https://www.phaser.cimr.cam.ac.uk/api.php?action=feedcontributions&user=Airlie&feedformat=atomPhaserwiki - User contributions [en]2024-03-28T12:39:14ZUser contributionsMediaWiki 1.31.8https://www.phaser.cimr.cam.ac.uk/index.php?title=Dtmin&diff=2502Dtmin2020-01-16T13:44:50Z<p>Airlie: </p>
<hr />
<div>The Mathematica script for study parameters as well as the scripts for generating figures in the 2020 cctbx dtmin article can be found [http://www-structmed.cimr.cam.ac.uk/dtmin here].</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Phaser_Crystallographic_Software&diff=2501Phaser Crystallographic Software2020-01-15T16:08:21Z<p>Airlie: </p>
<hr />
<div><br />
Phaser is a program for phasing macromolecular crystal structures with maximum likelihood methods. It has been developed by [[Developers | Randy Read's group]] at the [http://www.cimr.cam.ac.uk Cambridge Institute for Medical Research] (CIMR) in the [http://www.cam.ac.uk University of Cambridge] and is available through the [http://www.phenix-online.org Phenix] and [http://www.ccp4.ac.uk CCP4] software suites.<br />
<br />
Use the '''sidebar''' to navigate through the extensive documentation for Phaser. <br />
<!-- https://www.phaser.cimr.cam.ac.uk/index.php/MediaWiki:Sidebar --><br />
<br />
''This PhaserWiki supersedes the obsolete [http://www-structmed.cimr.cam.ac.uk/phaser/ Phaser homepage], which now redirects to this wiki. A copy of the obsolete Phaser homepage can be found [http://www-structmed.cimr.cam.ac.uk/phaser_obsolete/ here]''<br />
<br />
For Data Protection information see [http://www.cam.ac.uk/about-this-site/privacy-policy Cambridge University Privacy Policy]<br />
<br />
==Currently Supported Releases==<br />
<br />
====Phaser-2.8====<br />
:Download with Phenix Nightly Builds → [http://www.phenix-online.org/download/ Phenix ]<br />
:Documentation → [[Phaser-2.8: Manual | Manual]]<br />
<br />
====Phaser-2.7.17====<br />
:Download with Phenix Nightly Builds → [http://www.phenix-online.org/download/ Phenix ]<br />
:Download with CCP4 Update 7.0.023 <br />
:Documentation → [[Phaser-2.7.17: Manual | Manual]]<br />
''Changelog highlights''<br />
:* add feature to filter out data with low information content particularly in cases of high anisotropy<br />
:* bugfixes<br />
:: ''solution history formatting''<br />
:: ''R-value test with multiple search components failing''<br />
:: ''limit number of permutations in amalgamation to stop combinatorial explosion''<br />
:: ''correct handling of effect of experimental error in fast rotation function''<br />
:: ''search method full & permutations on had corrupted search ensemble copy numbers''<br />
<br />
====Phaser-2.7.16====<br />
<!--:Download with Phenix Nightly Builds → [http://www.phenix-online.org/download/ Phenix ]--><br />
:Download with Phenix Official Release 1.11.1 (October 2016) → [http://www.phenix-online.org/download/ Phenix ]<br />
:Documentation → [[Phaser-2.7.15: Manual | Manual]]<br />
''Changelog highlights''<br />
:* SOLUTION HISTORY tracks solution through positions in RF/TF/PAK/RNP peak lists<br />
:* selection by CHAIN and MODEL for PDB coordinate entry<br />
:* ensemble member rmsds adjusted to give values consistent with rmsd between members of an ensemble<br />
:* automatic search number for search ensemble(s)<br />
:* packing trace can be entered independently of coordinates and map (can mask larger volume than model)<br />
:* read TNCS/anisotropy binary files to avoid refinement (non-python interface)<br />
:* write TNCS and anisotropy parameters to binary files (non-python interface)<br />
:* default reading of I (or failing that, F) from mtz file (LABIN optional)<br />
:* trace for ensembles from maps = hexgrid of 1000+/-100 points <br />
:* trace for ensembles from coordinates above 1000 C-alpha = hexgrid of 1000+/-100 points<br />
:* trace for ensembles from coordinates between 1000 atoms and 1000 C-alpha = Calpha atoms<br />
:* trace for ensembles from coordinates under 1000 atoms = all atoms<br />
:* packing by pairwise percent only, other packing modes obsoleted<br />
:* packing test during FTF run by default with 50% pairwise packing cutoff<br />
:* automatic tNCS NMOL determination in presence of commensurate modulation<br />
:* added MODE GIMBLE, which splits ensembles by chain for rigid body refinement<br />
:* support for unicode<br />
:* solution coordinates placed nearest to input coordinates if possible<br />
<br />
<!--====Phaser-2.5.6-beta &nbsp;&nbsp; <span style="color:darkorange">''*unstable*''</span>==== --><br />
<br />
<!--:'''<span style="color:darkorange">CCP4 update coming soon</span>'''--><br />
<br />
==Referencing Phaser==<br />
Citing crystallographic software in your paper is important for funding new software development. We rely on your citations to convince funding bodies that our software is being used.<br />
<br />
If you solve a structure with Phaser, please cite<br />
<br />
;Phaser crystallographic software <br />
: McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ.<br />
:[http://scripts.iucr.org/cgi-bin/paper?he5368 '''J Appl Cryst'''] (2007). 40, 658-674. <br />
<br />
__NOTOC__</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Dtmin&diff=2500Dtmin2020-01-15T15:40:49Z<p>Airlie: Change of name</p>
<hr />
<div>The Wolfram Mathematica script for study parameters is found [http://www-structmed.cimr.cam.ac.uk/Dtmin here]</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Dtmin&diff=2498Dtmin2020-01-15T15:38:54Z<p>Airlie: Airlie moved page Mintbx to Dtmin: new name for directory</p>
<hr />
<div>The Wolfram Mathematica script for study parameters is found [http://www-structmed.cimr.cam.ac.uk/Mintbx here]</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Mintbx&diff=2499Mintbx2020-01-15T15:38:54Z<p>Airlie: Airlie moved page Mintbx to Dtmin: new name for directory</p>
<hr />
<div>#REDIRECT [[Dtmin]]</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=MediaWiki:Sidebar&diff=2497MediaWiki:Sidebar2020-01-15T15:38:21Z<p>Airlie: Change mintbx to dtmin</p>
<hr />
<div>** Phaser Crystallographic Software | PhaserWiki Home<br />
** Releases | Releases<br />
** Downloads | Downloads<br />
** Manuals | Manuals<br />
** Tutorials | Tutorials<br />
** FAQ | FAQ<br />
** Top Ten Tips | Top Ten Tips<br />
** Publications | Publications<br />
** External Links | External Links<br />
*users<br />
** Molecular Replacement | MR Phasing<br />
** Experimental Phasing | SAD Phasing<br />
*developers<br />
** Python Interface | Python Interface<br />
** Contact | Contact Developers<br />
** Developers | Developer Pages<br />
** Licences | Licences<br />
** Source Code | Source Code<br />
** phasertng | phasertng<br />
** dtmin | dtmin</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Dtmin&diff=2495Dtmin2019-12-02T17:53:36Z<p>Airlie: Created page with "The Wolfram Mathematica script for study parameters is found [http://www-structmed.cimr.cam.ac.uk/Mintbx here]"</p>
<hr />
<div>The Wolfram Mathematica script for study parameters is found [http://www-structmed.cimr.cam.ac.uk/Mintbx here]</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=MediaWiki:Sidebar&diff=2494MediaWiki:Sidebar2019-12-02T17:35:22Z<p>Airlie: Add mintbx link to developers section of MediaWiki:SideBar</p>
<hr />
<div>** Phaser Crystallographic Software | PhaserWiki Home<br />
** Releases | Releases<br />
** Downloads | Downloads<br />
** Manuals | Manuals<br />
** Tutorials | Tutorials<br />
** FAQ | FAQ<br />
** Top Ten Tips | Top Ten Tips<br />
** Publications | Publications<br />
** External Links | External Links<br />
*users<br />
** Molecular Replacement | MR Phasing<br />
** Experimental Phasing | SAD Phasing<br />
*developers<br />
** Python Interface | Python Interface<br />
** Contact | Contact Developers<br />
** Developers | Developer Pages<br />
** Licences | Licences<br />
** Source Code | Source Code<br />
** phasertng | phasertng<br />
** mintbx | mintbx</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=MediaWiki:Sidebar&diff=2489MediaWiki:Sidebar2019-07-15T11:52:22Z<p>Airlie: Add phaser-tng to developer pages</p>
<hr />
<div>** Phaser Crystallographic Software | PhaserWiki Home<br />
** Releases | Releases<br />
** Downloads | Downloads<br />
** Manuals | Manuals<br />
** Tutorials | Tutorials<br />
** FAQ | FAQ<br />
** Top Ten Tips | Top Ten Tips<br />
** Publications | Publications<br />
** External Links | External Links<br />
*users<br />
** Molecular Replacement | MR Phasing<br />
** Experimental Phasing | SAD Phasing<br />
*developers<br />
** Python Interface | Python Interface<br />
** Contact | Contact Developers<br />
** Developers | Developer Pages<br />
** Licences | Licences<br />
** Source Code | Source Code<br />
** phaser-tng | phaser-tng</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Phaser_Crystallographic_Software&diff=2452Phaser Crystallographic Software2018-04-17T08:14:28Z<p>Airlie: </p>
<hr />
<div><br />
Phaser is a program for phasing macromolecular crystal structures with maximum likelihood methods. It has been developed by [[Developers | Randy Read's group]] at the [http://www.cimr.cam.ac.uk Cambridge Institute for Medical Research] (CIMR) in the [http://www.cam.ac.uk University of Cambridge] and is available through the [http://www.phenix-online.org Phenix] and [http://www.ccp4.ac.uk CCP4] software suites.<br />
<br />
Use the '''sidebar''' to navigate through the extensive documentation for Phaser. <br />
<!-- index.php/MediaWiki:Sidebar--><br />
<br />
''This PhaserWiki supersedes the obsolete [http://www-structmed.cimr.cam.ac.uk/phaser/ Phaser homepage], which now redirects to this wiki. A copy of the obsolete Phaser homepage can be found [http://www-structmed.cimr.cam.ac.uk/phaser_obsolete/ here]''<br />
<br />
For Data Protection information see [http://www.cam.ac.uk/about-this-site/privacy-policy Cambridge University Privacy Policy]<br />
<br />
==Currently Supported Releases==<br />
<br />
====Phaser-2.8====<br />
:Download with Phenix Nightly Builds → [http://www.phenix-online.org/download/ Phenix ]<br />
:Documentation → [[Phaser-2.8: Manual | Manual]]<br />
<br />
====Phaser-2.7.17====<br />
:Download with Phenix Nightly Builds → [http://www.phenix-online.org/download/ Phenix ]<br />
:Download with CCP4 Update 7.0.023 <br />
:Documentation → [[Phaser-2.7.17: Manual | Manual]]<br />
''Changelog highlights''<br />
:* add feature to filter out data with low information content particularly in cases of high anisotropy<br />
:* bugfixes<br />
:: ''solution history formatting''<br />
:: ''R-value test with multiple search components failing''<br />
:: ''limit number of permutations in amalgamation to stop combinatorial explosion''<br />
:: ''correct handling of effect of experimental error in fast rotation function''<br />
:: ''search method full & permutations on had corrupted search ensemble copy numbers''<br />
<br />
====Phaser-2.7.16====<br />
<!--:Download with Phenix Nightly Builds → [http://www.phenix-online.org/download/ Phenix ]--><br />
:Download with Phenix Official Release 1.11.1 (October 2016) → [http://www.phenix-online.org/download/ Phenix ]<br />
:Documentation → [[Phaser-2.7.15: Manual | Manual]]<br />
''Changelog highlights''<br />
:* SOLUTION HISTORY tracks solution through positions in RF/TF/PAK/RNP peak lists<br />
:* selection by CHAIN and MODEL for PDB coordinate entry<br />
:* ensemble member rmsds adjusted to give values consistent with rmsd between members of an ensemble<br />
:* automatic search number for search ensemble(s)<br />
:* packing trace can be entered independently of coordinates and map (can mask larger volume than model)<br />
:* read TNCS/anisotropy binary files to avoid refinement (non-python interface)<br />
:* write TNCS and anisotropy parameters to binary files (non-python interface)<br />
:* default reading of I (or failing that, F) from mtz file (LABIN optional)<br />
:* trace for ensembles from maps = hexgrid of 1000+/-100 points <br />
:* trace for ensembles from coordinates above 1000 C-alpha = hexgrid of 1000+/-100 points<br />
:* trace for ensembles from coordinates between 1000 atoms and 1000 C-alpha = Calpha atoms<br />
:* trace for ensembles from coordinates under 1000 atoms = all atoms<br />
:* packing by pairwise percent only, other packing modes obsoleted<br />
:* packing test during FTF run by default with 50% pairwise packing cutoff<br />
:* automatic tNCS NMOL determination in presence of commensurate modulation<br />
:* added MODE GIMBLE, which splits ensembles by chain for rigid body refinement<br />
:* support for unicode<br />
:* solution coordinates placed nearest to input coordinates if possible<br />
<br />
<!--====Phaser-2.5.6-beta &nbsp;&nbsp; <span style="color:darkorange">''*unstable*''</span>==== --><br />
<br />
<!--:'''<span style="color:darkorange">CCP4 update coming soon</span>'''--><br />
<br />
==Referencing Phaser==<br />
Citing crystallographic software in your paper is important for funding new software development. We rely on your citations to convince funding bodies that our software is being used.<br />
<br />
If you solve a structure with Phaser, please cite<br />
<br />
;Phaser crystallographic software <br />
: McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ.<br />
:[http://scripts.iucr.org/cgi-bin/paper?he5368 '''J Appl Cryst'''] (2007). 40, 658-674. <br />
<br />
__NOTOC__</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Phaser:_Manual&diff=2447Phaser: Manual2018-03-09T12:37:14Z<p>Airlie: </p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
===Phaser Executable===<br />
<br />
The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the [[#MODE | MODE]] keyword. The different modes and the keywords relevant to each mode are described in [[Modes]].<br />
<br />
Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. However, some keywords are meaningful when entered multiple times. The order may or may not be important. <br />
<br />
*[[Image:User1.gif|link=]] [[#Basic Keywords | Basic Keywords]]<br />
<br />
*[[Image:Output.png|link=]] [[#Output Control Keywords | Output Control Keywords]]<br />
<br />
*[[Image:User2.gif|link=]] [[#Advanced Keywords |Advanced Keywords ]]<br />
<br />
*[[Image:Expert.gif|link=]] [[#Expert Keywords | Expert Keywords]]<br />
<br />
*[[Image:Developer.gif|link=]] [[#Developer Keywords | Developer Keywords]]<br />
<br />
str string<br />
int integer<br />
float double precision floating point<br />
dvect3 array of 3 doubles<br />
<br />
<br />
===Python Interface===<br />
<br />
Phaser can be compiled as a python library. The python interface takes a phaser keyword string as input.</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Phaser:_Manual&diff=2446Phaser: Manual2018-03-09T10:39:26Z<p>Airlie: </p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
===Phaser Executable===<br />
<br />
The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the [[#MODE | MODE]] keyword. The different modes and the keywords relevant to each mode are described in [[Modes]].<br />
<br />
Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. However, some keywords are meaningful when entered multiple times. The order may or may not be important. <br />
<br />
*[[Image:User1.gif|link=]] [[#Basic Keywords | Basic Keywords]]<br />
<br />
*[[Image:Output.png|link=]] [[#Output Control Keywords | Output Control Keywords]]<br />
<br />
*[[Image:User2.gif|link=]] [[#Advanced Keywords |Advanced Keywords ]]<br />
<br />
*[[Image:Expert.gif|link=]] [[#Expert Keywords | Expert Keywords]]<br />
<br />
*[[Image:Developer.gif|link=]] [[#Developer Keywords | Developer Keywords]]<br />
<br />
str string<br />
int integer<br />
float double precision floating point<br />
dvect3 array of 3 doubles<br />
<br />
<br />
===Python Interface===<br />
<br />
Phaser can be compiled as a python library. The python interface takes a phaser keyword string as input.<br />
<br />
<br />
<br />
<br />
<br />
==Basic Keywords==<br />
===[[Image:User1.gif|link=]]ATOM===<br />
<br />
<br />
<br />
<br />
==Output Control Keywords==<br />
===[[Image:Output.png|link=]]DEBUG===<br />
; DEBUG [ON|OFF]<br />
: Extra verbose output for debugging<br />
* Default: DEBUG OFF<br />
<br />
==Advanced Keywords==<br />
===[[Image:User2.gif|link=]]ELLG===<br />
; ELLG TARGET <TARGET><br />
: Target value for expected LLG for determining resolution limits and search order<br />
<!--; ELLG HIRES <HIRES> Internal control only--><br />
* Default: ELLG TARGET 225<br />
<br />
<br />
<br />
<br />
==Expert Keywords==<br />
<br />
===[[Image:Expert.gif|link=]]MACANO=== <br />
; MACANO PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for the refinement of SigmaN in the anisotropy correction<br />
; MACANO ANISO [ON|OFF] BINS [ON|OFF] SOLK [ON|OFF] SOLB [ON|OFF] ''{NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}''<br />
: Macrocycle for the custom refinement of SigmaN in the anisotropy correction. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACANO PROTOCOL DEFAULT<br />
<br />
<br />
<br />
==Developer Keywords==<br />
===[[Image:Developer.gif|link=]]BINS===<br />
; BINS DATA [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the data.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Phaser:_Manual&diff=2445Phaser: Manual2018-03-09T09:54:59Z<p>Airlie: Clear page ready for autogen wiki tests</p>
<hr />
<div></div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Developers&diff=2444Developers2018-03-09T09:52:19Z<p>Airlie: </p>
<hr />
<div>;Principal Investigator<br />
* [[Randy J. Read | Professor Randy J. Read]]<br />
<br />
<br />
;Group<br />
* [[ Tristan Croll | Dr Tristan Croll ]]<br />
* [[ Airlie J. McCoy | Dr Airlie McCoy ]]<br />
* [[ Robert Oeffner | Dr Robert Oeffner ]]<br />
<br />
<br />
;Alumni<br />
* [[ Gabor Bunkoczi | Dr Gabor Bunkoczi ]]<br />
* Dr Anne Baker<br />
* Dr Laurent Storoni<br />
* Dr Hamsapriye<br />
<br />
<br />
;Converting wiki page into rst for phenix docs<br />
# Copy and paste desired wiki source (not raw html) into text file, say Phenix-dev\modules\phenix_html\rst_files\reference\MRwiki.txt.<br />
# Copy any images referenced by MRwiki.txt to Phenix-dev\modules\phenix_html\rst_files\images\<br />
# Image references in MRwiki.txt need to be amended from Image:mypic.gif to Image:../images/mypic.gif<br />
# Install Pandoc on your PC<br />
# Change direcotry to Phenix-dev\modules\phenix_html\rst_files\reference and run Pandoc with command line: <br />
#:<pre>pandoc --columns=150 --toc -f mediawiki MRwiki.txt -t rst -o MRwiki_rst.txt</pre><br />
# Run phenix_html.rebuild_docs<br />
# Inspect new file Phenix\doc\reference\MRwiki_rst.html<br />
# If happy commit files to phenix_html svn server</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Airlie_J._McCoy&diff=2443Airlie J. McCoy2018-03-09T09:48:05Z<p>Airlie: /* 2016 */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
==Publications==<br />
<br />
<br />
===2017===<br />
<br />
;Structure and evolution of ENTH and VHS/ENTH-like domains in tepsin.<br />
:Archuleta TL, Frazier MN, Monken AE, Kendall AK, Harp J, <span style="color:darkmagenta">McCoy AJ</span>, Creanza N, Jackson LP.<br />
:Traffic. 2017 Sep;18(9):590-603. [http://dx.doi.org/10.1111/tra.12499'''link''']<br />
<br />
;Acknowledging Errors: Advanced Molecular Replacement with Phaser.<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Methods Mol Biol. 2017;1607:421-453. [http://dx.doi.org/10.1007/978-1-4939-7000-1_18 '''link'''] Review.<br />
<br />
;Ab initio solution of macromolecular crystal structures without direct methods.<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Oeffner RD, Wrobel AG, Ojala JR, Tryggvason K, Lohkamp B, Read RJ.<br />
:Proc Natl Acad Sci U S A. 2017 Apr 4;114(14):3637-3641. [http://dx.doi.org/10.1073/pnas.1701640114 '''link'''] Epub 2017 Mar 21.<br />
<br />
===2016===<br />
<br />
;Transient Fcho1/2⋅Eps15/R⋅AP-2 Nanoclusters Prime the AP-2 Clathrin Adaptor for Cargo Binding.<br />
:Ma L, Umasankar PK, Wrobel AG, Lymar A, <span style="color:darkmagenta">McCoy AJ</span>, Holkar SS, Jha A, Pradhan-Sundd T, Watkins SC, Owen DJ, Traub LM.<br />
:Dev Cell. 2016 May 24. pii: S1534-5807(16)30280-5. [http://dx.doi.org/10.1016/j.devcel.2016.05.003 '''link''']<br />
<br />
===2015===<br />
;A log-likelihood-gain intensity target for crystallographic phasing that accounts for experimental error.<br />
:Read RJ, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:Acta Crystallogr D Struct Biol. 2016 Mar 1;72(Pt 3):375-87. [http://dx.doi.org/10.1107/S2059798315013236 '''link''']. Epub 2016 Mar 1.<br />
<br />
;Advances in experimental phasing.<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Schneider T.<br />
:Acta Crystallogr D Struct Biol. 2016 Mar 1;72(Pt 3):291-2. [http://dx.doi.org/10.1107/S2059798316003375 '''link''']. Epub 2016 <br />
<br />
;X-ray structure determination using low-resolution electron microscopy maps for molecular replacement.<br />
:Jackson RN, <span style="color:darkmagenta">McCoy AJ</span>, Terwilliger TC, Read RJ, Wiedenheft B.<br />
:Nat Protoc. 2015 Sep;10(9):1275-84. [http://dx.doi.org/10.1038/nprot.2015.069 '''link''']. Epub 2015 Jul 30.<br />
<br />
;ANS complex of St John's wort PR-10 protein with 28 copies in the asymmetric unit: a fiendish combination of pseudosymmetry with tetartohedral twinning.<br />
:Sliwiak J, Dauter Z, Kowiel M, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ, Jaskolski M.<br />
:Acta Crystallogr D Biol Crystallogr. 2015 Apr;71(Pt 4):829-43. [http://dx.doi.org/10.1107/S1399004715001388 '''link'''] . Epub 2015 Mar 26.<br />
<br />
===2014===<br />
<br />
;Macromolecular X-ray structure determination using weak, single-wavelength anomalous data.<br />
:Bunkóczi G, <span style="color:darkmagenta">McCoy AJ</span>, Echols N, Grosse-Kunstleve RW, Adams PD, Holton JM, Read RJ, Terwilliger TC.<br />
:Nat Methods. 2015 Feb;12(2):127-30. [http://dx.doi.org/10.1038/nmeth.3212 '''link''']. Epub 2014 Dec 22.<br />
<br />
;VARP is recruited on to endosomes by direct interaction with retromer, where together they function in export to the cell surface.<br />
:Hesketh GG, Pérez-Dorado I, Jackson LP, Wartosch L, Schäfer IB, Gray SR, <span style="color:darkmagenta">McCoy AJ</span>, Zeldin OB, Garman EF, Harbour ME, Evans PR, Seaman MN, Luzio JP, Owen DJ.<br />
:Dev Cell. 2014 Jun 9;29(5):591-606. Epub 2014 May 22.<br />
:[http://dx.doi.org/10.1016/j.devcel.2014.04.010 '''Dev Cell link''']<br />
<br />
;Automated identification of elemental ions in macromolecular crystal structures.<br />
:Echols N, Morshed N, Afonine PV, <span style="color:darkmagenta">McCoy AJ</span>, Miller MD, Read RJ, Richardson JS, Terwilliger TC, Adams PD.<br />
:Acta Crystallogr D Biol Crystallogr. 2014 Apr;70(Pt 4):1104-14. Epub 2014 Mar 20.<br />
:[http://dx.doi.org/10.1107/S1399004714001308 '''IUCr link''']<br />
<br />
;Likelihood-based molecular-replacement solution for a highly pathological crystal with tetartohedral twinning and sevenfold translational noncrystallographic symmetry.<br />
:Sliwiak 1, Jaskolski M, Dauter Z, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2014 Feb;70(Pt 2):471-80. Epub 2014 Jan 29.<br />
:[http://dx.doi.org/10.1107/S1399004713030319 '''IUCr link''']<br />
<br />
;Automating crystallographic structure solution and refinement of protein-ligand complexes.<br />
:Echols N, Moriarty NW, Klei HE, Afonine PV, Bunkóczi G, Headd JJ, <span style="color:darkmagenta">McCoy AJ</span>, Oeffner RD, Read RJ, Terwilliger TC, Adams PD.<br />
:Acta Crystallogr D Biol Crystallogr. 2014 Jan;70(Pt 1):144-54 Epub 2013 Dec 25.<br />
:[http://dx.doi.org/10.1107/S139900471302748X '''IUCr link''']<br />
<br />
;Structures of yeast mitochondrial ADP/ATP carriers support a domain-based alternating-access transport mechanism.<br />
:Ruprecht JJ, Hellawell AM, Harding M, Crichton PG, <span style="color:darkmagenta">McCoy AJ</span>, Kunji ER.<br />
:Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):E426-34 Epub 2014 Jan 13.<br />
:[http://dx.doi.org/10.1073/pnas.1320692111 '''PNAS link''']<br />
<br />
===2013===<br />
;Cytokine Spatzle binds to the Drosophila immunoreceptor Toll with a neurotrophin-like specificity and couples receptor activation.<br />
:Lewis M, Arnot CJ, Beeston H, <span style="color:darkmagenta">McCoy A</span>., Ashcroft AE, Gay NJ, Gangloff M.<br />
:Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20461-6. Epub 2013 Nov 26.<br />
:[http://dx.doi.org/10.1073/pnas.1317002110 '''download pdf''']<br />
<br />
;Phaser.MRage<nowiki>:</nowiki> automated molecular replacement.<br />
:Bunkóczi G, Echols N, <span style="color:darkmagenta">McCoy AJ</span>, Oeffner RD, Adams PD, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2013 Nov;69(Pt 11):2276-86. Epub 2013 Oct 18.<br />
:[http://dx.doi.org/10.1107/S0907444913022750 '''IUCr link''']<br />
<br />
;SCEDS<nowiki>:</nowiki> protein fragments for molecular replacement in Phaser.<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Nicholls RA, Schneider TR.<br />
:Acta Crystallogr D Biol Crystallogr. 2013 Nov;69(Pt 11):2216-25. [http://dx.doi.org/10.1107/S0907444913021811 '''doi''']. Epub 2013 Oct 4.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5209 '''IUCr link''']<br />
<br />
;Improved estimates of coordinate error for molecular replacement.<br />
:Oeffner RD, Bunkóczi G, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2013 Nov;69(Pt 11):2209-15. [http://dx.doi.org/10.1107/S0907444913023512 '''doi''']. Epub 2013 Oct 12.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5212 '''IUCr link''']<br />
<br />
;Intensity statistics in the presence of translational noncrystallographic symmetry.<br />
:Read RJ, Adams PD, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:Acta Crystallogr D Biol Crystallogr 2013 Feb;69(Pt 2):176-83. Epub Jan 16.<br />
:[http://scripts.iucr.org/cgi-bin/paper?dz5268 '''IUCr link''']<br />
<br />
===2012===<br />
;Graphical tools for macromolecular crystallography in PHENIX.<br />
:Echols N, Grosse-Kunstleve RW, Afonine PV, Bunkóczi G, Chen VB, Headd JJ, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Adams PD.<br />
:J Appl Crystallogr. 2012 Jun 1;45(Pt 3):581-586. Epub 2012 May 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359726/pdf/j-45-00581.pdf '''download pdf''']<br />
<br />
===2011===<br />
;The Phenix software for automated determination of macromolecular structures.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung LW, Jain S, Kapral GJ, Grosse Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner RD, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Methods. 2011 Sep;55(1):94-106. doi: 10.1016/j.ymeth.2011.07.005. Epub 2011 Jul 29.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3193589/pdf/nihms319608.pdf '''download pdf''']<br />
<br />
;Overview of the CCP4 suite and current developments<br />
:Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, <span style="color:darkmagenta">McCoy A</span>, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS.<br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-242<br />
:[http://scripts.iucr.org/cgi-bin/paper?dz5219 '''Acta Cryst D''']<br />
<br />
;Using SAD data in Phaser<br />
:Read RJ, <span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):338-344<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5159 '''Acta Cryst D''']<br />
<br />
===2010===<br />
;A large-scale conformational change couples membrane recruitment to cargo binding in the AP2 clathrin adaptor complex.<br />
:Jackson LP, Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Gaffry T, James LC, Collins BM, Höning S, Evans PR, Owen DJ.<br />
:Cell. 2010 Jun 25;141(7):1220-9.<br />
:[http://www.cell.com/abstract/S0092-8674(10)00542-8 '''Cell'''] (subscription required)<br />
<br />
;Experimental phasing<nowiki>:</nowiki> best practice and pitfalls.<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):458-69. Epub 2010 Mar 24.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5142 '''Acta Cryst D''']<br />
<br />
;PHENIX<nowiki>:</nowiki> a comprehensive Python-based system for macromolecular structure solution.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21. Epub 2010 Jan 22.<br />
:[http://scripts.iucr.org/cgi-bin/paper?dz5186 '''Acta Cryst D''']<br />
<br />
===2009===<br />
;Decision-making in structure solution using Bayesian estimates of map quality<nowiki>:</nowiki> the PHENIX AutoSol wizard <br />
:Terwilliger TC, Adams PD, Read RJ, <span style="color:darkmagenta">McCoy AJ</span> , Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung LW.<br />
:Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):582-601<br />
:[http://scripts.iucr.org/cgi-bin/paper?ea5095 '''Acta Cryst''']<br />
<br />
===2008===<br />
;A structural explanation for the binding of endocytic dileucine motifs by the AP2 complex<br />
:Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Späte K, Miller SE, Evans PR, Höning S, Owen DJ.<br />
:Nature. 2008 Dec 18;456(7224):976-79<br />
:[http://www.nature.com/nature/journal/v456/n7224/abs/nature07422.html '''Nature'''] (subscription required)<br />
<br />
;An introduction to molecular replacement <br />
:Evans P, <span style="color:darkmagenta">McCoy A</span>.<br />
:Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):1-10. Epub 2007 Dec 5.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5108 '''Acta Cryst D''']<br />
<br />
;Automated structure solution with the PHENIX suite<br />
:Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, McKee E, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC, Adams PD.<br />
:Methods Mol Biol. 2008;426:419-35.<br />
:[http://dx.doi.org/10.1007/978-1-60327-058-8 '''doi'''] Digital Object Identifier<br />
<br />
===2007===<br />
;A SNARE-adaptor interaction is a new mode of cargo recognition in clathrin-coated vesicles <br />
:Miller SE, Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Robinson MS, Owen DJ.<br />
:Nature. 2007 Nov 22;450(7169):570-4<br />
:[http://www.nature.com/nature/journal/v450/n7169/abs/nature06353.html '''Nature'''] (subscription required)<br />
<br />
;High-resolution structure prediction and the crystallographic phase problem <br />
:Qian B, Raman S, Das R, Bradley P, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ, Baker D.<br />
:Nature. 2007 Nov 8;450(7167):259-64. Epub 2007 Oct 14.<br />
:[http://www.nature.com/nature/journal/v450/n7167/abs/nature06249.html '''Nature'''] (subscription required)<br />
<br />
;Solving structures of protein complexes by molecular replacement with Phaser <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2007 Jan;63(Pt 1):32-41. Epub 2006 Dec 13.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5095 '''Acta Cryst D'''] <br />
<br />
;Phaser crystallographic software <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC and Read RJ.<br />
:J. Appl. Cryst. (2007). 40, 658-674.<br />
:[http://scripts.iucr.org/cgi-bin/paper?he5368 '''J Appl Cryst''']<br />
<br />
;β-Edge interactions in a pentadecameric human antibody Vκ domain.<br />
:James LC, Jones PC, <span style="color:darkmagenta">McCoy A</span>, Tennent GA, Pepys MB, Famm K, Winter G.<br />
:J Mol Biol. 2007 Mar 30;367(3):603-8. Epub 2006 Nov 3.<br />
:[http://dx.doi.org/10.1016/j.jmb.2006.10.093 '''doi'''] Digital Object Identifier<br />
<br />
===2006===<br />
<br />
;Crystal structure of rab11 in complex with rab11 family interacting protein 2 <br />
:Jagoe WN, Lindsay AJ, Read RJ, <span style="color:darkmagenta">McCoy AJ</span>, McCaffrey MW, Khan AR.<br />
:Structure. 2006 Aug;14(8):1273-83.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0969212606002930 '''Structure'''] (subscription required)<br />
<br />
===2005===<br />
;Likelihood-enhanced fast translation functions <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):458-64. Epub 2005 Mar 24.<br />
:[http://scripts.iucr.org/cgi-bin/paper?gx5042.pdf '''Acta Cryst D'''] <br />
<br />
===2004===<br />
;Liking Likelihood <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2169-83. Epub 2004 Nov 26.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5064 '''Acta Cryst D''']<br />
<br />
;Simple algorithm for a maximum-likelihood SAD function <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Jul;60(Pt 7):1220-8. Epub 2004 Jun 22.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ea5015 '''Acta Cryst D''']<br />
<br />
;Likelihood-enhanced fast rotation functions <br />
:Storoni LC, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Mar;60(Pt 3):432-8. Epub 2004 Feb 25.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ad5007 '''Acta Cryst D'''] [http://www-structmed.cimr.cam.ac.uk/Personal/randy/pubs/ad5007.pdf '''pdf''']<br />
<br />
===2003===<br />
;Recent developments in the PHENIX software for automated crystallographic structure determination<br />
:Adams PD, Gopal K, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Pai RK, Read RJ, Romo TD, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC.<br />
:J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):53-5. Epub 2003 Nov 28.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ys0029.pdf '''J Synch Radia''']<br />
<br />
;Application of the complex multivariate normal distribution to crystallographic methods with insights into multiple isomorphous replacement phasing<br />
:Pannu NS, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2003 Oct;59(Pt 10):1801-8. Epub 2003 Sep 19.<br />
:[http://scripts.iucr.org/cgi-bin/paper?wd5000.pdf '''Acta Cryst D''']<br />
<br />
;Structure of β-antithrombin and the effect of glycosylation on antithrombin's heparin affinity and activity<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Pei XY, Skinner R, Abrahams JP, Carrell RW.<br />
:J Mol Biol. 2003 Feb 21;326(3):823-33.<br />
:[http://dx.doi.org/10.1016/S0022-2836(02)01382-7 '''doi'''] Digital Object Identifier<br />
<br />
===2002===<br />
;New applications of maximum likelihood and Bayesian statistics in macromolecular crystallography<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Curr Opin Struct Biol. 2002 Oct;12(5):670-3. Review.<br />
:[http://dx.doi.org/10.1016/S0959-440X(02)00373-1 '''doi'''] Digital Object Identifier<br />
<br />
;PHENIX<nowiki>:</nowiki> building new software for automated crystallographic structure determination <br />
:Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC.<br />
:Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1948-54. Epub 2002 Oct 21.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5027 '''Acta Cryst D''']<br />
<br />
;Molecular architecture and functional model of the endocytic AP2 complex <br />
:Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Evans PR, Owen DJ.<br />
:Cell. 2002 May 17;109(4):523-35.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0092867402007353 '''Cell'''] (subscription required)<br />
<br />
===2001===<br />
:No publications<br />
<br />
===2000===<br />
;ScFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> shortening of the linker in single-chain Fv fragment assembled in V(L) to V(H) orientation drives the formation of dimers, trimers, tetramers and higher molecular mass multimers <br />
:Dolezal O, Pearce LA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Hudson PJ, Kortt AA.<br />
:Protein Eng. 2000 Aug;13(8):565-74.<br />
:[http://dx.doi.org/10.1093/protein/13.8.565 '''doi'''] Digital Object Identifier<br />
<br />
;The conformational activation of antithrombin. A 2.85-A structure of a fluorescein derivative reveals an electrostatic link between the hinge and heparin binding regions. <br />
:Huntington JA*, <span style="color:darkmagenta">McCoy A</span>*, Belzar KJ, Pei XY, Gettins PG, Carrell RW.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Biol Chem. 2000 May 19;275(20):15377-83<br />
:[http://dx.doi.org/10.1074/jbc.275.20.15377 '''doi'''] Digital Object Identifier<br />
<br />
===1999===<br />
;Structural basis for dimerization of the Dictyostelium gelation factor (ABP120) rod <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Fucini P, Noegel AA, Stewart M.<br />
:Nat Struct Biol. 1999 Sep;6(9):836-41.<br />
:[http://www.nature.com/nsmb/journal/v6/n9/abs/nsb0999_836.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
;scFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> length of the linker between VH and VL domains dictates precisely the transition between diabodies and triabodies<br />
:Atwell JL, Breheney KA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Kortt AA, Hudson PJ.<br />
:Protein Eng. 1999 Jul;12(7):597-604.<br />
:[http://dx.doi.org/10.1093/protein/12.7.597 '''doi'''] Digital Object Identifier<br />
<br />
;Engineered mutants in the switch II loop of Ran define the contribution made by key residues to the interaction with nuclear transport factor 2 (NTF2) and the role of this interaction in nuclear protein import<br />
:Kent HM, Moore MS, Quimby BB, Baker AM, <span style="color:darkmagenta">McCoy AJ</span>, Murphy GA, Corbett AH, Stewart M.<br />
:J Mol Biol. 1999 Jun 11;289(3):565-77.<br />
:[http://dx.doi.org/10.1006/jmbi.1999.2775 '''doi'''] Digital Object Identifier<br />
<br />
===1998===<br />
;The structure of the Q69L mutant of GDP-Ran shows a major conformational change in the switch II loop that accounts for its failure to bind nuclear transport factor 2 (NTF2)<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Dec 18;284(5):1517-27.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.2204 '''doi'''] Digital Object Identifier<br />
<br />
;Three-dimensional structures of single-chain Fv-neuraminidase complexes<br />
:Malby RL*, <span style="color:darkmagenta">McCoy AJ</span>*, Kortt AA, Hudson PJ, Colman PM.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Mol Biol. 1998 Jun 19;279(4):901-10.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.1794 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Apr 3;277(3):635-46.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1602 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for amoeboid motility in nematode sperm <br />
:Bullock TL, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Roberts TM, Stewart M.<br />
:Nat Struct Biol. 1998 Mar;5(3):184-9.<br />
:[http://www.nature.com/nsmb/journal/v5/n3/abs/nsb0398-184.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
===1997===<br />
;Crystallization and preliminary X-Ray diffraction characterization of a dimerizing fragment of the rod domain of the Dictyostelium gelation factor (ABP-120)<br />
:Fucini P, <span style="color:darkmagenta">McCoy AJ</span>, Gomez-Ortiz M, Schleicher M, Noegel AA, Stewart M.<br />
:J Struct Biol. 1997 Nov;120(2):192-5<br />
:[http://dx.doi.org/10.1006/jsbi.1997.3930 '''doi'''] Digital Object Identifier<br />
<br />
;Nuclear protein import is decreased by engineered mutants of nuclear transport factor 2 (NTF2) that do not bind GDP-Ran<br />
:Clarkson WD, Corbett AH, Paschal BM, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>, Gerace L, Silver PA, Stewart M.<br />
:J Mol Biol. 1997 Oct 10;272(5):716-30.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1255 '''doi'''] Digital Object Identifier<br />
<br />
;The 1.8 Å crystal structure of winged bean albumin 1, the major albumin from ''Psophocarpus tetragonolobus (L.) DC''<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Kortt AA.<br />
:J Mol Biol. 1997 Jun 27;269(5):881-91.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1067 '''doi'''] Digital Object Identifier<br />
<br />
;Electrostatic complementarity at protein/protein interfaces<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Chandana Epa V, Colman PM.<br />
:J Mol Biol. 1997 May 2;268(2):570-84.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.0987 '''doi'''] Digital Object Identifier<br />
<br />
;Single-chain Fv fragments of anti-neuraminidase antibody NC10 containing five- and ten-residue linkers form dimers and with zero-residue linker a trimer <br />
:Kortt AA, Lah M, Oddie GW, Gruen CL, Burns JE, Pearce LA, Atwell JL, <span style="color:darkmagenta">McCoy AJ</span>, Howlett GJ, Metzger DW, Webster RG, Hudson PJ.<br />
:Protein Eng. 1997 Apr;10(4):423-33.<br />
:[http://dx.doi.org/10.1093/protein/10.4.423 '''doi'''] Digital Object Identifier<br />
<br />
===1996===<br />
;Protein Structure and Interaction<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Thesis (Ph. D) <br />
:[http://cat.lib.unimelb.edu.au/search~S30?/amccoy+aj/amccoy+aj/-3%2C0%2C0%2CB/frameset&FF=amccoy+airlie+janet&1%2C1%2C/indexsort=- '''University of Melbourne Library'''] (not available for loan)</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Phaser_Crystallographic_Software&diff=2442Phaser Crystallographic Software2018-02-27T16:14:05Z<p>Airlie: /* Currently Supported Releases */</p>
<hr />
<div><br />
Phaser is a program for phasing macromolecular crystal structures with maximum likelihood methods. It has been developed by [[Developers | Randy Read's group]] at the [http://www.cimr.cam.ac.uk Cambridge Institute for Medical Research] (CIMR) in the [http://www.cam.ac.uk University of Cambridge] and is available through the [http://www.phenix-online.org Phenix] and [http://www.ccp4.ac.uk CCP4] software suites.<br />
<br />
Use the '''sidebar''' to navigate through the extensive documentation for Phaser. <br />
<!-- index.php/MediaWiki:Sidebar--><br />
<br />
''This PhaserWiki supersedes the obsolete [http://www-structmed.cimr.cam.ac.uk/phaser/ Phaser homepage], which now redirects to this wiki. A copy of the obsolete Phaser homepage can be found [http://www-structmed.cimr.cam.ac.uk/phaser_obsolete/ here]''<br />
<br />
==Currently Supported Releases==<br />
<br />
====Phaser-2.8====<br />
:Download with Phenix Nightly Builds → [http://www.phenix-online.org/download/ Phenix ]<br />
:Documentation → [[Phaser-2.8: Manual | Manual]]<br />
<br />
====Phaser-2.7.17====<br />
:Download with Phenix Nightly Builds → [http://www.phenix-online.org/download/ Phenix ]<br />
:Download with CCP4 Update 7.0.023 <br />
:Documentation → [[Phaser-2.7.17: Manual | Manual]]<br />
''Changelog highlights''<br />
:* add feature to filter out data with low information content particularly in cases of high anisotropy<br />
:* bugfixes<br />
:: ''solution history formatting''<br />
:: ''R-value test with multiple search components failing''<br />
:: ''limit number of permutations in amalgamation to stop combinatorial explosion''<br />
:: ''correct handling of effect of experimental error in fast rotation function''<br />
:: ''search method full & permutations on had corrupted search ensemble copy numbers''<br />
<br />
====Phaser-2.7.16====<br />
<!--:Download with Phenix Nightly Builds → [http://www.phenix-online.org/download/ Phenix ]--><br />
:Download with Phenix Official Release 1.11.1 (October 2016) → [http://www.phenix-online.org/download/ Phenix ]<br />
:Documentation → [[Phaser-2.7.15: Manual | Manual]]<br />
''Changelog highlights''<br />
:* SOLUTION HISTORY tracks solution through positions in RF/TF/PAK/RNP peak lists<br />
:* selection by CHAIN and MODEL for PDB coordinate entry<br />
:* ensemble member rmsds adjusted to give values consistent with rmsd between members of an ensemble<br />
:* automatic search number for search ensemble(s)<br />
:* packing trace can be entered independently of coordinates and map (can mask larger volume than model)<br />
:* read TNCS/anisotropy binary files to avoid refinement (non-python interface)<br />
:* write TNCS and anisotropy parameters to binary files (non-python interface)<br />
:* default reading of I (or failing that, F) from mtz file (LABIN optional)<br />
:* trace for ensembles from maps = hexgrid of 1000+/-100 points <br />
:* trace for ensembles from coordinates above 1000 C-alpha = hexgrid of 1000+/-100 points<br />
:* trace for ensembles from coordinates between 1000 atoms and 1000 C-alpha = Calpha atoms<br />
:* trace for ensembles from coordinates under 1000 atoms = all atoms<br />
:* packing by pairwise percent only, other packing modes obsoleted<br />
:* packing test during FTF run by default with 50% pairwise packing cutoff<br />
:* automatic tNCS NMOL determination in presence of commensurate modulation<br />
:* added MODE GIMBLE, which splits ensembles by chain for rigid body refinement<br />
:* support for unicode<br />
:* solution coordinates placed nearest to input coordinates if possible<br />
<br />
<!--====Phaser-2.5.6-beta &nbsp;&nbsp; <span style="color:darkorange">''*unstable*''</span>==== --><br />
<br />
<!--:'''<span style="color:darkorange">CCP4 update coming soon</span>'''--><br />
<br />
==Referencing Phaser==<br />
Citing crystallographic software in your paper is important for funding new software development. We rely on your citations to convince funding bodies that our software is being used.<br />
<br />
If you solve a structure with Phaser, please cite<br />
<br />
;Phaser crystallographic software <br />
: McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ.<br />
:[http://scripts.iucr.org/cgi-bin/paper?he5368 '''J Appl Cryst'''] (2007). 40, 658-674. <br />
<br />
__NOTOC__</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Keywords&diff=2441Keywords2018-02-27T09:37:45Z<p>Airlie: /* link=SPACEGROUP */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
===Phaser Executable===<br />
<br />
The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the [[#MODE | MODE]] keyword. The different modes and the keywords relevant to each mode are described in [[Modes]].<br />
<br />
Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. However, some keywords are meaningful when entered multiple times. The order may or may not be important. <br />
<br />
*[[Image:User1.gif|link=]] [[#Basic Keywords | Basic Keywords]]<br />
<br />
*[[Image:Output.png|link=]] [[#Output Control Keywords | Output Control Keywords]]<br />
<br />
*[[Image:User2.gif|link=]] [[#Advanced Keywords |Advanced Keywords ]]<br />
<br />
*[[Image:Expert.gif|link=]] [[#Expert Keywords | Expert Keywords]]<br />
<br />
*[[Image:Developer.gif|link=]] [[#Developer Keywords | Developer Keywords]]<br />
<br />
<br />
===Python Interface===<br />
<br />
Phaser can be compiled as a python library. The mode is selected by calling the appropriate run-job. Input to the run-job is via input-objects, which are passed to the run-job. Setter function on the input objects are equivalent to the keywords for input to the phaser executable. The different modes and the keywords relevant to each mode are described in [[Modes]]. See [[Python Interface]] for details. <br />
<br />
The python interface uses standard python and cctbx/scitbx variable types.<br />
<br />
str string<br />
float double precision floating point<br />
Miller cctbx::miller::index<int> <br />
dvect3 scitbx::vec3<float> <br />
dmat33 scitbx::mat3<float> <br />
'''type'''_array scitbx::af::shared<'''type'''> arrays<br />
<br />
=Basic Keywords=<br />
==[[Image:User1.gif|link=]]ATOM== <br />
; ATOM CRYSTAL <XTALID> PDB <FILENAME><br />
: Definition of atom positions using a pdb file.<br />
; ATOM CRYSTAL <XTALID> HA <FILENAME><br />
: Definition of atom positions using a ha file (from RANTAN, MLPHARE etc.).<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> <br />
: Minimal definition of atom position. B-factor defaults to isotropic and Wilson B-factor. Use <TYPE>=TX for Ta6Br12 cluster and <TYPE>=XX for all other clusters. Scattering for cluster is spherically averaged. Coordinates of cluster compounds other than Ta6Br12 must be entered with CLUSTER keyword. Ta6Br12 coordinates are in phaser code and do not need to be given with CLUSTER keyword.<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> [ ISOB <ISOB> | ANOU <HH KK LL HK HL KL> | USTAR <HH KK LL HK HL KL>] FIXX [ON|OFF] FIXO [ON|OFF] FIXB [ON|OFF] BSWAP [ON|OFF] LABEL <SITE_NAME><br />
: Full definition of atom position including B-factor.<br />
;ATOM CHANGE BFACTOR WILSON [ON|OFF]<br />
: Reset all atomic B-factors to the Wilson B-factor.<br />
; ATOM CHANGE SCATTERER <SCATTERER><br />
:Reset all atomic scatterers to element (or cluster) type.<br />
setATOM_PDB(str <XTALID>,str <PDB FILENAME>)<br />
setATOM_IOTBX(str <XTALID>,iotbx::pdb::hierarchy::root <iotbx object>)<br />
setATOM_STR(str <XTALID>,str <pdb format string>)<br />
setATOM_HA(str <XTALID>,str <FILENAME>)<br />
addATOM(str <XTALID>,str <TYPE>,<br />
float <X>,float <Y>,float <Z>,float <OCC>)<br />
addATOM_FULL(str <XTALID>,str <TYPE>,bool <ORTH>,<br />
dvect3 <X Y Z>,float <OCC>,bool <ISO>,float <ISOB>,<br />
bool <ANOU>,dmat6 <HH KK LL HK HL KL>,<br />
bool <FIXX>,bool <FIXO>,bool <FIXB>,bool <SWAPB>,<br />
str <SITE_NAME>)<br />
setATOM_CHAN_BFAC_WILS(bool)<br />
setATOM_CHAN_SCAT(bool)<br />
setATOM_CHAN_SCAT_TYPE(str <TYPE>)<br />
<br />
==[[Image:User1.gif|link=]]CLUSTER== <br />
; CLUSTER PDB <PDBFILE><br />
: Sample coordinates for a cluster compound for experimental phasing. Clusters are specified with type XX. Ta6Br12 clusters do not need to have coordinates specified as the coordinates are in the phaser code. To use Ta6Br12 clusters, specify atomtypes/clusters as TX.<br />
setCLUS_PDB(str <PDBFILE>)<br />
addCLUS_PDB(str <ID>, str <PDBFILE>)<br />
<br />
==[[Image:User1.gif|link=]]COMPOSITION== <br />
; COMPOSITION BY [ <sup>1</sup>AVERAGE| <sup>2</sup>SOLVENT| <sup>3</sup>ASU ]<br />
: Alternative ways of defining composition<br />
: <sup>1</sup> AVERAGE solvent fraction for crystals (50%)<br />
: <sup>2</sup> Composition entered by solvent content.<br />
: <sup>3</sup> Explicit description of composition of ASU by sequence or molecular weight<br />
; <sup>2</sup>COMPOSITION PERCENTAGE <SOLVENT><br />
: Specified SOLVENT content<br />
; <sup>3</sup>COMPOSITION PROTEIN [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of protein in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION NUCLEIC [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of nucleic acid in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION ATOM <TYPE> NUMBER <NUM><br />
: Add NUM copies of an atom (usually a heavy atom) to the composition<br />
* Default: COMPOSITION BY ASU<br />
setCOMP_BY(str ["AVERAGE" | "SOLVENT" | "ASU" ])<br />
setCOMP_PERC(float <SOLVENT>)<br />
addCOMP_PROT_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_PROT_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_PROT_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_PROT_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_NUCL_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_NUCL_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_NUCL_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_NUCL_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_ATOM(str <TYPE>,float <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]CRYSTAL== <br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN Fpos =<F+> SIGFpos=<SIG+> Fneg=<F-> SIGFneg=<SIG-><br />
: Columns of MTZ file to read for this (anomalous) dataset<br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN F =<F> SIGF=<SIGF><br />
: Columns of MTZ file to read for this (non-anomalous) dataset. Used for LLG completion in SAD phasing when there is no anomalous signal (single atom MR protocol). Use LABIN for MR.<br />
setCRYS_ANOM_LABI(str <F+>,str <SIGF+>,str <F->,str <SIGF->) <br />
setCRYS_MEAN_LABI(str <F>,str <SIGF>)<br />
<br />
==[[Image:User1.gif|link=]]ENSEMBLE== <br />
; ENSEMBLE <MODLID> [PDB|CIF] <PDBFILE> [RMS <RMS><sup>1</sup> | ID <ID><sup>2</sup> | CARD ON<sup>3</sup>] ''CHAIN "<CHAIN>"<sup>4</sup> MODEL <NUM><sup>5</sup>''<br />
: The names of the PDB/CIF files used to build the ENSEMBLE, and either<br />
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
:: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file (e.g. "REMARK PHASER ENSEMBLE MODEL 1 ID 31.2") containing the superimposed models concatenated in the one file. This syntax enables simple automation of the use of ensembles. The pdb file can be non-standard because the atom list for the different models need not be the same.<br />
:: <sup>4</sup> CHAIN is selected from the pdb file. <br />
:: <sup>5</sup> MODEL number is selected from the pdb file.<br />
; ENSEMBLE <MODLID> HKLIN <MTZFILE> F=<F> PHI=<PHI> EXTENT <EX> <EY> <EZ> RMS <RMS> CENTRE <CX> <CY> <CZ> PROTEIN MW <PMW> NUCLEIC MW <NMW> ''CELL SCALE <SCALE>''<br />
: An ENSEMBLE defined from a map (via an mtz file). The molecular weight of the object the map represents is required for scaling. The effective RMS coordinate error is needed to judge how the map accuracy falls off with resolution. For density obtained from an EM image reconstruction, a good first guess would be to take the resolution where the FSC curve drops below 0.5 and divide by 3. The extent (difference between maximum and minimum x,y,z coordinates of region containing model density) is needed to determine reasonable rotation steps, and the centre is needed to carry out a proper interpolation of the molecular transform. The extent and the centre are both given in Ångstroms. The cell scale factor defaults to 1 and can be refined (for example, if the map is from electron microscopy when the cell scale may be unknown to within a few percent).<br />
; ENSEMBLE <MODLID> ATOM <TYPE> RMS <RMS><br />
: Define an ensemble as a single atom for single atom MR<br />
; ENSEMBLE <MODLID> HELIX <NUM> <br />
: Define an ensemble as a helix with NUM residues<br />
; ENSEMBLE <MODLID> HETATM [ON|OFF]<br />
: Use scattering from HETATM records in pdb file. See [[Molecular_Replacement#Coordinate_Editing | Coordinate Editing ]]<br />
; ENSEMBLE <MODLID> DISABLE CHECK [ON|OFF]<br />
: Toggle to disable checking of deviation between models in an ensemble. '''Use with extreme caution'''. Results of computations are not guaranteed to be sensible.<br />
; ENSEMBLE <MODLID> ESTIMATOR [OEFFNER | OEFFNERHI | OEFFNERLO | CHOTHIALESK ]<br />
: Define the estimator function for converting ID to RMS<br />
; ENSEMBLE <MODLID> PTGRP [COVERAGE | IDENTITY | RMSD | TOLANG | TOLSPC | EULER | SYMM ]<br />
: Define the pointgroup parameters <br />
; ENSEMBLE <MODLID> BINS [MIN <N>| MAX <M>| WIDTH <W> ]<br />
: Define the Fcalc reflection binning parameters <br />
; ENSEMBLE <MODLID> TRACE [PDB|CIF] <PDBFILE><br />
: Define the coordinates used for packing independent of the coordinates used for structure factor calculation<br />
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
:: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file <br />
; ENSEMBLE <MODLID> TRACE SAMPLING MIN <DIST> <br />
: Set the minimum distance for the sampling of packing grid<br />
; ENSEMBLE <MODLID> TRACE SAMPLING TARGET <NUM> <br />
: Set the target for the number of points to sample the smallest molecule to be packed<br />
; ENSEMBLE <MODLID> TRACE SAMPLING RANGE <NUM> <br />
: Target range (TARGET+/-RANGE) for search for hexgrid points in protein volume<br />
; ENSEMBLE <MODLID> TRACE SAMPLING USE [AUTO | ALL | CALPHA | HEXGRID ]<br />
: Sample trace coordinates using all atoms, C-alpha atoms, a hexagonal grid in the atomic volume or use an automatically determined choice<br />
; ENSEMBLE <MODLID> TRACE SAMPLING DISTANCE <DIST> <br />
: Set the distance for the sampling of the hexagonal grid explicitly and do not use TARGET to find default sampling distance<br />
; ENSEMBLE <MODLID> TRACE SAMPLING WANG <WANG> <br />
: Scale factor for the size of the Wang mask generated from an ensemble map<br />
; ENSEMBLE <MODLID> TRACE PDB <PDBFILE> <br />
: Use the given set of coordinates for packing rather than using the coordinates for structure factor calculation<br />
* Default: ENSEMBLE <MODLID> DISABLE CHECK OFF<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING MIN 1.0<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING TARGET 1000<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING RANGE 100<br />
addENSE_PDB_ID(str <MODLID>,str <FILE>,float <ID>) <br />
addENSE_PDB_RMS(str <MODLID>,str <FILE>,float <RMS>) <br />
setENSE_TRAC_SAMP_MIN(MODLID,float <MIN>)<br />
setENSE_TRAC_SAMP_TARG(MODLID,int <TARGET>)<br />
setENSE_TRAC_SAMP_RANG(MODLID,int <RANGE>)<br />
setENSE_TRAC_SAMP_USE(MODLID,str)<br />
setENSE_TRAC_SAMP_DIST(MODLID,float <DIST>)<br />
setENSE_TRAC_SAMP_WANG(MODLID,float <WANG>)r <FILE>,float <RMS>)<br />
addENSE_CARD(str <MODLID>,str <FILE>,bool)<br />
addENSE_MAP(str <MODLID>,str <MTZFILE>,str <F>,str <PHI>,dvect3 <EX EY EZ>,<br />
float <RMS>,dvect3 <CX CY CZ>,float <PMW>,float <NMW>,float <CELL>)<br />
setENSE_DISA_CHEC(bool)<br />
<br />
==[[Image:User1.gif|link=]]FIND==<br />
; FIND SCATTERER <ATOMTYPE><br />
: Phassade, type of scatterers to find<br />
; FIND NUMBER <NUMBER><br />
: Phassade, number of scatteres to find<br />
; FIND CLUSTER [ON|OFF]<br />
: Phassade, scatterer name is a cluster<br />
; FIND PEAK SELECT [PERCENT | SIGMA]<br />
: Phassade, peak selection method from Phassade FFT<br />
; FIND PEAK CUTOFF <CUTOFF><br />
: Phassade, peak selection method cutoff from Phassade FFT<br />
; FIND PURGE SELECT [PERCENT | SIGMA]<br />
: Phassade, purge selection method after all Phassade FFT<br />
; FIND PURGE CUTOFF <CUTOFF><br />
: Phassade, purge selection method cutoff after all Phassade FFT<br />
setFIND_SCAT(str <ATOMTYPE>)<br />
setFIND_NUMB(int <NUMBER>)<br />
setFIND_NUMB(int <NUMBER>)<br />
setFIND_CLUS(bool <CLUSTER>)<br />
setFIND_PEAK_SELE(str <SELECT>)<br />
setFIND_PEAK_CUTO(float <CUTOFF>)<br />
setFIND_PURG_SELE(str <SELECT>)<br />
setFIND_PURG_CUTO(float <CUTOFF>)<br />
<br />
==[[Image:User1.gif|link=]]HKLIN==<br />
; HKLIN <FILENAME><br />
: The mtz file containing the data<br />
setHKLI(str <FILENAME>)<br />
<br />
==[[Image:User1.gif|link=]]JOBS== <br />
; JOBS <NUM><br />
: Number of processors to use in parallelized sections of code<br />
* Default: JOBS 2<br />
setJOBS(int <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]LABIN== <br />
; LABIN F = <F> SIGF = <SIGF> <br />
: Columns in mtz file. F must be given. SIGF should be given but is optional<br />
; LABIN I = <nowiki><I></nowiki> SIGI = <SIGI> <br />
: Columns in mtz file. I must be given. SIGI should be given but is optional<br />
; LABIN FMAP = <PH> PHMAP = <PHMAP> <br />
: Columns in mtz file. FMAP/PHMAP are weighted coefficients for use in the Phased Translation Function.<br />
; LABIN FMAP = <PH> PHMAP = <PHMAP> FOM = <FOM><br />
: Columns in mtz file. FMAP/PHMAP are unweighted coefficients for use in the Phased Translation Function and FOM the figure of merit for weighting<br />
setLABI_F_SIGF(str <F>,str <SIGF>)<br />
setLABI_I_SIGI(str <nowiki><I></nowiki>,str <SIGI>)<br />
setLABI_PTF(str <FMAP>,str <PHMAP>,str <FOM>)<br />
<br />
''Data should be input to python run-jobs using one data_refl parameter''<br />
''This is extracted from the ResultMR_DAT object after a call to runMR_DAT''<br />
setREFL_DATA(data_ref)<br />
''Example:''<br />
i = InputMR_DAT()<br />
i.setHKLI("*.mtz")<br />
i.setLABI_F_SIGF("F","SIGF")<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputMR_LLG()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.setREFL_DATA(r.getDATA())<br />
''See also: '' [[Python Example Scripts]]<br />
<br />
''Alternatively, reflection arrays can be set using cctbx::af::shared<double>''<br />
setREFL_F_SIGF(float_array <F>,float_array <SIGF>)<br />
setREFL_I_SIGI(float_array <nowiki><I></nowiki>,float_array <SIGI>)<br />
setREFL_PTF(float_array <FMAP>,float_array <PHMAP>,float_array <FOM>)<br />
<br />
==[[Image:User1.gif|link=]]MODE==<br />
; MODE [ ANO | CCA | SCEDS | NMAXYZ | NCS | MR_ELLG | MR_AUTO | MR_GYRE | MR_ATOM | MR_ROT | MR_TRA | MR_RNP | | MR_OCC | MR_PAK | EP_AUTO | EP_SAD]<br />
: The mode of operation of Phaser. The different modes are described in a separate page on [[Keyword Modes]]<br />
ResultANO r = runANO(InputANO)<br />
ResultCCA r = runCCA(InputCCA)<br />
ResultNMA r = runSCEDS(InputNMA)<br />
ResultNMA r = runNMAXYZ(InputNMA)<br />
ResultNCS r = runNCS(InputNCS)<br />
ResultELLG r = runMR_ELLG(InputMR_ELLG)<br />
ResultMR r = runMR_AUTO(InputMR_AUTO)<br />
ResultEP r = runMR_ATOM(InputMR_ATOM)<br />
ResulrMR_RF r = runMR_FRF(InputMR_FRF)<br />
ResultMR_TF r = runMR_FTF(InputMR_FTF)<br />
ResultMR r = runMR_RNP(InputMR_RNP)<br />
ResultGYRE r = runMR_GYRE(InputMR_RNP)<br />
ResultMR r = runMR_OCC(InputMR_OCC)<br />
ResultMR r = runMR_PAK(InputMR_PAK)<br />
ResultEP r = runEP_AUTO(InputEP_AUTO)<br />
ResultEP_SAD r = runEP_SAD(InputEP_SAD)<br />
<br />
==[[Image:User1.gif|link=]]PARTIAL== <br />
; PARTIAL PDB <PDBFILE> [RMSIDENTITY] <RMS_ID><br />
: The partial structure for MR-SAD substructure completion. Note that this must already be correctly placed, as the experimental phasing module will not carry out molecular replacement.<br />
; PARTIAL HKLIN <MTZFILE> [RMS|IDENTITY] <RMS_ID><br />
: The partial electron density for MR-SAD substructure completion.<br />
; PARTIAL LABIN FC=<FC> PHIC=<PHIC><br />
: Column labels for partial electron density for MR-SAD substructure completion.<br />
setPART_PDB(str <PDBFILE>)<br />
setPART_HKLI(str <MTZFILE>) <br />
setPART_LABI_FC(str <FC>)<br />
setPART_LABI_PHIC(str <PHIC>) <br />
setPART_VARI(str ["ID"|"RMS"])<br />
setPART_DEVI(float <RMS_ID>)<br />
<br />
==[[Image:User1.gif|link=]]SEARCH==<br />
; SEARCH ENSEMBLE <MODLID> ''{OR ENSEMBLE <MODLID>}… NUMBER <NUM><sup>*</sup>''<br />
: The ENSEMBLE to be searched for in a rotation search or an automatic search. When multiple ensembles are given using the OR keyword, the search is performed for each ENSEMBLE in turn. When the keyword is entered multiple times, each SEARCH keyword refers to a new component of the structure. If the component is present multiple times the sub-keyword NUMber can be used (rather than entering the same SEARCH keyword NUMber times).<br />
: <sup>*</sup>For automatic determination of search number use NUMBER 0. If the composition is entered, the maximum number will be that defined by the composition, otherwise the maximum number will fill the asymmetric unit to a minimum solvent content of 20%. Searches for new components will continue until the TFZ score is above 8, and terminate if the TFZ score drops below 8 before the placement of the maximum number of components.<br />
; SEARCH METHOD [FULL|FAST]<br />
: Search using the [[Modes#Modes |full search]] or [[Modes#Modes | fast search]] algorithms.<br />
; SEARCH ORDER AUTO [ON|OFF]<br />
: Search in the "best" order as estimated using estimated rms deviation and completeness of models.<br />
; SEARCH PRUNE [ON|OFF]<br />
: For high TFZ solutions that fail the packing test, carry out a sliding-window occupancy refinement and prune residues that refine to low occupancy, in an effort to resolve packing clashes. If this flag is set to true, the flag for keeping high tfz score solutions (see [[#PACK | PACK]]) that don't pack is also set to true (PACK KEEP HIGH TFZ ON).<br />
; SEARCH AMALGAMATE USE [ON|OFF]<br />
: For multiple high TFZ solutions, enable amalgamation into a single solution<br />
; SEARCH BFACTOR <BFAC><br />
: B-factor applied to search molecule (or atom).<br />
; SEARCH OFACTOR <OFAC><br />
: Occupancy factor applied to search molecule (or atom).<br />
* Default: SEARCH METHOD FAST<br />
* Default: SEARCH ORDER AUTO ON<br />
* Default: SEARCH PRUNE ON<br />
* Default: SEARCH AMALGAMATE USE ON<br />
* Default: SEARCH BFACTOR 0<br />
* Default: SEARCH OFACTOR 1<br />
addSEAR_ENSE_NUM(str <MODLID>,int <NUM>) <br />
addSEAR_ENSE_OR_ENSE_NUM(string_array <MODLIDS>,int <NUM>) <br />
setSEAR_METH(str [ "FULL" | "FAST" ])<br />
setSEAR_ORDE_AUTO(bool)<br />
setSEAR_PRUN(bool <PRUNE>)<br />
setSEAR_AMAL_USE(bool <AMAL>)<br />
setSEAR_BFAC(float <BFAC>)<br />
setSEAR_OFAC(float <OFAC>)<br />
<br />
==[[Image:User1.gif|link=]]SGALTERNATIVE==<br />
; SGALTERNATIVE SELECT [<sup>1</sup>ALL| <sup>2</sup>HAND| <sup>3</sup>LIST| <sup>4</sup>NONE]<br />
: Selection of alternative space groups to test in translation functions i.e. those that are in same laue group as that given in [[#SPACEGROUP | SPACEGROUP]]<br />
: <sup>1</sup> Test all possible space groups, <br />
: <sup>2</sup> Test the given space group and its enantiomorph.<br />
: <sup>3</sup> Test the space groups listed with SGALTERNATIVE TEST <SG>.<br />
: <sup>4</sup> Do not test alternative space groups.<br />
; SGALTERNATIVE TEST <SG><br />
: Alternative space groups to test. Multiple test space groups can be entered.<br />
* Default: SGALTERNATIVE SELECT HAND<br />
setSGAL_SELE(str [ "ALL" | "HAND" | "LIST" | "NONE" ]) <br />
addSGAL_TEST(str <SG>)<br />
<br />
==[[Image:User1.gif|link=]]SOLUTION==<br />
; SOLUTION SET <ANNOTATION><br />
: Start new set of solutions <br />
; SOLUTION TEMPLATE <ANNOTATION><br />
: Specifies a template solution against which other solutions in this run will be compared. Given in place of SOLUTION SET. Template rotation and translations given by subsequent SOLUTION 6DIM cards as per SOLUTION SETS.<br />
; SOLUTION 6DIM ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> [ORTH|FRAC] <X> <Y> <Z> ''FIXR [ON|OFF] FIXT [ON|OFF] FIXB [ON|OFF] BFAC <BFAC> MULT <MULT>''<br />
: This keyword is repeated for each known position and orientation of an ENSEMBLE MODLID. A B G are the Euler angles (z-y-z convention) and X Y Z are the translation elements, expressed either in orthogonal Angstroms (ORTH) or fractions of a cell edge (FRAC). The input ensemble is transformed by a rotation around the origin of the coordinate system, followed by a translation. BFAC default to 0, MULT (for multiplicity) defaults to 1.<br />
; SOLUTION ENSEMBLE <MODLID> VRMS DELTA <DELTA> RMSD <RMSD><br />
: Refined RMS variance terms for pdb files (or map) in ensemble MODLID. RMSD is the input RMSD of the job that produced the sol file, DELTA is the shift with respect to this RMSD. If given as part of a solution, these values overwrite the values used for input in the ENSEMBLE keyword (if defined).<br />
; SOLUTION ENSEMBLE <MODLID> CELL SCALE <SCALE><br />
: Refined cell scale factor. Only applicable to ensembles that are maps<br />
; SOLUTION TRIAL ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> RF <RF> RFZ <RFZ><br />
: Rotation List for translation function<br />
; SOLUTION ORIGIN ENSEMBLE <MODLID><br />
: Create solution for ensemble MODLID at the origin<br />
; SOLUTION SPACEGROUP <SG><br />
: Space Group of the solution (if alternative spacegroups searched)<br />
; SOLUTION RESOLUTION <HIRES><br />
: High resolution limit of data used to find/refine this solution<br />
; SOLUTION PACKS <PACKS><br />
: Flag for whether solution has been retained despite failing packing test, due to having high TFZ<br />
setSOLU(mr_solution <SOL>) <br />
addSOLU_SET(str <ANNOTATION>) <br />
addSOLU_TEMPLATE(str <ANNOTATION>) <br />
addSOLU_6DIM_ENSE(str <MODLID>,dvect3 <A B C>,bool <FRAC>,dvect3 <X Y Z>,<br />
float <BFAC>,bool <FIXR>,bool <FIXT>,bool <FIXB>,int <MULT>, 1.0) <br />
addSOLU_ENSE_DRMS(str <MODLID>, float <DRMS>) <br />
addSOLU_ENSE_CELL(str <MODLID>, float <SCALE>)<br />
addSOLU_TRIAL_ENSE(string <MODLID>,dvect3 <A B C>,float <RF>, float <RFZ>)<br />
addSOLU_ORIG_ENSE(string <MODLID>)<br />
setSOLU_SPAC(str <SG>)<br />
setSOLU_RESO(float <HIRES>)<br />
setSOLU_PACK(bool <PACKS>)<br />
<br />
==[[Image:User1.gif|link=]]SPACEGROUP==<br />
; SPACEGROUP <SG><br />
; SPACEGROUP HALL <SG><br />
: Space group may be altered from the one on the MTZ file to a space group in the same point group. The space group can be entered in one of three ways<br />
#The Hermann-Mauguin symbol e.g. P212121 or P 21 21 21 (with or without spaces)<br />
#The international tables number, which gives standard setting e.g. 19 <br />
#The Hall symbols e.g. P 2ac 2ab<br />
: '''The space group can also be a subgroup of the merged space group'''. For example, P1 is always allowed. The reflections will be expanded to the symmetry of the given subgroup. This is only a valid approach when the true symmetry is the symmetry of the subgroup and perfect twinning causes the data to merge "perfectly" in the higher symmetry. <br />
:'''A list of the allowed space groups in the same point group as the given space group (or space group read from MTZ file) and allowed subgroups of these is given in the Cell Content Analysis logfile.'''<br />
* Default: Read from MTZ file<br />
setSPAC_NUM(int <NUM>)<br />
setSPAC_NAME(string <HM>)<br />
setSPAC_HALL(string <HALL>)<br />
<br />
==[[Image:User1.gif|link=]]WAVELENGTH== <br />
; WAVELENGTH <LAMBDA> <br />
: The wavelengh at which the SAD dataset was collected<br />
setWAVE(float <LAMBDA>)<br />
<br><br />
<br><br />
<br />
=Output Control Keywords=<br />
==[[Image:Output.png|link=]]DEBUG== <br />
; DEBUG [ON|OFF]<br />
: Extra verbose output for debugging<br />
* Default: DEBUG OFF<br />
setDEBU(bool) <br />
<br />
==[[Image:Output.png|link=]]EIGEN==<br />
; EIGEN WRITE [ON|OFF]<br />
; EIGEN READ <EIGENFILE><br />
: Read or write a file containing the eigenvectors and eigenvalues. If reading, the eigenvalues and eigenvectors of the Hessian are read from the file generated by a previous run, rather than calculated. This option must be used with the job that generated the eigenfile and the job reading the eigenfile must have identical input for the ENM parameters. Use WRITE to control whether or not the eigenfile is written when not using the READ mode.<br />
* Default: EIGEN WRITE ON<br />
setEIGE_WRIT(bool)<br />
setEIGE_READ(str <EIGENFILE>)<br />
<br />
==[[Image:Output.png|link=]]HKLOUT== <br />
; HKLOUT [ON|OFF]<br />
: Flags for output of an mtz file containing the phasing information<br />
* Default: HKLOUT ON<br />
setHKLO(bool) <br />
<br />
==[[Image:Output.png|link=]]KEYWORDS== <br />
; KEYWORDS [ON|OFF]<br />
: Write output Phaser .sol file (.rlist file for rotation function)<br />
* Default: KEYWORDS ON<br />
setKEYW(bool)<br />
<br />
==[[Image:Output.gif|link=]]LLGMAPS==<br />
; LLGMAPS [ON|OFF]<br />
: Write log-likelihood gradient map coefficients to MTZ file<br />
* Default: LLGMAPS OFF<br />
setLLGM(bool <True|False>)<br />
<br />
==[[Image:Output.png|link=]]MUTE== <br />
; MUTE [ON|OFF]<br />
: Toggle for running in silent/mute mode, where no logfile is written to ''standard output''.<br />
* Default: MUTE OFF<br />
setMUTE(bool) <br />
<br />
==[[Image:Output.png|link=]]KILL== <br />
; KILL TIME [MINS]<br />
: Kill Phaser after MINS minutes of CPU have elapsed, provided parallel section is complete<br />
; KILL FILE [FILENAME]<br />
: Kill Phaser if file FILENAME is present, provided parallel section is complete<br />
* Default: KILL TIME 0 ''Phaser runs to completion''<br />
* Detaulf: KILL FILE "" ''Phaser runs to completion''<br />
setKILL_TIME(float) <br />
setKILL_FILE(string)<br />
<br />
==[[Image:Output.png|link=]]OUTPUT== <br />
; OUTPUT LEVEL [SILENT|CONCISE|SUMMARY|LOGFILE|VERBOSE|DEBUG]<br />
: Output level for logfile<br />
; OUTPUT LEVEL [0|1|2|3|4|5]<br />
: Output level for logfile (equivalent to keyword level setting)<br />
* Default: OUTPUT LEVEL LOGFILE<br />
setOUTP_LEVE(string)<br />
setOUTP(enum)<br />
<br />
==[[Image:Output.png|link=]]TITLE==<br />
; TITLE <TITLE><br />
: Title for job<br />
* Default: TITLE [no title given]<br />
setTITL(str <TITLE>)<br />
<br />
==[[Image:Output.png|link=]]TOPFILES== <br />
; TOPFILES <NUM><br />
: Number of top pdbfiles or mtzfiles to write to output.<br />
* Default: TOPFILES 1<br />
setTOPF(int <NUM>) <br />
<br />
==[[Image:Output.png|link=]]ROOT== <br />
; ROOT <FILEROOT><br />
: Root filename for output files (e.g. FILEROOT.log)<br />
* Default: ROOT PHASER<br />
setROOT(string <FILEROOT>)<br />
<br />
==[[Image:Output.png|link=]]VERBOSE== <br />
; VERBOSE [ON|OFF] <br />
: Toggle to send verbose output to log file.<br />
* Default: VERBOSE OFF<br />
setVERB(bool) <br />
<br />
==[[Image:Output.png|link=]]XYZOUT== <br />
; XYZOUT [ON|OFF] ''ENSEMBLE [ON|OFF]<sup>1</sup> PACKING [ON|OFF]<sup>2</sup>''<br />
: Toggle for output coordinate files. <br />
::<sup>1</sup> If the optional ENSEMBLE keyword is ON, then each placed ensemble is written to its own pdb file. The files are named FILEROOT.#.#.pdb with the first # being the solution number and the second # being the number of the placed ensemble (representing a SOLU 6DIM entry in the .sol file). <br />
::<sup>2</sup> If the optional PACKING keyword is ON, then the hexagonal grid used for the packing analysis is output to its own pdb file FILEROOT.pak.pdb<br />
* Default: XYZOUT OFF (Rotation functions)<br />
* Default: XYZOUT ON ENSEMBLE OFF (all other relevant modes)<br />
* Default: XYZOUT ON PACKING OFF (all other relevant modes)<br />
setXYZO(bool) <br />
setXYZO_ENSE(bool)<br />
setXYZO_PACK(bool)<br />
<br><br />
<br><br />
<br />
=Advanced Keywords=<br />
==[[Image:User2.gif|link=]]ELLG==<br />
([[Molecular_Replacement#Should_Phaser_Solve_It.3F|explained here]])<br />
; ELLG TARGET <TARGET><br />
: Target value for expected LLG for determining resolution limits and search order<br />
<!--; ELLG HIRES <HIRES> Internal control only--><br />
* Default: ELLG TARGET 225<br />
setELLG_TARG(float <TARGET>)<br />
<br />
==[[Image:User2.gif|link=]]FORMFACTORS==<br />
; FORMFACTORS [XRAY | ELECTRON | NEUTRON]<br />
: Use scattering factors from x-ray, electron or neutrons<br />
* Default: FORMFACTORS XRAY<br />
setFORM(string XRAY)<br />
<br />
==[[Image:User2.gif|link=]]HAND==<br />
; HAND [ <sup>1</sup>ON| <sup>2</sup>OFF| <sup>3</sup>BOTH]<br />
: Hand of heavy atoms for experimental phasing<br />
: <sup>1</sup>Phase using the other hand of heavy atoms <br />
: <sup>2</sup>Phase using given hand of heavy atoms <br />
: <sup>3</sup>Phase using both hands of heavy atoms<br />
* Default: HAND BOTH<br />
setHAND(str [ "OFF" | "ON" | "BOTH" ])<br />
<br />
==[[Image:User2.gif|link=]]LLGCOMPLETE==<br />
; LLGCOMPLETE COMPLETE [ON|OFF]<br />
: Toggle for structure completion by log-likelihood gradient maps<br />
; LLGCOMPLETE SCATTERER <TYPE> <br />
: Atom/Cluster type(s) to be used for log-likelihood gradient completion. If more than one element is entered for log-likelihood gradient completion, the atom type that gives the highest Z-score for each peak is selected. Type = "RX" is a purely real scatterer and type="AX" is purely anomalous scatterer<br />
; LLGCOMPLETE REAL ON<br />
: Use a purely real scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER RX)<br />
; LLGCOMPLETE ANOMALOUS ON<br />
: Use a purely anomalous scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER AX)<br />
; LLGCOMPLETE CLASH <CLASH> <br />
: Minimum distance between atoms in log-likelihood gradient maps and also the distance used for determining anisotropy of atoms (default determined by resolution, flagged by CLASH=0)<br />
; LLGCOMPLETE SIGMA <Z><br />
: Z-score (sigma) for accepting peaks as new atoms in log-likelihood gradient maps<br />
; LLGCOMPLETE NCYC <NMAX><br />
: Maximum number of cycles of log-likelihood gradient structure completion. By default, NMAX is 50, but this limit should never be reached, because all features in the log-likelihood gradient maps should be assigned well before 50 cycles are finished. This keyword should be used to reduce the number of cycles to 1 or 2.<br />
; LLGCOMPLETE METHOD [IMAGINARY|ATOMTYPE]<br />
: Pick peaks from the imaginary map only or from all the completion atomtype maps.<br />
* Default: LLGCOMPLETE COMPLETE OFF<br />
* Default: LLGCOMPLETE CLASH 0<br />
* Default: LLGCOMPLETE SIGMA 6<br />
* Default: LLGComplete NCYC 50<br />
* Default: LLGComplete METHOD ATOMTYPE<br />
setLLGC_COMP(bool <True|False>) <br />
setLLGC_CLAS(float <CLASH>) <br />
setLLGC_SIGM(float <Z>) <br />
setLLGC_NCYC(int <NMAX>)<br />
setLLGC_METH(str ["IMAGINARY"|"ATOMTYPE"])<br />
<br />
==[[Image:User2.gif|link=]]NMA== <br />
; NMA MODE <M1> ''{MODE <M2>…}'' <br />
: The MODE keyword gives the mode along which to perturb the structure. If multiple modes are entered, the structure is perturbed along all the modes AND combinations of the modes given. There is no limit on the number of modes that can be entered, but the number of pdb files explodes combinatorially. The first 6 modes are the pure rotation and translation modes and do not lead to perturbation of the structure. If the number M is less than 7 then M is interpreted as the first M modes starting at 7, so for example, MODE 5 would give modes 7 8 9 10 11.<br />
; NMA COMBINATION <NMAX><br />
: Controls how many modes are present in any combination.<br />
* Default: NMA MODE 5<br />
* Default: NMA COMBINATION 2<br />
addNMA_MODE(int <MODE>) <br />
setNMA_COMB(int <NMAX>)<br />
<br />
==[[Image:User2.gif|link=]]PACK==<br />
; PACK SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>ALL ]<br />
: <sup>1</sup>Allow up to the PERCENT of sampling points to clash, considering only pairwise clashes.<br />
: <sup>2</sup>Allow all solutions (no packing test). <i>Only use this to force output of PDB file for inspection of clashes.</i><br />
; PACK CUTOFF <PERCENT> <br />
: Limit on total number (or percent) of clashes <br />
; PACK QUICK [ON|OFF]<br />
: Packing check stops when ALLOWED_CLASHES or MAX_CLASHES is reached. However, all clashes are found when the solution has a high Z-score (see [[#ZSCORE | ZSCORE]]).<br />
; PACK COMPACT [ON|OFF]<br />
: Pack ensembles into a compact association (minimize distances between centres of mass for the addition of each component in a solution).<br />
; PACK KEEP HIGH TFZ [ON|OFF]<br />
: Solutions with high tfz (see [[#ZSCORE | ZSCORE]]) but that fail to pack are retained in the solution list. Set to true if SEARCH PRUNE ON (see [[#SEARCH | SEARCH]]).<br />
* Default: PACK SELECT PERCENT<br />
* Default: PACK CUTOFF 10<br />
* Default: PACK COMPACT ON<br />
* Default: PACK QUICK ON<br />
* Default: PACK KEEP HIGH TFZ OFF<br />
* Default: PACK CONSERVATION DISTANCE 1,5<br />
setPACK_SELE(str ["PERCENT"|"ALL"]) <br />
setPACK_CUTO(float <ALLOWED_CLASHES>)<br />
setPACK_QUIC(bool)<br />
setPACK_KEEP_HIGH_TFZ(bool)<br />
setPACK_COMP(bool)<br />
<br />
==[[Image:User2.gif|link=]]PEAKS==<br />
; PEAKS TRA SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL] <br />
; PEAKS ROT SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL]<br />
: Peaks for individual rotation functions (ROT) or individual translation functions (TRA) satisfying selection criteria are saved. To be used for subsequent steps, peaks must also satisfy the overall [[#PURGE | PURGE]] selection criteria, so it will usually be appropriate to set only the PURGE criteria (which over-ride the defaults for the PEAKS criteria if not explicitly set). See [[Molecular_Replacement#How_to_Select_Peaks | How to Select Peaks]]<br />
: <sup>1</sup> Select peaks by taking all peaks over CUTOFF percent of the difference between the top peak and the mean value.<br />
: <sup>2</sup> Select peaks by taking all peaks with a Z-score greater than CUTOFF.<br />
: <sup>3</sup> Select peaks by taking top CUTOFF.<br />
: <sup>4</sup> Select all peaks.<br />
; PEAKS ROT CUTOFF <CUTOFF><br />
; PEAKS TRA CUTOFF <CUTOFF><br />
: Cutoff value for the rotation function (ROT) or translation function (TRA) peak selection criteria.<br />
: If selection is by percent and [[#PURGE | PURGE PERCENT]] is changed from the default, then the PEAKS percent value is set to the lower PURGE percent value.<br />
; PEAKS ROT CLUSTER [ON|OFF] <br />
; PEAKS TRA CLUSTER [ON|OFF]<br />
: Toggle selects clustered or unclustered peaks for rotation function (ROT) or translation function (TRA).<br />
; PEAKS ROT DOWN [PERCENT] <br />
: [[#SEARCH | SEARCH METHOD FAST]] only. Percentage to reduce rotation function cutoff if there is no TFZ over the zscore cutoff that determines a true solution (see [[#ZSCORE | ZSCORE]]) in first search.<br />
* Default: PEAKS ROT SELECT PERCENT<br />
* Default: PEAKS TRA SELECT PERCENT<br />
* Default: PEAKS ROT CUTOFF 75<br />
* Default: PEAKS TRA CUTOFF 75<br />
* Default: PEAKS ROT CLUSTER ON<br />
* Default: PEAKS TRA CLUSTER ON<br />
setPEAK_ROTA_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"]) <br />
setPEAK_TRAN_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"])<br />
setPEAK_ROTA_CUTO(float <CUTOFF>)<br />
setPEAK_TRAN_CUTO(float <CUTOFF>) <br />
setPEAK_ROTA_CLUS(bool <CLUSTER>) <br />
setPEAK_TRAN_CLUS(bool <CLUSTER>)<br />
setPEAK_ROTA_DOWN(float <PERCENT>)<br />
<br />
==[[Image:User2.gif|link=]]PERMUTATIONS== <br />
; PERMUTATIONS [ON|OFF]<br />
: Only relevant to [[#SEARCH | SEARCH METHOD FULL]]. Toggle for whether the order of the search set is to be permuted.<br />
* Default: PERMUTATIONS OFF<br />
setPERM(bool <PERMUTATIONS>)<br />
<br />
==[[Image:User2.gif|link=]]PERTURB== <br />
; PERTURB RMS STEP <RMS><br />
: Increment in rms Ångstroms between pdb files to be written. <br />
; PERTURB RMS MAX <MAXRMS><br />
: The structure will be perturbed along each mode until the MAXRMS deviation has been reached.<br />
; PERTURB RMS DIRECTION [FORWARD|BACKWARD|TOFRO] <br />
: The structure is perturbed either forwards or backwards or to-and-fro (FORWARD|BACKWARD|TOFRO) along the eigenvectors of the modes specified.<br />
; PERTURB INCREMENT [RMS| DQ] <br />
: Perturb the structure by rms devitations along the modes, or by set dq increments<br />
; PERTURB DQ <DQ1> ''{DQ <DQ2>…}''<br />
: Alternatively, the DQ factors (as used by the Elnemo server (K. Suhre & Y-H. Sanejouand, NAR 2004 vol 32) ) by which to perturb the atoms along the eigenvectors can be entered directly.<br />
* Default: PERTURB INCREMENT RMS<br />
* Default: PERTURB RMS STEP 0.2<br />
* Default: PERTURB RMS MAXRMS 0.3<br />
* Default: PERTURB RMS DIRECTION TOFRO<br />
setPERT_INCR(str [ "RMS" | "DQ" ])<br />
setPERT_RMS_MAXI(float <MAX>)<br />
setPERT_RMS_DIRE(str [ "FORWARDS" | "BACKWARDS" | "TOFRO" ]) <br />
addPERT_DQ(float <DQ>)<br />
<br />
==[[Image:User2.gif|link=]]PURGE== <br />
; PURGE ROT ENABLE [ON|OFF]<sup>1</sup><br />
; PURGE ROT PERCENT <PERC><sup>2</sup><br />
; PURGE ROT NUMBER <NUM><sup>3</sup><br />
: Purging criteria for rotation function (RF), where PERCENT and NUMBER are alternative selection criteria (''OR'' criteria)<br />
::<sup>1</sup> Toggle for whether to purge the solution list from the RF according to the top solution found. If there are a number of RF searches with different partial solution backgrounds, the PURGE is applied to the total list of peaks. If there is one clearly significant RF solution from one of the backgrounds it acts to purge all the less significant solutions. If there is only one RF (a single partial solution background) the PURGE gives no additional selection over and above the PEAKS command. <br />
::<sup>2</sup> [[Molecular_Replacement#How_to_Select_Peaks | Selection by percent]]. PERC is percentage of the top peak, where the value of the top peak is defined as 100% and the value of the mean is defined as 0%. Note that this criterion is applied subsequent to any selection criteria applied through the [[#PEAKS | PEAKS]] command. If the [[#PEAKS | PEAKS]] selection is by percent, then the percent cutoff given in the PURGE command over-rides that for [[#PEAKS | PEAKS]], so as to rationalize results in the case of only a single RF (single partial solution background.)<br />
::<sup>3</sup> NUM is the number of solutions to retain in purging. If NUMBER is given (non-zero) it overrides the PERCENT option. NUMBER given as zero is the flag for not applying this criterion.<br />
; PURGE TRA ENABLE [ON|OFF]<br />
; PURGE TRA PERCENT <PERC><br />
; PURGE TRA NUMBER <NUM><br />
: As above, but for translation function<br />
; PURGE RNP ENABLE [ON|OFF]<br />
; PURGE RNP PERCENT <PERC><br />
; PURGE RNP NUMBER <NUM><br />
: As above but for refinement, but with the important distinction that PERCENT and NUMBER are concurrent selection criteria (''AND'' criteria)<br />
* Default: PURGE ROT ENABLE ON <br />
* Default: PURGE ROT PERC 75<br />
* Default: PURGE ROT NUM 0<br />
* Default: PURGE TRA ENABLE ON<br />
* Default: PURGE TRA PERC 75<br />
* Default: PURGE TRA NUM 0<br />
* Default: PURGE RNP ENABLE ON<br />
* Default: PURGE RNP PERC 75<br />
* Default: PURGE RNP NUM 0<br />
setPURG_ROTA_ENAB(bool <ENABLE>)<br />
setPURG_TRAN_ENAB(bool <ENABLE>) <br />
setPURG_RNP_ENAB(bool <ENABLE>)<br />
setPURG_ROTA_PERC(float <PERC>) <br />
setPURG_TRAN_PERC(float <PERC>) <br />
setPURG_RNP_PERC(float <PERC>)<br />
setPURG_ROTA_NUMB(float <NUM>) <br />
setPURG_TRAN_NUMB(float <NUM>)<br />
setPURG_TRAN_NUMB(float <NUM>)<br />
setPURG_RNP_NUMB(float <NUM>)<br />
<br />
==[[Image:User2.gif|link=]]RESOLUTION== <br />
; RESOLUTION HIGH <HIRES> <br />
: High resolution limit in Ångstroms. <br />
; RESOLUTION LOW <LORES><br />
: Low resolution limit in Ångstroms.<br />
; RESOLUTION AUTO HIGH <HIRES> <br />
: High resolution limit in Ångstroms for final high resolution refinement in MR_AUTO mode.<br />
* Default for molecular replacement: Set by [[#ELLG | ELLG TARGET]] for structure solution, final refinement uses all data<br />
* Default for experimental phasing: All data used<br />
setRESO_HIGH(float <HIRES>) <br />
setRESO_LOW(float <LORES>)<br />
setRESO_AUTO_HIGH(float <HIRES>) <br />
setRESO(float <HIRES>,float <LORES>)<br />
<br />
==[[Image:User2.gif|link=]]ROTATE== <br />
; ROTATE VOLUME FULL<br />
: Sample all unique angles <br />
; ROTATE VOLUME AROUND EULER <A> <nowiki><B></nowiki> <C> RANGE <RANGE> <br />
: Restrict the search to the region of +/- RANGE degrees around orientation given by EULER<br />
setROTA_VOLU(string ["FULL"|"AROUND"|) <br />
setROTA_EULE(dvect3 <A B C>) <br />
setROTA_RANG(float <RANGE>)<br />
<br />
==[[Image:User2.gif|link=]]SCATTERING==<br />
; SCATTERING TYPE <TYPE> FP=<FP> FDP=<FDP> FIX [ON|OFF|EDGE]<br />
: Measured scattering factors for a given atom type, from a fluorescence scan. FIX EDGE (default) fixes the fdp value if it is away from an edge, but refines it if it is close to an edge, while FIX ON or FIX OFF does not depend on proximity of edge.<br />
; SCATTERING RESTRAINT [ON|OFF]<br />
: use Fdp restraints<br />
; SCATTERING SIGMA <SIGMA><br />
: Fdp restraint sigma used is SIGMA multiplied by initial fdp value<br />
* Default: SCATTERING SIGMA 0.2<br />
* Default: SCATTERING RESTRAINT ON<br />
addSCAT(str <TYPE>,float <FP>,float <FDP, string <FIXFDP>) <br />
setSCAT_REST(bool) <br />
setSCAT_SIGM(float <SIGMA>)<br />
<br />
==[[Image:User2.gif|link=]]SCEDS== <br />
; SCEDS NDOM <NDOM><br />
:Number of domains into which to split the protein<br />
; SCEDS WEIGHT SPHERICITY <WS><br />
: Weight factor for the the Density Test in the SCED Score. The Sphericity Test scores boundaries that divide the protein into more spherical domains more highly.<br />
; SCEDS WEIGHT CONTINUITY <WC><br />
: Weight factor for the the Continuity Test in the SCED Score. The Continuity Test scores boundaries that divide the protein into domains contigous in sequence more highly. <br />
; SCEDS WEIGHT EQUALITY <WE><br />
: Weight factor for the the Equality Test in the SCED Score. The Equality Test scores boundaries that divide the protein more equally more highly.<br />
; SCEDS WEIGHT DENSITY <WD><br />
: Weight factor for the the Equality Test in the SCED Score. The Density Test scores boundaries that divide the protein into domains more densely packed with atoms more highly. <br />
* Default: SCEDS NDOM 2<br />
* Default: SCEDS WEIGHT EQUALITY 1<br />
* Default: SCEDS WEIGHT SPHERICITY 4 <br />
* Default: SCEDS WEIGHT DENSITY 1<br />
* Default: SCEDS WEIGHT CONTINUITY 0<br />
setSCED_NDOM(int <NDOM>) <br />
setSCED_WEIG_SPHE(float <WS>) <br />
setSCED_WEIG_CONT(float <WC>)<br />
setSCED_WEIG_EQUA(float <WE>) <br />
setSCED_WEIG_DENS(float <WD>)<br />
<br />
==[[Image:User2.gif|link=]]TARGET==<br />
; TARGET ROT [FAST | BRUTE]<br />
: Target function for fast rotation searches (2). BRUTE searches all angles on a grid with the full rotation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these rotations with the full rotation likelihood target.<br />
; TARGET TRA [FAST | BRUTE | PHASED]<br />
: Target function for fast translation searches (3). BRUTE searches all positions on a grid with the full translation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these positions with the full translation likelihood target. PHASED selects the "phased translation function", for which a LABIN command should also be given, specifying FMAP, PHMAP and (optionally) FOM.<br />
* Default: TARGET ROT FAST<br />
* Default: TARGET TRA FAST<br />
setTARG_ROTA(str ["FAST"|"BRUTE"])<br />
setTARG_TRAN(str ["FAST"|"BRUTE"|"PHASED"])<br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS NMOL <NMOL><br />
: Number of molecules/molecular assemblies related by single TNCS vector (usually only 2). If the TNCS is a pseudo-tripling of the cell then NMOL=3, a pseudo-quadrupling then NMOL=4 etc.<br />
* Default: TNCS NMOL 2<br />
setTNCS_NMOL(int <NMOL>)<br />
<br><br />
<br />
==[[Image:User2.gif|link=]]TRANSLATION== <br />
; TRANSLATION VOLUME [ <sup>1</sup>FULL | <sup>2</sup>REGION | <sup>3</sup>LINE | <sup>4</sup>AROUND ])<br />
: Search volume for brute force translation function.<br />
: <sup>1</sup> Cheshire cell or Primitive cell volume. <br />
: <sup>2</sup> Search region.<br />
: <sup>3</sup> Search along line. <br />
: <sup>4</sup> Search around a point.<br />
; <sup>1 2 3</sup>TRANSLATION START <X Y Z> <br />
; <sup>1 2 3</sup>TRANSLATION END <X Y Z><br />
: Search within region or line bounded by START and END.<br />
; <sup>4</sup>TRANSLATION POINT <X Y Z><br />
; <sup>4</sup>TRANSLATION RANGE <RANGE><br />
: Search within +/- RANGE Ångstroms (not fractional coordinates, even if the search point is given as fractional coordinates) of a point <X Y Z>.<br />
; TRANSLATION [ORTH | FRAC]<br />
: Coordinates are given in orthogonal or fractional values.<br />
; TRANSLATION PACKING USE [ON | OFF]<br />
: Top translation function peak will be tested for packing.<br />
; TRANSLATION PACKING CUTOFF <PERC><br />
: Percent pairwise packing used for packing function test of top TF peak. Equivalent to PACK CUTOFF <PERC> for packing function. <br />
; TRANSLATION PACKING NUM <NUM><br />
: Number of translation function peaks to test for packing before bailing out of packing test. Set to 0 to pack all translation function peaks (slow for large packing volumes). <br />
* Default: TRANSLATION VOLUME FULL<br />
* Default: TRANSLATION PACK CUTOFF 50<br />
* Default: TRANSLATION PACK NUM 0 (helices - all packing checked)<br />
* Default: TRANSLATION PACK NUM 500 (non-helices)<br />
setTRAN_VOLU(string ["FULL"|"REGION"|"LINE"|"AROUND"])<br />
setTRAN_START(dvect <START>)<br />
setTRAN_END(dvect <END>)<br />
setTRAN_POINT(dvect <POINT>)<br />
setTRAN_RANGE(float <RANGE>)<br />
setTRAN_FRAC(bool <True=FRAC False=ORTH>)<br />
setTRAN_PACK_USE(bool)<br />
setTRAN_PACK_CUTO(float)<br />
<br />
==[[Image:User2.gif|link=]]ZSCORE== <br />
; ZSCORE USE [ON|OFF]<br />
: Use the TFZ tests. Only applicable with [[#SEARCH | SEARCH METHOD FAST]]. (Note Phaser-2.4.0 and below use "ZSCORE SOLVED 0" to turn off the TFZ tests)<br />
; ZSCORE SOLVED <ZSCORE_SOLVED><br />
: Set the minimum TFZ that indicates a definite solution for amalgamating solutions in FAST search method. <br />
;ZSCORE STOP [ON|OFF]<br />
: Stop adding components beyond point where TFZ is below cutoff when adding multiple components in FAST mode. However, FAST mode will always add one component even if TFZ is below cutoff, or two components if starting search with no components input (no input solution).<br />
; ZSCORE HALF [ON|OFF]<br />
: Set the TFZ for amalgamating solutions in the FAST search method to the maximum of ZSCORE_SOLVED and half the maximum TFZ, to accommodate cases of partially correct solutions in very high TFZ cases (e.g. TFZ > 16)<br />
* Default: ZSCORE USE ON<br />
* Default: ZSCORE SOLVED 8<br />
* Default: ZSCORE HALF ON<br />
* Default: ZSCORE STOP ON<br />
setZSCO_USE(bool <True=ON False=OFF>)<br />
setZSCO_SOLV(floatType ZSCORE_SOLVED)<br />
setZSCO_HALF(bool <True=ON False=OFF>)<br />
setZSCO_STOP(bool <True=ON False=OFF>)<br />
<br><br />
<br><br />
<br />
=Expert Keywords=<br />
<br />
==[[Image:Expert.gif|link=]]MACANO== <br />
; MACANO PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for the refinement of SigmaN in the anisotropy correction<br />
; MACANO ANISO [ON|OFF] BINS [ON|OFF] SOLK [ON|OFF] SOLB [ON|OFF] ''{NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}''<br />
: Macrocycle for the custom refinement of SigmaN in the anisotropy correction. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACANO PROTOCOL DEFAULT<br />
setMACA_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACA(bool <ANISO>,bool <BINS>,bool <SOLK>,bool <SOLB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACMR== <br />
; MACMR PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACMR ROT [ON|OFF] TRA [ON|OFF] BFAC [ON|OFF] VRMS [ON|OFF] ''CELL [ON|OFF] LAST [ON|OFF] NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of molecular replacement solutions. Macrocycles are performed in the order in which they are entered. For description of VRMS see the [[FAQ]]. CELL is the scale factor for the unit cell for maps (EM maps). LAST is a flag that refines the parameters for the last component of a solution only, fixing all the others.<br />
; MACMR CHAINS [ON|OFF]<br />
: Split the ensembles into chains for refinement<br />
: Not possible as part of an automated mode<br />
* Default: MACMR PROTOCOL DEFAULT<br />
* Default: MACMR CHAINS OFF<br />
setMACM_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACM(bool <ROT>,bool <TRA>,bool <BFAC>,bool <VRMS>,bool <CELL>,bool <LAST>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
setMACM_CHAI(bool])<br />
<br />
==[[Image:Expert.gif|link=]]MACOCC== <br />
; MACOCC PROTOCOL [ DEFAULT | CUSTOM | OFF | ALL ]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACOCC NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of occupancy for solutions. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACOCC PROTOCOL DEFAULT<br />
setMACO_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACO(int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACGYRE== <br />
; MACGYRE PROTOCOL [ DEFAULT | CUSTOM | OFF | ALL ]<br />
: Protocol for refinement of gyre rotations<br />
; MACGYRE ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] ''ANCHOR [ON|OFF] SIGROT <SIGR> SIGTRA <SIGT> NCYCLE <NCYC> MINIMIZER [ BFGS | NEWTON | DESCENT ]''<br />
: Macrocycle for custom refinement of gyre refinement for solutions. Macrocycles are performed in the order in which they are entered.<br />
; MACGYRE SIGROT <SIGROT> <br />
; MACGYRE SIGTRA <SIGTRA> <br />
; MACGYRE ANCHOR [ON|OFF]<br />
: Override default values for harmonic restraints for rotation and translation refinement, and whether or not to anchor one fragment (no translation) for all macrocycles<br />
* Default: MACGYRE PROTOCOL DEFAULT<br />
setMACG_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACG(bool <REF>,bool <REF>, bool <REF>)<br />
addMACG_FULL(bool <REF>,bool <REF>,bool<REF>,bool <ANCHOR>,float <SIGROT>,float <SIGTRA>,int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
setMACG_SIGR(bool <SIGROT>)<br />
setMACG_SIGT(bool <SIGTRA>)<br />
setMACG_ANCH(bool <ANCHOR>)<br />
<br />
==[[Image:Expert.gif|link=]]MACSAD== <br />
; MACSAD PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for SAD refinement.<br />
:''n.b. PROTOCOL ALL will crash phaser and is only useful for debugging - see code for details''<br />
; MACSAD XYZ [ON|OFF] OCC [ON|OFF] BFAC [ON|OFF] FDP [ON|OFF] SA [ON|OFF] SB [ON|OFF] SP [ON|OFF] SD [ON|OFF] ''{PK [ON|OFF]} {PB [ON|OFF]} {NCYCLE <NCYC>} MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for SAD refinement. Macrocycles are performed in the order in which they are entered.<br />
*Default: MACSAD PROTOCOL DEFAULT<br />
setMACS_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACS(<br />
bool <XYZ>,bool <OCC>,bool <BFAC>,bool <FDP><br />
bool <SA>,bool <SB>,bool <SP>,bool <SD>,<br />
bool <PK>, bool <PB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACTNCS== <br />
; MACTNCS PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for pseudo-translational NCS refinement.<br />
; MACTNCS ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] ''NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for pseudo-translational NCS refinement. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACTNCS PROTOCOL DEFAULT<br />
setMACT_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACT(bool <ROT>,bool <TRA>,bool <VRMS>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]OCCUPANCY== <br />
; OCCUPANCY WINDOW ELLG <ELLG><br />
: Target eLLG for determining number of residues in window for occupancy refinement. The number of residues in a window will be an odd number. Occupancy refinement will be done for each offset of the refinement window.<br />
; OCCUPANCY WINDOW NRES <NRES><br />
: As an alternative to using the eLLG to define the number of residues in window for occupancy refinement, the number may be input directly. NRES must be an odd number.<br />
; OCCUPANCY WINDOW MAX <NRES><br />
: Maximum number of residues in an occupancy window (determined either by ellg or given as NRES) for which occupancy is refined. Prevents the refinement windows from spanning non-local regions of space.<br />
; OCCUPANCY MIN <MINOCC> MAX <MAXOCC><br />
: Minimum and maximum values of occupancy during refinement.<br />
; OCCUPANCY MERGE [ON/OFF]<br />
: Merge refined occupancies from different window offsets to give final occupancies per residue. If OFF, occupancies from a single window offset will be used, selected using OCCUPANCY OFFSET <N><br />
; OCCUPANCY FRAC <FRAC><br />
: Minimum fraction of the protein for which the occupancy may be set to zero.<br />
; OCCUPANCY OFFSET <N><br />
: If OCCUPANCY MERGE OFF, then <N> defines the single window offset from which final occupancies will be taken<br />
* Default: OCCUPANCY WINDOW ELLG 5<br />
* Default: OCCUPANCY WINDOW MAX 111<br />
* Default: OCCUPANCY MIN 0.01 MAX 1<br />
* Default: OCCUPANCY NCYCLES 1<br />
* Default: OCCUPANCY MERGE ON<br />
* Default: OCCUPANCY FRAC 0.5<br />
* Default: OCCUPANCY OFFSET 0<br />
setOCCU_WIND_ELLG(float <ELLG>)<br />
setOCCU_WIND_NRES(int <NRES>)<br />
setOCCU_WIND_MAX(int <NRES>)<br />
setOCCU_MIN(float <MIN>)<br />
setOCCU_MAX(float <MAX>)<br />
setOCCU_MERG(float <FRAC>)<br />
setOCCU_FRAC(bool)<br />
setOCCU_OFFS(int <N>)<br />
<br />
==[[Image:Expert.gif|link=]]RESCORE== <br />
; RESCORE ROT [ON|OFF]<br />
; RESCORE TRA [ON|OFF]<br />
: Toggle for rescoring of fast rotation function (ROT) or fast translation function (TRA) search peaks. <br />
* Default: RESCORE ROT ON<br />
* Default: RESCORE TRA ON|OFF will depend on whether phaser is running in the mode [[#MODE | MODE MR_AUTO]] with [[#SEARCH | SEARCH METHOD FAST]] or with [[#SEARCH | SEARCH METHOD FULL]], or running the translation function separately [[#MODE | MODE MR_FTF]]. For [[#SEARCH | SEARCH METHOD FAST]] the default also depends on whether or not the expected LLG target [[#ELLG | ELLG TARGET <TARGET>]] value is reached.<br />
setRESC_ROTA(bool)<br />
setRESC_TRAN(bool)<br />
<br />
==[[Image:Expert.gif|link=]]RFACTOR== <br />
; RFACTOR USE [ON|OFF]<br />
: For cases of searching for one ensemble when there is one ensemble in the asymmetric unit, the R-factor for the ensemble at the orientation and position in the input is calculated. If this value is low then MR is not performed in the MR_AUTO job in FAST search mode. Instead, rigid body refinement is performed before exiting. Note that the same R-factor test and cutoff is used for judging success in single-atom molecular replacement (MR_ATOM mode).<br />
; RFACTOR CUTOFF <VALUE><br />
: Rfactor in percent used as cutoff for deciding whether or not the R-factor indicates that MR is not necessary.<br />
* Default: RFACTOR USE ON CUTOFF 35<br />
setRFAC_USE(bool)<br />
setRFAC_CUTO(float <PERCENT>)<br />
<br />
==[[Image:Expert.gif|link=]]SAMPLING==<br />
; SAMPLING ROT <SAMP><br />
; SAMPLING TRA <SAMP><br />
: Sampling of search given in degrees for a rotation search and Ångstroms for a translation search. Sampling for rotation search depends on the mean radius of the Ensemble and the high resolution limit (dmin) of the search.<br />
* Default: SAMP = 2*atan(dmin/(4*meanRadius)) (ROTATION FUNCTION)<br />
* Default: SAMP = dmin/5; (BRUTE TRANSLATION FUNCTION)<br />
* Default: SAMP = dmin/4; (FAST TRANSLATION FUNCTION)<br />
setSAMP_ROTA(float <SAMP>)<br />
setSAMP_TRAN(float <SAMP>)<br />
<br><br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS USE [ON|OFF]<br />
: Use TNCS if present: apply TNCS corrections. (Note: was TNCS IGNORE [ON|OFF] in Phaser-2.4.0)<br />
; TNCS RLIST ADD [ON | OFF]<br />
: Supplement the rotation list used in the translation function with rotations already present in the list of known solutions. New molecules in the same orientation as those in the known search (as occurs with translational ncs) may not have peaks associated with them from the rotation function because the known molecules mask the presence of the ones not yet found. <br />
; TNCS PATT HIRES <hires><br />
: High resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT LORES <lores><br />
: Low resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT PERCENT <percent><br />
: Percent of origin Patterson peak that qualifies as a TNCS vector<br />
; TNCS PATT DISTANCE <distance><br />
: Minimum distance of Patterson peak from origin that qualifies as a TNCS vector<br />
; TNCS TRANSLATION PERTURB [ON | OFF]<br />
: If the TNCS translation vector is on a special position, perturb the vector from the special position before refinement<br />
; TNCS ROTATION RANGE <angle><br />
: Maximum deviation from initial rotation from which to look for rotational deviation. Default uses internally determined value based on resolution of data and size of G-function effective molecular radius. Value of 0 turns rotational refinement off.<br />
; TNCS ROTATION SAMPLING <sampling><br />
: Sampling for rotation search. Default uses internally determined value based on resolution of data and size of G-function effective molecular radius. Value of 0 turns rotational refinement off.<br />
* Default: TNCS USE ON<br />
* Default: TNCS RLIST ADD ON<br />
* Default: TNCS PATT HIRES 5<br />
* Default: TNCS PATT LORES 10<br />
* Default: TNCS PATT PERCENT 20<br />
* Default: TNCS PATT DISTANCE 15 <br />
* Default: TNCS TRANSLATION PERTURB ON<br />
setTNCS_USE(bool)<br />
setTNCS_RLIS_ADD(bool)<br />
setTNCS_PATT_HIRE(float <HIRES>)<br />
setTNCS_PATT_LORE(float <LORES>) <br />
setTNCS_PATT_PERC(float <PERCENT>) <br />
setTNCS_PATT_DIST(float <DISTANCE>)<br />
setTNCS_TRAN_PERT(bool)<br />
setTNCS_ROTA_RANG(float <RANGE>) <br />
setTNCS_ROTA_SAMP(float <SAMPLING>) <br />
<br><br />
<br><br />
<br />
=Developer Keywords=<br />
==[[Image:Developer.gif|link=]]BINS== <br />
; BINS DATA [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the data.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections<br />
; BINS ENSE [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the calaculated structure factos for the ensembles.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections<br />
* Default: BINS DATA MIN 6 MAX 50 WIDTH 500 <br />
* Default: BINS ENSE MIN 6 MAX 1000 WIDTH 1000 <br />
setBINS_DATA_MINI(float <L>)<br />
setBINS_DATA_MAXI(float <H>)<br />
setBINS_DATA_WIDT(float <W>)<br />
setBINS_ENSE_MINI(float <L>)<br />
setBINS_ENSE_MAXI(float <H>)<br />
setBINS_ENSE_WIDT(float <W>)<br />
<br />
==[[Image:Developer.gif|link=]]BFACTOR==<br />
; BFACTOR WILSON RESTRAINT [ON|OFF]<br />
: Toggle to use the Wilson restraint on the isotropic component of the atomic B-factors in SAD phasing.<br />
; BFACTOR SPHERICITY RESTRAINT [ON|OFF] <br />
: Toggle to use the sphericity restraint on the anisotropic B-factors in SAD phasing<br />
; BFACTOR REFINE RESTRAINT [ON|OFF] <br />
: Toggle to use the restraint to zero for the molecular B-factor in molecular replacement.<br />
; BFACTOR WILSON SIGMA <SIGMA><br />
: The sigma of the Wilson restraint.<br />
; BFACTOR SPHERICITY SIGMA <SIGMA><br />
: The sigma of the sphericity restraint.<br />
; BFACTOR REFINE SIGMA <SIGMA><br />
: The sigma of the restraint to zero for the molecular B-factor in molecular replacement.<br />
* Default: BFACTOR WILSON RESTRAINT ON <br />
* Default: BFACTOR SPHERICITY RESTRAINT ON <br />
* Default: BFACTOR REFINE RESTRAINT ON <br />
* Default: BFACTOR WILSON SIGMA 5<br />
* Default: BFACTOR SPHERICITY SIGMA 5<br />
* Default: BFACTOR REFINE SIGMA 6<br />
setBFAC_WILS_REST(bool <True|False>)<br />
setBFAC_SPHE_REST(bool <True|False>)<br />
setBFAC_REFI_REST(bool <True|False>) <br />
setBFAC_WILS_SIGM(float <SIGMA>) <br />
setBFAC_SPHE_SIGM(float <SIGMA>) <br />
setBFAC_REFI_SIGM(float <SIGMA>)<br />
<br />
==[[Image:Developer.gif|link=]]BOXSCALE==<br />
; BOXSCALE <BOXSCALE><br />
: Scale for box for calculating structure factors. The ensembles are put in a box equal to (extent of molecule)*BOXSCALE<br />
* Default: BOXSCALE 4<br />
setBOXS<float <BOXSCALE>)<br />
<br />
==[[Image:Developer.gif|link=]]CELL==<br />
; <span style="color:darkorange">Python Only</span> <br />
: Unit cell dimensions<br />
* Default: Cell read from MTZ file<br />
setCELL(float <A>,float <nowiki><B></nowiki>,float <C>,float <ALPHA>,float <BETA>,float <GAMMA>)<br />
setCELL6(float_array <A B C ALPHA BETA GAMMA>)<br />
<br />
==[[Image:Developer.gif|link=]]COMPOSITION== <br />
; COMPOSITION MIN SOLVENT <PERC><br />
: Minimum solvent to give maximum asu packing volume for automated search copy determination (NUM 0)<br />
* Default: COMPOSITION MIN SOLVENT 0.2<br />
setCOMP_MIN_SOLV(float)<br />
<br />
==[[Image:Developer.gif|link=]]DDM== <br />
; DDM SLIDER <VAL> <br />
: The SLIDER window width is used to smooth the Difference Distance Matrix. <br />
; DDM DISTANCE MIN <VAL> MAX <VAL> STEP <VAL><br />
: The range and step interval, as the fraction of the difference between the lowest and highest DDM values used to step.<br />
; DDM SEPARATION MIN <VAL> MAX <VAL><br />
: Through space separation in Angstroms used.<br />
; DDM SEQUENCE MIN <VAL> MAX <VAL><br />
: The range of sequence separations between matrix pairs.<br />
; DDM JOIN MIN <VAL> MAX <VAL><br />
: The range of lengths of the sequences to join if domain segments are discontinuous in percentages of the polypeptide chain.<br />
* Default: DDM SLIDER 0<br />
* Default: DDM DISTANCE MIN 1 MAX 5 STEP 50<br />
* Default: DDM SEPARATION MIN 7 MAX 14<br />
* Default: DDM SEQUENCE MIN 0 MAX 1<br />
* Default: DDM JOIN MIN 2 MAX 12<br />
setDDM_SLID(int <VAL>) <br />
setDDM_DIST_STEP(int <VAL>) <br />
setDDM_DIST_MINI(int <VAL>) <br />
setDDM_DIST_MAXI(int <VAL>) <br />
setDDM_SEPA_MINI(float <VAL>) <br />
setDDM_SEPA_MAXI(float <VAL>)<br />
setDDM_JOIN_MINI(int <VAL>) <br />
setDDM_JOIN_MAXI(int <VAL>) <br />
setDDM_SEQU_MINI(int <VAL>) <br />
setDDM_SEQU_MAXI(int <VAL>)<br />
<br />
==[[Image:Developer.gif|link=]]ENM== <br />
; ENM OSCILLATORS [ <sup>1</sup>RTB | <sup>2</sup>ALL ] <br />
: Define the way the atoms are used for the elastic network model.<br />
: <sup>1</sup>Use the rotation-translation block method.<br />
: <sup>2</sup>Use all atoms to determine the modes (only for use on very small molecules, less than 250 atoms). <br />
; ENM MAXBLOCKS <MAXBLOCKS><br />
: MAXBLOCKS is the number of rotation-translation blocks for the RTB analysis.<br />
; ENM NRES <NRES><br />
: For the RTB analysis, by default NRES=0 and then it is calculated so that it is as small as it can be without reaching MAXBlocks. <br />
; ENM RADIUS <RADIUS><br />
: Elastic Network Model interaction radius (Angstroms)<br />
; ENM FORCE <FORCE><br />
: Elastic Network Model force constant<br />
* Default: ENM OSCILLATORS RTB MAXBLOCKS 250 NRES 0 RADIUS 5 FORCE 1<br />
setENM_OSCI(str ["RTB"|"CA"|"ALL"])<br />
setENM_RTB_MAXB(float <MAXB>)<br />
setENM_RTB_NRES(float <NRES>) <br />
setENM_RADI(float <RADIUS>) <br />
setENM_FORC(float <FORCE>)<br />
<br />
==[[Image:Developer.gif|link=]]NORMALIZATION==<br />
; <span style="color:darkorange">Scripting Only</span><br />
; NORM EPSFAC WRITE <FILENAME><br />
: The normalization factors that correct for anisotropy in the data are written to BINARY file FILENAME<br />
; NORM EPSFAC READ <FILENAME><br />
: The normalization factors that correct for anisotropy in the data are read from BINARY file FILENAME. Further refinement is automatically turned off.<br />
; <span style="color:darkorange">Python Only</span><br />
The normalization factors that correct for anisotropy in the data, extracted from ResultANO object with getSigmaN(). Anisotropy should subsequently be turned off with setMACA_PROT("OFF").<br />
setNORM_DATA(data_norm <SIGMAN>)<br />
<br />
==[[Image:Developer.gif|link=]]OUTLIER==<br />
; OUTLIER REJECT [ON|OFF]<br />
: Reject low probability data outliers<br />
; OUTLIER PROB <PROB><br />
: Cutoff for rejection of low probablity outliers<br />
* Default: OUTLIER REJECT ON PROB 0.000001<br />
setOUTL_REJE(bool) <br />
setOUTL_PROB(float <PROB>)<br />
<br />
==[[Image:Developer.gif|link=]]PTGROUP== <br />
; PTGROUP COVERAGE <COVERAGE><br />
: Percentage coverage for two sequences to be considered in same pointgroup<br />
; PTGROUP IDENTITY <IDENTITY><br />
: Percentage identity for two sequences to be considered in same pointgroup<br />
; PTGROUP RMSD <RMSD><br />
: Percentage rmsd for two models to be considered in same pointgroup<br />
; PTGROUP TOLERANCE ANGULAR <ANG><br />
: Angular tolerance for pointgroup<br />
; PTGROUP TOLERANCE SPATIAL <DIST><br />
: Spatial tolerance for pointgroup<br />
setPTGR_COVE(float <COVERAGE>) <br />
setPTGR_IDEN(float <IDENTITY>) <br />
setPTGR_RMSD(float <RMSD>) <br />
setPTGR_TOLE_ANGU(float <ANG>) <br />
setPTGR_TOLE_SPAT(float <DIST>)<br />
<br />
==[[Image:Developer.gif|link=]]RESHARPEN== <br />
; RESHARPEN PERCENTAGE <PERC><br />
: Perecentage of the B-factor in the direction of lowest fall-off (in anisotropic data) to add back into the structure factors F_ISO and FWT and FDELWT so as to sharpen the electron density maps<br />
* Default: RESHARPEN PERCENT 100<br />
setRESH_PERC(float <PERCENT>)<br />
<br />
==[[Image:Developer.gif|link=]]SOLPARAMETERS==<br />
; SOLPARAMETERS SIGA FSOL <FSOL> BSOL <BSOL> MIN <MINSIGA><br />
: Babinet solvent parameters for Sigma(A) curves. MINSIGA is the minimum SIGA for Babinet solvent term (low resolution only). The solvent term in the Sigma(A) curve is given by <BR>max(1 - FSOL*exp(-BSOL/(4d^2)),MINSIGA).<br />
; SOLPARAMETERS BULK USE [ON|OFF]<br />
: Toggle for use of solvent mask scaling parameters for ensemble structure factors, applied to Fmask.<br />
; SOLPARAMETERS BULK FSOL <FSOL> BSOL <BSOL> <br />
: Solvent mask scaling parameters for ensemble structure factors, applied to Fmask.<br />
* Default: SOLPARAMETERS SIGA FSOL 1.05 BSOL 501 MIN 0.1<br />
* Default: SOLPARAMETERS SIGA RESTRAINT ON<br />
* Default: SOLPARAMETERS BULK USE OFF<br />
* Default: SOLPARAMETERS BULK FSOL 0.35 BSOL 45<br />
setSOLP_SIGA_FSOL(float <FSOL>) <br />
setSOLP_SIGA_BSOL(float <BSOL>)<br />
setSOLP_SIGA_MIN(float <MINSIGA>)<br />
setSOLP_BULK_USE(bool)<br />
setSOLP_BULK_FSOL(float <FSOL>) <br />
setSOLP_BULK_BSOL(float <BSOL>)<br />
<br />
==[[Image:Developer.gif|link=]]TARGET== <br />
; TARGET ROT FAST TYPE [LERF1 | CROWTHER]<br />
: Target function type for fast rotation searches<br />
; TARGET TRA FAST TYPE [LETF1 | LETF2 | CORRELATION]<br />
: Target function type for fast translation searches<br />
setTARG_ROTA_TYPE(string TYPE)<br />
setTARG_TRAN_TYPE(string TYPE)<br />
<br />
==[[Image:Developer.gif|link=]]TNCS==<br />
; TNCS ROTATION ANGLE <A> <nowiki><B></nowiki> <C><br />
: Input rotational difference between molecules related by the pseudo-translational symmetry vector, specified as rotations in degrees about x, y and z axes. Central value for grid search (RANGE > 0).<br />
; TNCS ROTATION RANGE <A><br />
: Range of angular difference in rotation angles to explore around central angle.<br />
; TNCS ROTATION SAMPLING <A><br />
: Sampling step for rotational grid search.<br />
; TNCS TRA VECTOR <x y z> <br />
: Input pseudo-translational symmetry vector (fractional coordinates). By default the translation is determined from the Patterson.<br />
; TNCS VARIANCE RMSD <num><br />
: Input estimated rms deviation between pseudo-translational symmetry vector related molecules.<br />
; TNCS VARIANCE FRAC <num><br />
: Input estimated fraction of cell content that obeys pseudo-translational symmetry.<br />
; TNCS LINK RESTRAINT [ON | OFF]<br />
: Link the occupancy of atoms related by TNCS in SAD phasing<br />
; TNCS LINK SIGMA <sigma><br />
: Sigma of link restraint of the occupancy of atoms related by TNCS in SAD phasing<br />
* Default: TNCS ROTATION ANGLE 0 0 0<br />
* Default: TNCS ROTATION RANGE -999 (determine from structure size and resolution)<br />
* Default: TNCS ROTATION SAMPLING -999 (determine from structure size and resolution)<br />
* Default: TNCS TRANSLATION VECTOR determined from position of Patterson peak<br />
* Default: TNCS VARIANCE RMSD 0.4 <br />
* Default: TNCS VARIANCE FRAC 1 <br />
* Default: TNCS LINK RESTRAINT ON<br />
* Default: TNCS LINK SIGMA 0.1<br />
setTNCS_ROTA_ANGL(dvect3 <A B C>) <br />
setTNCS_TRAN_VECT(dvect3 <X Y Z>) <br />
setTNCS_VARI_RMSD(float <RMSD>) <br />
setTNCS_VARI_FRAC(float <FRAC>)<br />
setTNCS_LINK_REST(bool)<br />
setTNCS_LINK_SIGM(float <SIGMA>)<br />
; <span style="color:darkorange">Scripting Only</span><br />
; TNCS EPSFAC WRITE <FILENAME><br />
: The normalization factors that correct for tNCS in the data are written to BINARY file FILENAME<br />
; TNCS EPSFAC READ <FILENAME><br />
: The normalization factors that correct for tNCS in the data are read from BINARY file FILENAME. Further refinement is automatically turned off.<br />
; <span style="color:darkorange">Python Only</span><br />
The normalization factors that correct for tNCS in the data, extracted from ResultNCS object with getPtNcs(). tNCS refinement should subsequently be turned off with setMACT_PROT("OFF").<br />
setTNCS(data_tncs <PTNCS>)<br />
<br />
==[[Image:Developer.gif|link=]]TRANSLATION== <br />
; TRANSLATION MAPS [ON | OFF]<br />
: Output maps of fast translation function FSS scoring functions<br />
: Maps take the names <ROOT>.<ensemble>.k.e.map where k is the Known backgound number and e is the Euler angle number for that known background<br />
* Default: TRANSLATION MAPS OFF<br />
setTRAN_MAPS(bool)</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Molecular_Replacement&diff=2415Molecular Replacement2018-01-26T12:01:56Z<p>Airlie: /* Has Phaser Solved It? */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
'''Quicklink to example scripts''' → [[MR using keyword input]]<br />
<br />
'''Quicklink to phaser.famos (find_alt_orig_sym_mate) documentation''' → [[Famos]]<br />
<br />
Phaser should be able to solve most structures with the Automated Molecular Replacement mode, and this is the first mode that you should try. Give Phaser your data ([[#How to Define Data|How to Define Data]]) and your models ([[#How to Define Models|How to Define Models]]), tell Phaser what to search for, and a list of possible spacegroups (in the same point group).<br />
<br />
If this doesn't work (see [[#Has Phaser Solved It?| Has Phaser Solved It?]]), you can try selecting peaks of lower significance in the rotation function in case the real orientation was not within the selection criteria. By default peaks above 75% of the top peak are selected (see [[#How to Select Peaks| How to Select Peaks]]). See [[#What to do in Difficult Cases| What to do in Difficult Cases]] for more hints and tips. If the automated molecular replacement mode doesn't work even with non-default input you need to run the modes of Phaser separately. The possibilities are endless - you can even try exhaustive searches (translations of all orientations) if you want - but experience has shown that most structures that can be solved by Phaser can be solved by relatively simple strategies.<br />
<br />
==Automated Molecular Replacement==<br />
Automated Molecular Replacement combines the anisotropy correction, likelihood enhanced fast rotation function, likelihood enhanced fast translation function, packing and refinement modes for multiple search models and a set of possible spacegroups to automatically solve a structure by molecular replacement. Top solutions are output to the files FILEROOT.sol, FILEROOT.#.mtz and FILEROOT.#.pdb (where "#" refers to the sorted solution number, 1 being the best, and only 1 is output by default). Many structures can be solved by running an automated molecular replacement search with defaults, giving the ensembles that you expect to be easiest to find first.<br />
<br />
At the completion of Molecular Replacement you may wish to place your solutions on a common origin with a previous solution, for which [[Famos | Famos ]] can be used.<br />
<br />
[[Image:Phaser_MR_auto.gif|Flow Diagram for Automated MR]]<br />
<br />
==Should Phaser Solve It?==<br />
The difficulty of a molecular replacement problem depends primarily on two major factors: how well the model will be able to explain the diffraction data (which depends both on the accuracy of the model and on its completeness), and how many reflections can be explained, at least in part. Each reflection provides a piece of information that helps to identify correct MR solutions.<br />
<br />
It is possible to make a reasonable prediction of whether or not a solution will be found. If the quality of the model (its accuracy and completeness) can be estimated, then the expected contribution of each reflection to the total LLG can also be estimated. From a large battery of tests, we know that an LLG of 40 or greater usually indicates a correct solution (at least in the absence of complicating factors such as translational non-crystallographic symmetry, tNCS). Building on this understanding, if it is estimated that the LLG will be 60 or less, then Phaser will assume that the problem is a difficult one, and will implement search procedures optimised for difficult problems.<br />
<br />
==What Resolution of Data Should be Used?==<br />
The signal for a molecular replacement solution should be very clear if the expected value of the LLG is much higher than the minimum required to be fairly certain of a solution. Currently Phaser aims for a minimum LLG of 120 and, if it is possible to achieve an even higher value, given the quality of the model and the quantity of diffraction data, then the resolution for the initial search is limited to the value required to achieve an expected LLG of 120. Data to the full resolution are still used for a final rigid-body refinement, or in a second pass if a clear solution is not found in the first attempt.<br />
<br />
However, if the model is expected to have a large RMS error (based usually on the correlation between sequence identity and RMS error), then data to high resolution will not contribute any significant signal. Regardless of the expected LLG at the highest resolution limit, the resolution used is limited to 1.8 times the estimated RMS error of the model, because this resolution limit gives about 99% of the LLG that could be achieved.<br />
<br />
Because Phaser implements strategies designed to solve structures with as much confidence as possible, as efficiently as possible, it is best to leave the choice of resolution to Phaser, at least in the first instance.<br />
<br />
==Has Phaser Solved It?==<br />
{| class="wikitable" style="text-align:center" style="margin-left: 30px" <br />
|-<br />
! TF Z-score !! Have I solved it?<br />
|-<br />
| less than 5 || no<br />
|-<br />
| 5 - 6 || unlikely<br />
|-<br />
| 6 - 7 || possibly<br />
|-<br />
| 7 - 8 || probably<br />
|-<br />
| more than 8* ||definitely<br />
|-<br />
|colspan="2" style="text-align: center;" | *''6 for 1st model in monoclinic space groups''<br />
|} <br />
<br />
Ideally, a unique solution with a strong signal will be found at the end of the search. If you are searching for multiple components, then ideally the search for each component will also give a strong signal. However if the signal-to-noise of your search is low, there will be noise peaks and multiple ambiguous solutions. Signal-to-noise is judged using the '''Z-score''', which is computed by comparing the LLG values from the rotation or translation search with LLG values for a set of random rotations or translations. The mean and the RMS deviation from the mean are computed from the random set, then the Z-score for a search peak is defined as its LLG minus the mean, all divided by the RMS deviation, ''i.e. '' '''the number of standard deviations above (or below) the mean. '''<br />
<br />
For a rotation function, the correct orientation may be well down the list with a Z-score (number of standard deviations above the mean value, or RFZ) under 4, and it is often not possible to identify the correct orientation until a translation function is performed and yields a clear solution. Note that the signal-to-noise of the rotation function drops with increasing number of primitive symmetry operations (the number of different orientations for symmetry-related molecules), because there is more uncertainty about how the structure factor contributions from symmetry-related copies will add up.<br />
<br />
For a translation function the correct solution will generally have a Z-score (TFZ) over 5 and be well separated from the rest of the solutions. Of course, there will always be exceptions! The table gives a very rough guide to interpreting TFZ scores. This table will be updated, as we learn more from systematic molecular replacement trials.<br />
<br />
When you are searching for multiple components, the signal may be low for the first few components but, as the model becomes more complete, the signal should become stronger. Finding a clear solution for a new component is a good sign that the partial solution to which that component was added was indeed correct.<br />
<br />
You should always at least glance through the summary of the logfile. One thing to look for, in particular, is whether any translation solutions with a high Z-score have been rejected by the packing step. By default up to 5 percent of marker atoms (C-alpha atoms for protein) are allowed to be involved in clashes. A solution with more clashes may still be correct, and the clashes may arise only because of differences in small surface loops. If this happens, repeat the run allowing a suitable number of clashes. Note that, unless there is specific evidence in the logfile that a high TFZ-score solution is being rejected with a few clashes, it is much better to edit the model to remove the loops than to increase the number of allowed clashes. Packing criteria are a very powerful constraint on the translation function, and increasing the number of allowed clashes beyond the default will increase the search time enormously without the possibility of generating any correct solutions that would not have otherwise been found.<br />
<br />
Note that, by default, Phaser will produce a single PDB file corresponding to the top solution found (if any), so finding a single PDB file in your output directory is not an indication that the search succeeded! You have to look, at least, at the summary of the logfile, or at the list of possible solutions in the .sol file that is produced if you run Phaser from ccp4i or command-line scripts.<br />
<br />
==Annotation==<br />
<br />
A highly compact summary of the history of the statistics of a solution is given in the SOLUTION SET in the .sol file. This is a good place to start your analysis of the output. The annotation gives the Z-score of the solution at each rotation and translation function, the number of clashes in the packing, and the refined LLG.<br />
<br />
{| class="wikitable" style="text-align:center" style="margin-left: 30px" <br />
|-<br />
! Annotation !! Meaning<br />
|-<br />
| RFZ= || Rotation Function Z-score<br />
|-<br />
| TFZ= || Translation Function Z-score<br />
|-<br />
| PAK= || Number of packing clashes<br />
|-<br />
| LLG= || LLG after refinement. Will be repeated when a low resolution refinement is followed by a high resolution refinement.<br />
|-<br />
| TFZ== || Translation Function Z-score equivalent, only calculated for the top solution after refinement (or for the number of top files specified by TOPFILES)<br />
|-<br />
| RF++ || Rotation angle from previous strong solution has been used in the addition of next solution<br />
|-<br />
| RF*0 || Rotation angle 000 identified by low R-factor of input model<br />
|-<br />
| TFZ=* || First molecule in P1 (arbitrary origin, no Translation Function required)<br />
|-<br />
| TF*0 || Translation vector 000 identified by low R-factor of input model<br />
|-<br />
| (&&nbsp;... & ...) || Set of TFZ PAK and LLG values for placements that were amalgamated (more than one placement from a single Translation Function)<br />
|-<br />
| LLG+=(...&nbsp;&&nbsp;...)&nbsp;|| Set of LLG values calculated during amalgamation, which will always be increasing in value<br />
|-<br />
| +TNCS || Components added by Translational NCS relation<br />
|-<br />
| *T=<i>n</i> || Solution matches template solution <i>n</i><br />
|} <br />
<br />
Two versions of TFZ (the translation function Z-score) now appear for each component. The first ("TFZ=") is the Z-score from the actual translation search, which depends on the accuracy of the orientation used for that search. The second ("TFZ==") is the TFZ-equivalent, which indicates what the TFZ score would have been with the correct (refined) orientation. You should see the TFZ-equivalent is high at least for the final components of the solution, and that the LLG (log-likelihood gain) increases as each component of the solution is added. For example, in the case of beta-blip the annotation for the single solution output in the .sol file shows these features<br />
<br />
SOLU SET RFZ=10.7 TFZ=24.3 PAK=0 LLG=472 TFZ==24.7 RFZ=6.4 TFZ=24.4 PAK=0 LLG=1006 TFZ==29.7 LLG=1006 TFZ==29.7<br />
SOLU 6DIM ENSE beta EULER 200.849 41.269 183.909 FRAC -0.49604 -0.15830 -0.28092 BFAC 0.00000<br />
SOLU 6DIM ENSE blip EULER 43.749 80.793 117.292 FRAC -0.12289 0.29435 -0.09266 BFAC 0.00000<br />
<br />
Note that the Euler angles in Phaser follow the same convention as those defined for the Crowther fast rotation function, i.e. z-y-z (rotate around the z-axis, followed by the new y-axis, followed by the new z-axis).<br />
<br />
==History==<br />
<br />
A highly compact summary of the history of the peak positions of a solution is given in the SOLUTION HISTORY in the .sol file. Together with the SOLUTION SET annotation, this is useful in your analysis of the output. <br />
<br />
{| class="wikitable" style="text-align:center" style="margin-left: 30px" <br />
|-<br />
! History !! Meaning<br />
|-<br />
| RF/TF(r/t:n) || (r) Rotation Function peak number/(t) Translation Function peak number for the rotation function : (n) number of peak in final merged and sorted list<br />
|-<br />
| PAK(n:m) || (n) input solution number : (m) output solution number after packing condition applied<br />
|-<br />
| RNP(m,a,b,c,... : p) || All input peaks amalgamated after refinement to give output solution number (m and others): (p) output solution number<br />
|-<br />
| FUSE(A,B,C) || Solution numbers merged in amalgamation<br />
|} <br />
<br />
For example, in the case of beta-blip the annotation for the single solution output in the .sol file shows these features<br />
<br />
SOLU HISTORY RF/TF(1/1:1)PAK(1:1)RNP(1:1)RNP(1:1)<br />
SOLU 6DIM ENSE beta EULER 200.849 41.269 183.909 FRAC -0.49604 -0.15830 -0.28092 BFAC 0.00000<br />
SOLU 6DIM ENSE blip EULER 43.749 80.793 117.292 FRAC -0.12289 0.29435 -0.09266 BFAC 0.00000<br />
<br />
A more complicated structure solution may have<br />
<br />
SOLU HISTORY RF/TF(7/1:10)PAK(10:10)RNP(10,12,13,11,17,16,18,25,3,8,22,21,20,7,969,6,5,201,9,4,390,2,1,19:1)RNP(1:1)<br />
<br />
==What to do in Difficult Cases==<br />
<br />
Not every structure can be solved by molecular replacement, but the right strategy can push the limits. What to do when the default jobs fail depends on why your structure is difficult.<br />
*'''Flexible Structure'''<br />
*:The relative orientations of the domains may be different in your crystal than in the model. If that may be the case, break the model into separate PDB files containing rigid-body units, enter these as separate ensembles, and search for them separately. If you find a convincing solution for one domain, but fail to find a solution for the next domain, you can take advantage of the knowledge that its orientation is likely to be similar to that of the first domain. The ROTAte&nbsp;AROUnd option of the brute rotation search can be used to restrict the search to orientations within, say, 30 degrees of that of the known domain. Allow for close approach of the domains by increasing the allowed clashes with the PACK keyword by, say, 1 for each domain break that you introduce. Note that it is possible to use the brute rotation search as part of the automated molecular replacement pipeline, by changing the choice of the type of rotation search. Alternatively, you could try generating a series of models perturbed by normal modes, with the NMAPdb keyword. One of these may duplicate the hinge motion and provide a good single model.<br />
*'''Poor or Incomplete Model'''<br />
*:Signal-to-noise is reduced by coordinate errors or incompleteness of the model. Since the rotation search has lower signal to begin with than the translation search, it is usually more severely affected. For this reason, it can be very useful to use the subsequent translation search as a way to choose among many (say 1000) orientations. THe MR_AUTO FAST search mode automatically reduces the cutoff for accepting peaks from the fast rotation function if the decault pass does not find a solution with a high z-score, but you can manually reduce this further with the PEAKS and PURGE keywords. You can also try turning off the clustering of fast rotation function peaks because the correct orientation may sit on the shoulder of a peak in the rotation function. <br />
*:As shown convincingly by Schwarzenbacher ''et al.'' (Schwarzenbacher, Godzik, Grzechnik &amp; Jaroszewski, ''Acta Cryst.'' D'''60''', 1229-1236, 2004), judicious editing can make a significant difference in the quality of a distant model. In a number of tests with their data on models below 30% sequence identity, we have found that Phaser works best with a "mixed model" (non-identical sidechains longer than Ser replaced by Ser). In agreement with their results, the best models are generally derived using more sophisticated alignment protocols, such as their FFAS protocol. Use [http://www.phenix-online.org/documentation/sculptor.htm phenix.sculptor] to edit your model.<br />
*'''High Degree of Non-crystallographic Symmetry'''<br />
*:If there are clear peaks in the self-rotation function, you can expect orientations to be related by this known NCS. Methods to automatically use such information will be implemented in a future version of Phaser. In the meantime, you can work out for yourself the orientations that would be consistent with NCS and use the ROTAte&nbsp;AROUnd option to sample similar orientations. Alternatively, you may have an oligomeric model and expect similar NCS in the crystal. First search with the oligomeric model; if this fails, search with a monomer. If that succeeds, you can again use the ROTAte&nbsp;AROUnd option to force a subsequent monomer to adopt an orientation similar to the one you expect.<br />
*'''What <u>not</u> to do'''<br />
*:The automated mode of Phaser is fast when Phaser finds a high Z-score solution to your problem. When Phaser cannot find a solution with a significant Z-score, it "thrashes", meaning it maintains a list of 100-1000's of low Z-score potential solutions and tries to improve them. This can lead to exceptionally long Phaser runs (over a week of CPU time). Such runs are possible because the highly automated script allows many consecutive MR jobs to be run without you having to manually set 100-1000's of jobs running and keep track of the results. "Thrashing" generally does not produce a solution: solutions generally appear relatively quickly or not at all. It is more useful to go back and analyse your models and your data to see where improvements can be made. Your system manager will appreciate you terminating these jobs.<br />
*:It is also not a good idea to effectively remove the packing test. Unless there is specific evidence in the logfile that a high TF-function Z-score solution is being rejected with a few clashes, it is much better to edit the model to remove the loops than to increase the number of allowed clashes. Packing criteria are a very powerful constraint on the translation function, and increasing the number of allowed clashes beyond a few (e.g. 1-5) will increase the search time enormously without the possibility of generating any correct solutions that would not have otherwise been found.<br />
*'''Other suggestions'''<br />
*:Phaser has powerful input, output and scripting facilities that allow a large number of possibilities for altering default behaviour and forcing Phaser to do what you think it should. However, you will need to read the information in the manual below to take advantage of these facilities!<br />
<br />
==How to Define Data==<br />
You need to tell Phaser the name of the mtz file containing your data and the columns in the mtz file to be used using the HKLIn and LABIn keywords. Additional keywords (BINS CELL OUTLier RESOlution SPACegroup) define how the data are used.<br />
<br />
==How to Define Models==<br />
Phaser must be given the models that it will use for molecular replacement. A model in Phaser is referred to as an "ensemble", even when it is described by a single file. This is because it is possible to provide a set of aligned structures as an ensemble, from which a statistically-weighted averaged model is calculated. A molecular replacement model is provided either as one or more aligned pdb files, or as an electron density map, entered as structure factors in an mtz file. Each ensemble is treated as a separate type of rigid body to be placed in the molecular replacement solution. An ensemble should only be defined once, even if there are several copies of the molecule in the asymmetric unit.<br />
<br />
Fundamental to the way in which Phaser uses MR models (either from coordinates or maps) is to estimate how the accuracy of the model falls off as a function of resolution, represented by the Sigma(A) curve. To generate the Sigma(A) curve, Phaser needs to know the RMS coordinate error expected for the model and the fraction of the scattering power in the asymmetric unit that this model contributes.<br />
<br />
A Babinet-style correction is used to account for the effects of disordered solvent on the completeness of the model at low resolution.<br />
<br />
Molecular replacement models are defined with the ENSEmble keyword and the COMPosition keyword. The ENSEmble keyword gives (amongst other things) the RMS deviation for the Sigma(A) curve. The COMPosition keyword is used to deduce the fraction of the scattering power in the asymmetric unit that each ensemble contributes. The composition of the asymmetric unit is defined either by entering the molecular weights or sequences of the components in the asymmetric unit, and giving the number of copies of each. Expert users can also enter the fraction of the scattering of each component directly, although the composition must still be entered for the absolute scale calculation. Please note that the composition supplied to Phaser has to include everything in the asymmetric unit, not just what is being looked for in the current search!<br />
<br />
===Building an Ensemble from Coordinates===<br />
The RMS deviation is determined directly from RMS or indirectly from IDENtity in the ENSEmble<br />
keyword using a formula that depends on the sequence identity and the number of residues in the model.<br />
<br />
The RMS deviation estimated from ID may be an underestimate of the true value if there is a slight conformational change between the model and target structures. To find a solution in these cases it may be necessary to increase the RMS from the default value generated from the ID, by say 0.5 Ångstroms. On the other hand, when Phaser succeeds in solving a structure from a model with sequence identity much below 30%, it is often found that the fold is preserved better than the average for that level of sequence identity. So it may be worth submitting a run in which the RMS error is set at, say, 1.5, even if the sequence identity is low. The table below can be used as a guide as to the default RMS value corresponding to ID.<br />
<br />
If you construct a model by homology modelling, remember that the RMS error you expect is essentially the error you expect from the template structure (if not worse!). So specify the sequence identity of the template, not of the homology model.<br />
<br />
Only the model with the highest sequence identity is reported in the output pdb file. Also, HETATM cards in the input pdb file are ignored in the calculation of the structure factors for the ensemble, but are carried through to the output pdb file. Thus, the phases on the output mtz file (which come from the structure factors of the ensemble) do not correspond to those that would be calculated from the output pdb file, when there is more than one pdb file in an ensemble and/or the pdbfile(s) have HETATM records.<br />
<br />
<br />
{| class="wikitable" style="text-align:center" style="margin-left: 30px" <br />
|colspan="11" style="text-align: center;" | Initial estimate of RMS deviation<br />
|-<br />
|colspan="11" style="text-align: center;" | Number of residues in model versus sequence identity<br />
|-<br />
! !! #50 !! #100 !! #200 !! #300 !! #400 !! #600 !! #850 !! #1000 !! #1500 !! #2000<br />
|-<br />
|'''ID=0%''' || 1.579 || 1.689 || 1.875 || 2.030 || 2.164 || 2.391 || 2.625 || 2.748 || 3.093 || 3.375<br />
|-<br />
|'''ID=10%''' || 1.356 || 1.451 || 1.610 || 1.743 || 1.858 || 2.053 || 2.255 || 2.360 || 2.657 || 2.899<br />
|-<br />
|'''ID=20%''' || 1.165 || 1.246 || 1.383 || 1.497 || 1.596 || 1.764 || 1.936 || 2.027 || 2.281 || 2.489<br />
|-<br />
|'''ID=30%''' || 1.000 || 1.070 || 1.188 || 1.286 || 1.371 || 1.515 || 1.663 || 1.741 || 1.959 || 2.138<br />
|-<br />
|'''ID=40%''' || 0.859 || 0.919 || 1.020 || 1.104 || 1.177 || 1.301 || 1.428 || 1.495 || 1.683 || 1.836<br />
|-<br />
|'''ID=50%''' || 0.738 || 0.789 || 0.876 || 0.948 || 1.011 || 1.117 || 1.227 || 1.284 || 1.445 || 1.577<br />
|-<br />
|'''ID=60%''' || 0.634 || 0.678 || 0.752 || 0.814 || 0.868 || 0.959 || 1.053 || 1.103 || 1.241 || 1.354<br />
|-<br />
|'''ID=70%''' || 0.544 || 0.582 || 0.646 || 0.699 || 0.746 || 0.824 || 0.905 || 0.947 || 1.066 || 1.163<br />
|-<br />
|'''ID=80%''' || 0.467 || 0.500 || 0.555 || 0.601 || 0.640 || 0.708 || 0.777 || 0.813 || 0.915 || 0.999<br />
|-<br />
|'''ID=90%''' || 0.401 || 0.429 || 0.477 || 0.516 || 0.550 || 0.608 || 0.667 || 0.698 || 0.786 || 0.858<br />
|-<br />
|'''ID=100%''' || 0.345 || 0.369 || 0.409 || 0.443 || 0.472 || 0.522 || 0.573 || 0.600 || 0.675 || 0.737<br />
|-<br />
|}<br />
<br />
<br />
====Coordinate Editing====<br />
=====HETATM/LIGANDS=====<br />
Phaser ignores the scattering from HETATM records. The HETATM records are carried though to output with occupancy set to zero. Ligands will therefore not contribute to the scattering used for molecular replacement. The exceptions to this rule are the HETATM records for MSE (seleno-methionine) MSO (seleno-methionine selenoxide) CSE (seleno-cysteine) CSO (seleno-cysteine selenoxide) ALY (acetyllysine) MLY (n-dimethyl-lysine) and MLZ (n-methyl-lysine) which are used in the scattering and carried through to output with their original occupancy. If you wish to include any HETATM records in the scattering the record name use the keyword ENSE modlid HETATOM ON<br />
<br />
=====WATER=====<br />
Water molecules (identified by the residue name OW WAT HOH H2O OH2 MOH WTR or TIP) are deleted from the pdb file on input, are not used in the scattering and are not carried through to file output. If you want to retain water molecules you will need to change the residue name to something other than this (e.g. WWW) so that the atoms are not identified as water. To include the water molecules in the scattering, the HETATM records will also have to be changed to ATOM records as described above.<br />
<br />
===Building an Ensemble from Electron Density===<br />
When using density as a model, it is necessary to specify both the extent (x,y,z limits) of the cut-out region of density, and the centre of this region. With coordinates, Phaser can work this out by itself. This information is needed, for instance, to decide how large rotational steps can be in the rotation search and to carry out the molecular transform interpolation correctly. In the case of electron density, the RMS value does not have the same physical meaning that it has when the model is specified by atomic coordinates, but it is used to judge how the accuracy of the calculated structure factors drops off with resolution. A suitable value for RMS can be obtained, in the case of density from an experimentally-phased map, by choosing a value that makes the SigmaA curve fall off with resolution similarly to the mean figures-of-merit. In the case of density from an EM image reconstruction, the RMS value should make the SigmaA curve fall off similarly to a Fourier correlation curve used to judge the resolution of the EM image.<br />
<br />
For detailed information, including a tutorial with example scripts, see<br />
[[Using Electron Density as a Model| Using density as a model]]<br />
<br />
==How to Define Composition==<br />
The composition defines the total amount of protein and nucleic acid that you have in the asymmetric unit not the fraction of the asymmetric unit that you are searching for.<br />
<br />
===Default Composition===<br />
For convenience, the composition defaults to 50% protein scattering by volume (the average for protein crystals). It is better to enter it explicitly, even if only to check that you have correctly deduced the probable content of your crystal. If your crystal has higher or lower solvent content than this, or contains nucleic acid, then the composition should be entered explicitly.<br />
===Composition by Solvent Content===<br />
Scattering is determined from the solvent content of the crystal, assuming that the crystal contains protein only, and the average distribution of amino acids in protein. If your crystal contains nucleic acid or your protein has an unusual amino acid distribution then the composition should be entered explicitly using the MW or sequence options.<br />
===Composition by Number of Residues in ASU===<br />
Scattering is determined from the number of residues in the asymmetric unit, assuming that the crystal contains protein only or nucleic acid only, and assuming an average distribution of residues for either. If your crystal contains a mixture then the composition should be entered explicitly using the MW or sequence options. If your crystal has an unusual residue distribution then the composition should be entered explicitly using the sequence options.<br />
===Composition by Molecular Weight===<br />
The composition is calculated from the molecular weight of the protein and nucleic acid assuming the protein and nucleic acid have the average distribution of amino acids and bases. If your protein or nucleic acid has an unusual amino acid or base distribution the composition should be entered by sequence. You can mix compositions entered by molecular weight with those entered by sequence.<br />
===Composition by Sequence===<br />
The composition is calculated from the amino acid sequence of the protein and the base sequence of the nucleic acid in fasta format. You can mix compositions entered by molecular weight with those entered by sequence. Individual atoms can be added to the composition with the COMPOSITION ATOM keyword. This allows the explicit addition of heavy atoms in the structure e.g. Fe atoms.<br />
===Composition by Percentage Scattering===<br />
The fraction scattering of each ensemble can be entered directly. The fraction scattering of each ensemble is normally automatically worked out from the average scattering from each ensemble (calculated from the pdb files if entered as coordinates, or from the protein and nucleic acid molecular weights if entered as a map) divided by the total scattering given by the composition, but entering the fraction scattering directly overrides this calculation. This option is for use when the pdb files of the models in the ensemble are unusual e.g. consist only of C-alpha atoms, or only of hydrogen atoms (as in the CLOUDS method for NMR).<br />
<br />
==How to Define Solutions==<br />
Phaser writes out files ending in ".sol" and ".rlist" that contain the solution information from the job. The root of the files is given by the ROOT keyword. By default, the root filename is PHASER. These files can be read back into subsequent runs of Phaser to build up solutions containing more than one molecule in the asymmetric unit.<br />
<br />
"PHASER.sol" files are generated by all modes (rotation function modes with VERBOSE output), and contain the current idea of potential molecular replacement solutions.<br />
<br />
"PHASER.rlist" files are generated by the rotation function modes, and are used as input for performing translation functions.<br />
<br />
For simple MR cases you don't really need to know how to define molecular replacement solutions. However, for difficult cases you might need to edit the files "PHASER.sol" and "PHASER.rlist" files manually<br />
<br />
=== "sol" Files===<br />
SOLUtion 6DIM keywords describe Ensembles that have been oriented by a rotation search and positioned by a translation search. Each Ensemble in the asymmetric unit has its own SOLUtion keyword. When more than one (potential) molecular replacement solution is present, the solutions are separated with the SOLUTION SET keywords.<br />
<br />
==="rlist" Files===<br />
These files define a rotation function list. The peak list is given with a series of SOLUtion TRIAl keywords.<br />
<br />
If a partial solution is already known, then the information for the currently "known" parts of the asymmetric unit is given in the form used for the PHASER.sol file, followed by the list of trial orientations for which a translation function is to be performed.<br />
<br />
===Fixed partial structure===<br />
If you have the coordinates of a partial solution with the pdb coordinates of the known structure in the correct orientation and position, then you can force Phaser to use these coordinates. Use the SOLUTION keyword to fix a rotation of 0 0 0 and a position of 0 0 0 for these coordinates.<br />
<br />
==How to Select Peaks==<br />
<br />
<br />
<br />
The selection of peaks saved for output in the rotation and translation functions can be done in four different ways.<br />
*'''Select by Percentage'''<br />
*: Percentage of the top peak, where the value of the top peak is defined as 100% and the value of the mean is defined as 0%.<br />
*: Default, cutoff=75%. This criteria has the advantange that at least one peak (the top peak) always survives the selection. If the top solution is clear, then only the one solution will be output, but if the distribution of peaks is rather flat, then many peaks will be output for testing in the next part of the MR procedure (e.g. many peaks selected from the rotation function for testing with a translation function). <br />
*'''Select by Z-score'''<br />
*: Number of standard deviations (sigmas) over the mean (the Z-score). <br />
*: Absolute significance test. Not all searches will produce output if the cutoff value is too high (e.g. 5 sigma). <br />
*'''Select by Number'''<br />
*: Number of top peaks to select. <br />
*: If the distribution is very flat then it might be better to select a fixed large number (e.g. 1000) of top rotation peaks for testing in the translation function.<br />
*'''No selection'''<br />
*: All peaks are selected. <br />
*: Enables full 6 dimensional searches, where all the solutions from the rotation function are output for testing in the translation function. This should never be necessary; it would be much faster and probably just as likely to work if the top 1000 peaks were used in this way.<br />
<br />
[[Image:Phaser_selection.gif| Selection criteria]]<br />
<br />
Peaks can also be clustered or not clustered prior to selection in steps 1 and 2.<br />
*'''Clustering Off'''<br />
: All high peaks on the search grid are selected<br />
*'''Clustering On'''<br />
: Points on the search grid with higher neighbouring points are removed from the selection<br />
<br />
<br />
[[Image:Phaser_clustering.gif| Clustering]]<br />
<br />
==How to Control Output==<br />
The output of Phaser can be controlled with optional keywords. <br />
<br />
The ROOT keyword is not compulsory (the default root filename is "PHASER"), but should always be given, so that your jobs have separate and meaningful output filenames.<br />
<br />
The TOPFiles keyword controls the number of potential MR solutions for which PDB and (in the appropriate modes) MTZ files are produced.<br />
<br />
For the MR_AUTO, MR_RNP and MR_LLG modes, unless HKLOut OFF is given as an optional keyword, Phaser produces an MTZ file with "SigmaA" type weighted Fourier map coefficients for producing electron density maps for rebuilding.<br />
<br />
{| class="wikitable" style="text-align:left" width=100%<br />
|-<br />
! MTZ Column Labels !! Description<br />
|-<br />
| FWT/PHWT || Amplitude and phase for 2''m''&#124;F<sub>obs</sub>&#124;-''D''&#124;F<sub>calc</sub>&#124; exp(''i''&alpha;<sub>calc</sub>) map<br />
|-<br />
| DELFWT/PHDELWT || Amplitude and phase for ''m''&#124;F<sub>obs</sub>&#124;-''D''&#124;F<sub>calc</sub>&#124; exp(''i''&alpha;<sub>calc</sub>) map<br />
|-<br />
| FOM || ''m'', analogous to the "Sim" weight, to estimate the reliability of &alpha;<sub>calc</sub><br />
|-<br />
| HLA/HLB/HLC/HLD || Hendrickson-Lattman coefficients encoding the phase probability distribution<br />
|}<br />
<br />
==Translational Non-crystallographic Symmetry==<br />
<br />
<span style="color:crimson">'''*Warning*''' Solution by MR in the presence of translational non-crystallographic symmetry is not fully automated.</span><br />
<br />
Phaser calculates correction factors for the expected intensities in the presence of translational non-crystallographic symmetry (tNCS), and is able to solve structures with complex patterns of tNCS. '''However, the use of Phaser in the presence of tNCS requires the nature of the tNCS to be understood by the user.''' In simple cases, solution is no more difficult than solution without tNCS, but in complex cases, separate Phaser runs with tNCS turned on and off, and/or the use of different tNCS vectors, may be necessary.<br />
<br />
The output of Phaser will help the user in detecting and understanding the tNCS, but '''the tNCS is not completely characterised by Phaser'''. The default behaviour may or may not be correct for the particular crystal under study.<br />
<br />
Characterization of the tNCS involves understanding the number of copies of the molecule in the asymmetric unit and the translation vectors between them. Molecules related by a tNCS vector will have an associated peak in the native Patterson. Phaser calculates the native Patterson (MODE TNCS) and lists the peaks that are more than 20% of the origin peak. Any given crystal with tNCS may have one or more peaks meeting this criteria.<br />
<br />
===Default tNCS detection and correction===<br />
<span style="color:crimson">Documentation for Phaser-2.7.16 and above</span><br />
<br />
====No tNCS====<br />
No tNCS correction is applied by default if there is<br />
# no peak in the native Patterson <br />
# more than one peak in the native Patterson over 20% of the origin and these peaks are not all the result of a commensurate modulation<br />
<br />
====Pairs of molecules====<br />
By default, if Phaser detects a peak in the native Patterson then Phaser will search for molecules in pairs related by the tNCS vector given by the peak in the native Patterson.<br />
<br />
This will be the correct behaviour if and only if there are an even number of copies of the molecule in the asymmetric unit, clustered into two groups related by a single tNCS vector. There will only be one significant peak in the native Patterson. Fortunately, this is a reasonably common scenario.<br />
<br />
Phaser refines the relative orientation of the molecules in the two groups (rotations of up to 10 degrees will still give rise to a significant native Patterson peak) and uses this information to generate expected intensity factors for the reflections. Solution should be straightforward, with the usual caveat for MR that there is a sufficiently good model.<br />
<br />
Where there is a single peak in the native Patterson, it is often located at a position half way along a unit cell axis or diagonal, representing a pseudo-halving of the unit cell dimensions. However, Phaser is by no means restricted to these sorts of pseudo-cells in its handling of two-fold tNCS, and the tNCS vector can be in a general position.<br />
<br />
===Non-default tNCS correction===<br />
====Higher order tNCS====<br />
Frequently, tNCS does not associate 2 clusters of molecules in the asymmetric unit, but rather there are 3 or more (n) clusters of molecules associated by a series of vectors that are multiples of 1, 2, 3 ... (n-1) times a basic translation vector. Where n times the basic translation vector equates to (very close to) integer multiples of unit cell axes, the tNCS represents a pseudo-cell, and this case is known as commensurate modulation. <br />
<br />
Phaser attempts to automatically detect commensurate modulation. The peaks of the native Patterson are analyzed to find the n-fold relationship. The series will not generally have all peaks the same height. Lower peaks in the series represent relationships where the relative rotations between related molecules are larger. Missing peaks in the series may be below the default 20% of origin cut-off. This can be lowered with TNCS PATT PERCENT <x><br />
<br />
Phaser then sets TNCS NMOL <n> and the vector for the tNCS, and searches for ensembles in multiples of NMOL.<br />
<br />
When there are more than two molecules related by tNCS, Phaser does not refine the orientations between the molecules related by the tNCS.<br />
<br />
However, as for two-fold tNCS, Phaser is not restricted to these sorts of pseudo-cells and the basic tNCS vector can be in a general position, as can the number of copies.<br />
<br />
'''The automatic detection may not give the true tNCS relationship'''. For example, the true commensurate modulation may be a factor of the NMOL automatically detected by Phaser, or there may not be commensurate modulation at all, or commensurate modulation may not be found with the default Pattesron peak height cutoff. In difficult cases, please inspect the Patterson for peaks.<br />
<br />
====Complex tNCS====<br />
If there are many molecules in the asymmetric unit but they are not all related by tNCS, or there are sub-groups of molecules related by different tNCS vectors, then the modulations of the expected intensities due to the tNCS will be much less significant than the cases described above. '''In these cases it is possible that structure solution will be achieved without any tNCS correction factors being applied.''' Indeed, searching for all the copies as tNCS-related multiples when some molecules are not related by tNCS will cause structure solution to fail. To turn off the automatic detection and use of tNCS use the keyword TNCS USE OFF.<br />
<br />
If turning off the TNCS correction factors fails to give a solution, then a good approach is to proceed step-wise. Consider the highest native Patterson peak first and determine that nature of the tNCS associated with it. Use the appropriate correction factors to locate all the molecules with this tNCS. Then take the second independent native Patterson peak and apply the correction factors associated with it to find the second set of molecules, fixing the first, etc. Finally, turn TNCS off to find any orphan molecules.</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Molecular_Replacement&diff=2414Molecular Replacement2018-01-26T12:01:17Z<p>Airlie: /* Building an Ensemble from Coordinates */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
'''Quicklink to example scripts''' → [[MR using keyword input]]<br />
<br />
'''Quicklink to phaser.famos (find_alt_orig_sym_mate) documentation''' → [[Famos]]<br />
<br />
Phaser should be able to solve most structures with the Automated Molecular Replacement mode, and this is the first mode that you should try. Give Phaser your data ([[#How to Define Data|How to Define Data]]) and your models ([[#How to Define Models|How to Define Models]]), tell Phaser what to search for, and a list of possible spacegroups (in the same point group).<br />
<br />
If this doesn't work (see [[#Has Phaser Solved It?| Has Phaser Solved It?]]), you can try selecting peaks of lower significance in the rotation function in case the real orientation was not within the selection criteria. By default peaks above 75% of the top peak are selected (see [[#How to Select Peaks| How to Select Peaks]]). See [[#What to do in Difficult Cases| What to do in Difficult Cases]] for more hints and tips. If the automated molecular replacement mode doesn't work even with non-default input you need to run the modes of Phaser separately. The possibilities are endless - you can even try exhaustive searches (translations of all orientations) if you want - but experience has shown that most structures that can be solved by Phaser can be solved by relatively simple strategies.<br />
<br />
==Automated Molecular Replacement==<br />
Automated Molecular Replacement combines the anisotropy correction, likelihood enhanced fast rotation function, likelihood enhanced fast translation function, packing and refinement modes for multiple search models and a set of possible spacegroups to automatically solve a structure by molecular replacement. Top solutions are output to the files FILEROOT.sol, FILEROOT.#.mtz and FILEROOT.#.pdb (where "#" refers to the sorted solution number, 1 being the best, and only 1 is output by default). Many structures can be solved by running an automated molecular replacement search with defaults, giving the ensembles that you expect to be easiest to find first.<br />
<br />
At the completion of Molecular Replacement you may wish to place your solutions on a common origin with a previous solution, for which [[Famos | Famos ]] can be used.<br />
<br />
[[Image:Phaser_MR_auto.gif|Flow Diagram for Automated MR]]<br />
<br />
==Should Phaser Solve It?==<br />
The difficulty of a molecular replacement problem depends primarily on two major factors: how well the model will be able to explain the diffraction data (which depends both on the accuracy of the model and on its completeness), and how many reflections can be explained, at least in part. Each reflection provides a piece of information that helps to identify correct MR solutions.<br />
<br />
It is possible to make a reasonable prediction of whether or not a solution will be found. If the quality of the model (its accuracy and completeness) can be estimated, then the expected contribution of each reflection to the total LLG can also be estimated. From a large battery of tests, we know that an LLG of 40 or greater usually indicates a correct solution (at least in the absence of complicating factors such as translational non-crystallographic symmetry, tNCS). Building on this understanding, if it is estimated that the LLG will be 60 or less, then Phaser will assume that the problem is a difficult one, and will implement search procedures optimised for difficult problems.<br />
<br />
==What Resolution of Data Should be Used?==<br />
The signal for a molecular replacement solution should be very clear if the expected value of the LLG is much higher than the minimum required to be fairly certain of a solution. Currently Phaser aims for a minimum LLG of 120 and, if it is possible to achieve an even higher value, given the quality of the model and the quantity of diffraction data, then the resolution for the initial search is limited to the value required to achieve an expected LLG of 120. Data to the full resolution are still used for a final rigid-body refinement, or in a second pass if a clear solution is not found in the first attempt.<br />
<br />
However, if the model is expected to have a large RMS error (based usually on the correlation between sequence identity and RMS error), then data to high resolution will not contribute any significant signal. Regardless of the expected LLG at the highest resolution limit, the resolution used is limited to 1.8 times the estimated RMS error of the model, because this resolution limit gives about 99% of the LLG that could be achieved.<br />
<br />
Because Phaser implements strategies designed to solve structures with as much confidence as possible, as efficiently as possible, it is best to leave the choice of resolution to Phaser, at least in the first instance.<br />
<br />
==Has Phaser Solved It?==<br />
{| class="wikitable" style="text-align:center" align="right" style="margin-left: 30px" <br />
|-<br />
! TF Z-score !! Have I solved it?<br />
|-<br />
| less than 5 || no<br />
|-<br />
| 5 - 6 || unlikely<br />
|-<br />
| 6 - 7 || possibly<br />
|-<br />
| 7 - 8 || probably<br />
|-<br />
| more than 8* ||definitely<br />
|-<br />
|colspan="2" style="text-align: center;" | *''6 for 1st model in monoclinic space groups''<br />
|} <br />
<br />
Ideally, a unique solution with a strong signal will be found at the end of the search. If you are searching for multiple components, then ideally the search for each component will also give a strong signal. However if the signal-to-noise of your search is low, there will be noise peaks and multiple ambiguous solutions. Signal-to-noise is judged using the '''Z-score''', which is computed by comparing the LLG values from the rotation or translation search with LLG values for a set of random rotations or translations. The mean and the RMS deviation from the mean are computed from the random set, then the Z-score for a search peak is defined as its LLG minus the mean, all divided by the RMS deviation, ''i.e. '' '''the number of standard deviations above (or below) the mean. '''<br />
<br />
For a rotation function, the correct orientation may be well down the list with a Z-score (number of standard deviations above the mean value, or RFZ) under 4, and it is often not possible to identify the correct orientation until a translation function is performed and yields a clear solution. Note that the signal-to-noise of the rotation function drops with increasing number of primitive symmetry operations (the number of different orientations for symmetry-related molecules), because there is more uncertainty about how the structure factor contributions from symmetry-related copies will add up.<br />
<br />
For a translation function the correct solution will generally have a Z-score (TFZ) over 5 and be well separated from the rest of the solutions. Of course, there will always be exceptions! The table gives a very rough guide to interpreting TFZ scores. This table will be updated, as we learn more from systematic molecular replacement trials.<br />
<br />
When you are searching for multiple components, the signal may be low for the first few components but, as the model becomes more complete, the signal should become stronger. Finding a clear solution for a new component is a good sign that the partial solution to which that component was added was indeed correct.<br />
<br />
You should always at least glance through the summary of the logfile. One thing to look for, in particular, is whether any translation solutions with a high Z-score have been rejected by the packing step. By default up to 5 percent of marker atoms (C-alpha atoms for protein) are allowed to be involved in clashes. A solution with more clashes may still be correct, and the clashes may arise only because of differences in small surface loops. If this happens, repeat the run allowing a suitable number of clashes. Note that, unless there is specific evidence in the logfile that a high TFZ-score solution is being rejected with a few clashes, it is much better to edit the model to remove the loops than to increase the number of allowed clashes. Packing criteria are a very powerful constraint on the translation function, and increasing the number of allowed clashes beyond the default will increase the search time enormously without the possibility of generating any correct solutions that would not have otherwise been found.<br />
<br />
Note that, by default, Phaser will produce a single PDB file corresponding to the top solution found (if any), so finding a single PDB file in your output directory is not an indication that the search succeeded! You have to look, at least, at the summary of the logfile, or at the list of possible solutions in the .sol file that is produced if you run Phaser from ccp4i or command-line scripts.<br />
<br />
==Annotation==<br />
<br />
A highly compact summary of the history of the statistics of a solution is given in the SOLUTION SET in the .sol file. This is a good place to start your analysis of the output. The annotation gives the Z-score of the solution at each rotation and translation function, the number of clashes in the packing, and the refined LLG.<br />
<br />
{| class="wikitable" style="text-align:center" style="margin-left: 30px" <br />
|-<br />
! Annotation !! Meaning<br />
|-<br />
| RFZ= || Rotation Function Z-score<br />
|-<br />
| TFZ= || Translation Function Z-score<br />
|-<br />
| PAK= || Number of packing clashes<br />
|-<br />
| LLG= || LLG after refinement. Will be repeated when a low resolution refinement is followed by a high resolution refinement.<br />
|-<br />
| TFZ== || Translation Function Z-score equivalent, only calculated for the top solution after refinement (or for the number of top files specified by TOPFILES)<br />
|-<br />
| RF++ || Rotation angle from previous strong solution has been used in the addition of next solution<br />
|-<br />
| RF*0 || Rotation angle 000 identified by low R-factor of input model<br />
|-<br />
| TFZ=* || First molecule in P1 (arbitrary origin, no Translation Function required)<br />
|-<br />
| TF*0 || Translation vector 000 identified by low R-factor of input model<br />
|-<br />
| (&&nbsp;... & ...) || Set of TFZ PAK and LLG values for placements that were amalgamated (more than one placement from a single Translation Function)<br />
|-<br />
| LLG+=(...&nbsp;&&nbsp;...)&nbsp;|| Set of LLG values calculated during amalgamation, which will always be increasing in value<br />
|-<br />
| +TNCS || Components added by Translational NCS relation<br />
|-<br />
| *T=<i>n</i> || Solution matches template solution <i>n</i><br />
|} <br />
<br />
Two versions of TFZ (the translation function Z-score) now appear for each component. The first ("TFZ=") is the Z-score from the actual translation search, which depends on the accuracy of the orientation used for that search. The second ("TFZ==") is the TFZ-equivalent, which indicates what the TFZ score would have been with the correct (refined) orientation. You should see the TFZ-equivalent is high at least for the final components of the solution, and that the LLG (log-likelihood gain) increases as each component of the solution is added. For example, in the case of beta-blip the annotation for the single solution output in the .sol file shows these features<br />
<br />
SOLU SET RFZ=10.7 TFZ=24.3 PAK=0 LLG=472 TFZ==24.7 RFZ=6.4 TFZ=24.4 PAK=0 LLG=1006 TFZ==29.7 LLG=1006 TFZ==29.7<br />
SOLU 6DIM ENSE beta EULER 200.849 41.269 183.909 FRAC -0.49604 -0.15830 -0.28092 BFAC 0.00000<br />
SOLU 6DIM ENSE blip EULER 43.749 80.793 117.292 FRAC -0.12289 0.29435 -0.09266 BFAC 0.00000<br />
<br />
Note that the Euler angles in Phaser follow the same convention as those defined for the Crowther fast rotation function, i.e. z-y-z (rotate around the z-axis, followed by the new y-axis, followed by the new z-axis).<br />
<br />
==History==<br />
<br />
A highly compact summary of the history of the peak positions of a solution is given in the SOLUTION HISTORY in the .sol file. Together with the SOLUTION SET annotation, this is useful in your analysis of the output. <br />
<br />
{| class="wikitable" style="text-align:center" style="margin-left: 30px" <br />
|-<br />
! History !! Meaning<br />
|-<br />
| RF/TF(r/t:n) || (r) Rotation Function peak number/(t) Translation Function peak number for the rotation function : (n) number of peak in final merged and sorted list<br />
|-<br />
| PAK(n:m) || (n) input solution number : (m) output solution number after packing condition applied<br />
|-<br />
| RNP(m,a,b,c,... : p) || All input peaks amalgamated after refinement to give output solution number (m and others): (p) output solution number<br />
|-<br />
| FUSE(A,B,C) || Solution numbers merged in amalgamation<br />
|} <br />
<br />
For example, in the case of beta-blip the annotation for the single solution output in the .sol file shows these features<br />
<br />
SOLU HISTORY RF/TF(1/1:1)PAK(1:1)RNP(1:1)RNP(1:1)<br />
SOLU 6DIM ENSE beta EULER 200.849 41.269 183.909 FRAC -0.49604 -0.15830 -0.28092 BFAC 0.00000<br />
SOLU 6DIM ENSE blip EULER 43.749 80.793 117.292 FRAC -0.12289 0.29435 -0.09266 BFAC 0.00000<br />
<br />
A more complicated structure solution may have<br />
<br />
SOLU HISTORY RF/TF(7/1:10)PAK(10:10)RNP(10,12,13,11,17,16,18,25,3,8,22,21,20,7,969,6,5,201,9,4,390,2,1,19:1)RNP(1:1)<br />
<br />
==What to do in Difficult Cases==<br />
<br />
Not every structure can be solved by molecular replacement, but the right strategy can push the limits. What to do when the default jobs fail depends on why your structure is difficult.<br />
*'''Flexible Structure'''<br />
*:The relative orientations of the domains may be different in your crystal than in the model. If that may be the case, break the model into separate PDB files containing rigid-body units, enter these as separate ensembles, and search for them separately. If you find a convincing solution for one domain, but fail to find a solution for the next domain, you can take advantage of the knowledge that its orientation is likely to be similar to that of the first domain. The ROTAte&nbsp;AROUnd option of the brute rotation search can be used to restrict the search to orientations within, say, 30 degrees of that of the known domain. Allow for close approach of the domains by increasing the allowed clashes with the PACK keyword by, say, 1 for each domain break that you introduce. Note that it is possible to use the brute rotation search as part of the automated molecular replacement pipeline, by changing the choice of the type of rotation search. Alternatively, you could try generating a series of models perturbed by normal modes, with the NMAPdb keyword. One of these may duplicate the hinge motion and provide a good single model.<br />
*'''Poor or Incomplete Model'''<br />
*:Signal-to-noise is reduced by coordinate errors or incompleteness of the model. Since the rotation search has lower signal to begin with than the translation search, it is usually more severely affected. For this reason, it can be very useful to use the subsequent translation search as a way to choose among many (say 1000) orientations. THe MR_AUTO FAST search mode automatically reduces the cutoff for accepting peaks from the fast rotation function if the decault pass does not find a solution with a high z-score, but you can manually reduce this further with the PEAKS and PURGE keywords. You can also try turning off the clustering of fast rotation function peaks because the correct orientation may sit on the shoulder of a peak in the rotation function. <br />
*:As shown convincingly by Schwarzenbacher ''et al.'' (Schwarzenbacher, Godzik, Grzechnik &amp; Jaroszewski, ''Acta Cryst.'' D'''60''', 1229-1236, 2004), judicious editing can make a significant difference in the quality of a distant model. In a number of tests with their data on models below 30% sequence identity, we have found that Phaser works best with a "mixed model" (non-identical sidechains longer than Ser replaced by Ser). In agreement with their results, the best models are generally derived using more sophisticated alignment protocols, such as their FFAS protocol. Use [http://www.phenix-online.org/documentation/sculptor.htm phenix.sculptor] to edit your model.<br />
*'''High Degree of Non-crystallographic Symmetry'''<br />
*:If there are clear peaks in the self-rotation function, you can expect orientations to be related by this known NCS. Methods to automatically use such information will be implemented in a future version of Phaser. In the meantime, you can work out for yourself the orientations that would be consistent with NCS and use the ROTAte&nbsp;AROUnd option to sample similar orientations. Alternatively, you may have an oligomeric model and expect similar NCS in the crystal. First search with the oligomeric model; if this fails, search with a monomer. If that succeeds, you can again use the ROTAte&nbsp;AROUnd option to force a subsequent monomer to adopt an orientation similar to the one you expect.<br />
*'''What <u>not</u> to do'''<br />
*:The automated mode of Phaser is fast when Phaser finds a high Z-score solution to your problem. When Phaser cannot find a solution with a significant Z-score, it "thrashes", meaning it maintains a list of 100-1000's of low Z-score potential solutions and tries to improve them. This can lead to exceptionally long Phaser runs (over a week of CPU time). Such runs are possible because the highly automated script allows many consecutive MR jobs to be run without you having to manually set 100-1000's of jobs running and keep track of the results. "Thrashing" generally does not produce a solution: solutions generally appear relatively quickly or not at all. It is more useful to go back and analyse your models and your data to see where improvements can be made. Your system manager will appreciate you terminating these jobs.<br />
*:It is also not a good idea to effectively remove the packing test. Unless there is specific evidence in the logfile that a high TF-function Z-score solution is being rejected with a few clashes, it is much better to edit the model to remove the loops than to increase the number of allowed clashes. Packing criteria are a very powerful constraint on the translation function, and increasing the number of allowed clashes beyond a few (e.g. 1-5) will increase the search time enormously without the possibility of generating any correct solutions that would not have otherwise been found.<br />
*'''Other suggestions'''<br />
*:Phaser has powerful input, output and scripting facilities that allow a large number of possibilities for altering default behaviour and forcing Phaser to do what you think it should. However, you will need to read the information in the manual below to take advantage of these facilities!<br />
<br />
==How to Define Data==<br />
You need to tell Phaser the name of the mtz file containing your data and the columns in the mtz file to be used using the HKLIn and LABIn keywords. Additional keywords (BINS CELL OUTLier RESOlution SPACegroup) define how the data are used.<br />
<br />
==How to Define Models==<br />
Phaser must be given the models that it will use for molecular replacement. A model in Phaser is referred to as an "ensemble", even when it is described by a single file. This is because it is possible to provide a set of aligned structures as an ensemble, from which a statistically-weighted averaged model is calculated. A molecular replacement model is provided either as one or more aligned pdb files, or as an electron density map, entered as structure factors in an mtz file. Each ensemble is treated as a separate type of rigid body to be placed in the molecular replacement solution. An ensemble should only be defined once, even if there are several copies of the molecule in the asymmetric unit.<br />
<br />
Fundamental to the way in which Phaser uses MR models (either from coordinates or maps) is to estimate how the accuracy of the model falls off as a function of resolution, represented by the Sigma(A) curve. To generate the Sigma(A) curve, Phaser needs to know the RMS coordinate error expected for the model and the fraction of the scattering power in the asymmetric unit that this model contributes.<br />
<br />
A Babinet-style correction is used to account for the effects of disordered solvent on the completeness of the model at low resolution.<br />
<br />
Molecular replacement models are defined with the ENSEmble keyword and the COMPosition keyword. The ENSEmble keyword gives (amongst other things) the RMS deviation for the Sigma(A) curve. The COMPosition keyword is used to deduce the fraction of the scattering power in the asymmetric unit that each ensemble contributes. The composition of the asymmetric unit is defined either by entering the molecular weights or sequences of the components in the asymmetric unit, and giving the number of copies of each. Expert users can also enter the fraction of the scattering of each component directly, although the composition must still be entered for the absolute scale calculation. Please note that the composition supplied to Phaser has to include everything in the asymmetric unit, not just what is being looked for in the current search!<br />
<br />
===Building an Ensemble from Coordinates===<br />
The RMS deviation is determined directly from RMS or indirectly from IDENtity in the ENSEmble<br />
keyword using a formula that depends on the sequence identity and the number of residues in the model.<br />
<br />
The RMS deviation estimated from ID may be an underestimate of the true value if there is a slight conformational change between the model and target structures. To find a solution in these cases it may be necessary to increase the RMS from the default value generated from the ID, by say 0.5 Ångstroms. On the other hand, when Phaser succeeds in solving a structure from a model with sequence identity much below 30%, it is often found that the fold is preserved better than the average for that level of sequence identity. So it may be worth submitting a run in which the RMS error is set at, say, 1.5, even if the sequence identity is low. The table below can be used as a guide as to the default RMS value corresponding to ID.<br />
<br />
If you construct a model by homology modelling, remember that the RMS error you expect is essentially the error you expect from the template structure (if not worse!). So specify the sequence identity of the template, not of the homology model.<br />
<br />
Only the model with the highest sequence identity is reported in the output pdb file. Also, HETATM cards in the input pdb file are ignored in the calculation of the structure factors for the ensemble, but are carried through to the output pdb file. Thus, the phases on the output mtz file (which come from the structure factors of the ensemble) do not correspond to those that would be calculated from the output pdb file, when there is more than one pdb file in an ensemble and/or the pdbfile(s) have HETATM records.<br />
<br />
<br />
{| class="wikitable" style="text-align:center" style="margin-left: 30px" <br />
|colspan="11" style="text-align: center;" | Initial estimate of RMS deviation<br />
|-<br />
|colspan="11" style="text-align: center;" | Number of residues in model versus sequence identity<br />
|-<br />
! !! #50 !! #100 !! #200 !! #300 !! #400 !! #600 !! #850 !! #1000 !! #1500 !! #2000<br />
|-<br />
|'''ID=0%''' || 1.579 || 1.689 || 1.875 || 2.030 || 2.164 || 2.391 || 2.625 || 2.748 || 3.093 || 3.375<br />
|-<br />
|'''ID=10%''' || 1.356 || 1.451 || 1.610 || 1.743 || 1.858 || 2.053 || 2.255 || 2.360 || 2.657 || 2.899<br />
|-<br />
|'''ID=20%''' || 1.165 || 1.246 || 1.383 || 1.497 || 1.596 || 1.764 || 1.936 || 2.027 || 2.281 || 2.489<br />
|-<br />
|'''ID=30%''' || 1.000 || 1.070 || 1.188 || 1.286 || 1.371 || 1.515 || 1.663 || 1.741 || 1.959 || 2.138<br />
|-<br />
|'''ID=40%''' || 0.859 || 0.919 || 1.020 || 1.104 || 1.177 || 1.301 || 1.428 || 1.495 || 1.683 || 1.836<br />
|-<br />
|'''ID=50%''' || 0.738 || 0.789 || 0.876 || 0.948 || 1.011 || 1.117 || 1.227 || 1.284 || 1.445 || 1.577<br />
|-<br />
|'''ID=60%''' || 0.634 || 0.678 || 0.752 || 0.814 || 0.868 || 0.959 || 1.053 || 1.103 || 1.241 || 1.354<br />
|-<br />
|'''ID=70%''' || 0.544 || 0.582 || 0.646 || 0.699 || 0.746 || 0.824 || 0.905 || 0.947 || 1.066 || 1.163<br />
|-<br />
|'''ID=80%''' || 0.467 || 0.500 || 0.555 || 0.601 || 0.640 || 0.708 || 0.777 || 0.813 || 0.915 || 0.999<br />
|-<br />
|'''ID=90%''' || 0.401 || 0.429 || 0.477 || 0.516 || 0.550 || 0.608 || 0.667 || 0.698 || 0.786 || 0.858<br />
|-<br />
|'''ID=100%''' || 0.345 || 0.369 || 0.409 || 0.443 || 0.472 || 0.522 || 0.573 || 0.600 || 0.675 || 0.737<br />
|-<br />
|}<br />
<br />
<br />
====Coordinate Editing====<br />
=====HETATM/LIGANDS=====<br />
Phaser ignores the scattering from HETATM records. The HETATM records are carried though to output with occupancy set to zero. Ligands will therefore not contribute to the scattering used for molecular replacement. The exceptions to this rule are the HETATM records for MSE (seleno-methionine) MSO (seleno-methionine selenoxide) CSE (seleno-cysteine) CSO (seleno-cysteine selenoxide) ALY (acetyllysine) MLY (n-dimethyl-lysine) and MLZ (n-methyl-lysine) which are used in the scattering and carried through to output with their original occupancy. If you wish to include any HETATM records in the scattering the record name use the keyword ENSE modlid HETATOM ON<br />
<br />
=====WATER=====<br />
Water molecules (identified by the residue name OW WAT HOH H2O OH2 MOH WTR or TIP) are deleted from the pdb file on input, are not used in the scattering and are not carried through to file output. If you want to retain water molecules you will need to change the residue name to something other than this (e.g. WWW) so that the atoms are not identified as water. To include the water molecules in the scattering, the HETATM records will also have to be changed to ATOM records as described above.<br />
<br />
===Building an Ensemble from Electron Density===<br />
When using density as a model, it is necessary to specify both the extent (x,y,z limits) of the cut-out region of density, and the centre of this region. With coordinates, Phaser can work this out by itself. This information is needed, for instance, to decide how large rotational steps can be in the rotation search and to carry out the molecular transform interpolation correctly. In the case of electron density, the RMS value does not have the same physical meaning that it has when the model is specified by atomic coordinates, but it is used to judge how the accuracy of the calculated structure factors drops off with resolution. A suitable value for RMS can be obtained, in the case of density from an experimentally-phased map, by choosing a value that makes the SigmaA curve fall off with resolution similarly to the mean figures-of-merit. In the case of density from an EM image reconstruction, the RMS value should make the SigmaA curve fall off similarly to a Fourier correlation curve used to judge the resolution of the EM image.<br />
<br />
For detailed information, including a tutorial with example scripts, see<br />
[[Using Electron Density as a Model| Using density as a model]]<br />
<br />
==How to Define Composition==<br />
The composition defines the total amount of protein and nucleic acid that you have in the asymmetric unit not the fraction of the asymmetric unit that you are searching for.<br />
<br />
===Default Composition===<br />
For convenience, the composition defaults to 50% protein scattering by volume (the average for protein crystals). It is better to enter it explicitly, even if only to check that you have correctly deduced the probable content of your crystal. If your crystal has higher or lower solvent content than this, or contains nucleic acid, then the composition should be entered explicitly.<br />
===Composition by Solvent Content===<br />
Scattering is determined from the solvent content of the crystal, assuming that the crystal contains protein only, and the average distribution of amino acids in protein. If your crystal contains nucleic acid or your protein has an unusual amino acid distribution then the composition should be entered explicitly using the MW or sequence options.<br />
===Composition by Number of Residues in ASU===<br />
Scattering is determined from the number of residues in the asymmetric unit, assuming that the crystal contains protein only or nucleic acid only, and assuming an average distribution of residues for either. If your crystal contains a mixture then the composition should be entered explicitly using the MW or sequence options. If your crystal has an unusual residue distribution then the composition should be entered explicitly using the sequence options.<br />
===Composition by Molecular Weight===<br />
The composition is calculated from the molecular weight of the protein and nucleic acid assuming the protein and nucleic acid have the average distribution of amino acids and bases. If your protein or nucleic acid has an unusual amino acid or base distribution the composition should be entered by sequence. You can mix compositions entered by molecular weight with those entered by sequence.<br />
===Composition by Sequence===<br />
The composition is calculated from the amino acid sequence of the protein and the base sequence of the nucleic acid in fasta format. You can mix compositions entered by molecular weight with those entered by sequence. Individual atoms can be added to the composition with the COMPOSITION ATOM keyword. This allows the explicit addition of heavy atoms in the structure e.g. Fe atoms.<br />
===Composition by Percentage Scattering===<br />
The fraction scattering of each ensemble can be entered directly. The fraction scattering of each ensemble is normally automatically worked out from the average scattering from each ensemble (calculated from the pdb files if entered as coordinates, or from the protein and nucleic acid molecular weights if entered as a map) divided by the total scattering given by the composition, but entering the fraction scattering directly overrides this calculation. This option is for use when the pdb files of the models in the ensemble are unusual e.g. consist only of C-alpha atoms, or only of hydrogen atoms (as in the CLOUDS method for NMR).<br />
<br />
==How to Define Solutions==<br />
Phaser writes out files ending in ".sol" and ".rlist" that contain the solution information from the job. The root of the files is given by the ROOT keyword. By default, the root filename is PHASER. These files can be read back into subsequent runs of Phaser to build up solutions containing more than one molecule in the asymmetric unit.<br />
<br />
"PHASER.sol" files are generated by all modes (rotation function modes with VERBOSE output), and contain the current idea of potential molecular replacement solutions.<br />
<br />
"PHASER.rlist" files are generated by the rotation function modes, and are used as input for performing translation functions.<br />
<br />
For simple MR cases you don't really need to know how to define molecular replacement solutions. However, for difficult cases you might need to edit the files "PHASER.sol" and "PHASER.rlist" files manually<br />
<br />
=== "sol" Files===<br />
SOLUtion 6DIM keywords describe Ensembles that have been oriented by a rotation search and positioned by a translation search. Each Ensemble in the asymmetric unit has its own SOLUtion keyword. When more than one (potential) molecular replacement solution is present, the solutions are separated with the SOLUTION SET keywords.<br />
<br />
==="rlist" Files===<br />
These files define a rotation function list. The peak list is given with a series of SOLUtion TRIAl keywords.<br />
<br />
If a partial solution is already known, then the information for the currently "known" parts of the asymmetric unit is given in the form used for the PHASER.sol file, followed by the list of trial orientations for which a translation function is to be performed.<br />
<br />
===Fixed partial structure===<br />
If you have the coordinates of a partial solution with the pdb coordinates of the known structure in the correct orientation and position, then you can force Phaser to use these coordinates. Use the SOLUTION keyword to fix a rotation of 0 0 0 and a position of 0 0 0 for these coordinates.<br />
<br />
==How to Select Peaks==<br />
<br />
<br />
<br />
The selection of peaks saved for output in the rotation and translation functions can be done in four different ways.<br />
*'''Select by Percentage'''<br />
*: Percentage of the top peak, where the value of the top peak is defined as 100% and the value of the mean is defined as 0%.<br />
*: Default, cutoff=75%. This criteria has the advantange that at least one peak (the top peak) always survives the selection. If the top solution is clear, then only the one solution will be output, but if the distribution of peaks is rather flat, then many peaks will be output for testing in the next part of the MR procedure (e.g. many peaks selected from the rotation function for testing with a translation function). <br />
*'''Select by Z-score'''<br />
*: Number of standard deviations (sigmas) over the mean (the Z-score). <br />
*: Absolute significance test. Not all searches will produce output if the cutoff value is too high (e.g. 5 sigma). <br />
*'''Select by Number'''<br />
*: Number of top peaks to select. <br />
*: If the distribution is very flat then it might be better to select a fixed large number (e.g. 1000) of top rotation peaks for testing in the translation function.<br />
*'''No selection'''<br />
*: All peaks are selected. <br />
*: Enables full 6 dimensional searches, where all the solutions from the rotation function are output for testing in the translation function. This should never be necessary; it would be much faster and probably just as likely to work if the top 1000 peaks were used in this way.<br />
<br />
[[Image:Phaser_selection.gif| Selection criteria]]<br />
<br />
Peaks can also be clustered or not clustered prior to selection in steps 1 and 2.<br />
*'''Clustering Off'''<br />
: All high peaks on the search grid are selected<br />
*'''Clustering On'''<br />
: Points on the search grid with higher neighbouring points are removed from the selection<br />
<br />
<br />
[[Image:Phaser_clustering.gif| Clustering]]<br />
<br />
==How to Control Output==<br />
The output of Phaser can be controlled with optional keywords. <br />
<br />
The ROOT keyword is not compulsory (the default root filename is "PHASER"), but should always be given, so that your jobs have separate and meaningful output filenames.<br />
<br />
The TOPFiles keyword controls the number of potential MR solutions for which PDB and (in the appropriate modes) MTZ files are produced.<br />
<br />
For the MR_AUTO, MR_RNP and MR_LLG modes, unless HKLOut OFF is given as an optional keyword, Phaser produces an MTZ file with "SigmaA" type weighted Fourier map coefficients for producing electron density maps for rebuilding.<br />
<br />
{| class="wikitable" style="text-align:left" width=100%<br />
|-<br />
! MTZ Column Labels !! Description<br />
|-<br />
| FWT/PHWT || Amplitude and phase for 2''m''&#124;F<sub>obs</sub>&#124;-''D''&#124;F<sub>calc</sub>&#124; exp(''i''&alpha;<sub>calc</sub>) map<br />
|-<br />
| DELFWT/PHDELWT || Amplitude and phase for ''m''&#124;F<sub>obs</sub>&#124;-''D''&#124;F<sub>calc</sub>&#124; exp(''i''&alpha;<sub>calc</sub>) map<br />
|-<br />
| FOM || ''m'', analogous to the "Sim" weight, to estimate the reliability of &alpha;<sub>calc</sub><br />
|-<br />
| HLA/HLB/HLC/HLD || Hendrickson-Lattman coefficients encoding the phase probability distribution<br />
|}<br />
<br />
==Translational Non-crystallographic Symmetry==<br />
<br />
<span style="color:crimson">'''*Warning*''' Solution by MR in the presence of translational non-crystallographic symmetry is not fully automated.</span><br />
<br />
Phaser calculates correction factors for the expected intensities in the presence of translational non-crystallographic symmetry (tNCS), and is able to solve structures with complex patterns of tNCS. '''However, the use of Phaser in the presence of tNCS requires the nature of the tNCS to be understood by the user.''' In simple cases, solution is no more difficult than solution without tNCS, but in complex cases, separate Phaser runs with tNCS turned on and off, and/or the use of different tNCS vectors, may be necessary.<br />
<br />
The output of Phaser will help the user in detecting and understanding the tNCS, but '''the tNCS is not completely characterised by Phaser'''. The default behaviour may or may not be correct for the particular crystal under study.<br />
<br />
Characterization of the tNCS involves understanding the number of copies of the molecule in the asymmetric unit and the translation vectors between them. Molecules related by a tNCS vector will have an associated peak in the native Patterson. Phaser calculates the native Patterson (MODE TNCS) and lists the peaks that are more than 20% of the origin peak. Any given crystal with tNCS may have one or more peaks meeting this criteria.<br />
<br />
===Default tNCS detection and correction===<br />
<span style="color:crimson">Documentation for Phaser-2.7.16 and above</span><br />
<br />
====No tNCS====<br />
No tNCS correction is applied by default if there is<br />
# no peak in the native Patterson <br />
# more than one peak in the native Patterson over 20% of the origin and these peaks are not all the result of a commensurate modulation<br />
<br />
====Pairs of molecules====<br />
By default, if Phaser detects a peak in the native Patterson then Phaser will search for molecules in pairs related by the tNCS vector given by the peak in the native Patterson.<br />
<br />
This will be the correct behaviour if and only if there are an even number of copies of the molecule in the asymmetric unit, clustered into two groups related by a single tNCS vector. There will only be one significant peak in the native Patterson. Fortunately, this is a reasonably common scenario.<br />
<br />
Phaser refines the relative orientation of the molecules in the two groups (rotations of up to 10 degrees will still give rise to a significant native Patterson peak) and uses this information to generate expected intensity factors for the reflections. Solution should be straightforward, with the usual caveat for MR that there is a sufficiently good model.<br />
<br />
Where there is a single peak in the native Patterson, it is often located at a position half way along a unit cell axis or diagonal, representing a pseudo-halving of the unit cell dimensions. However, Phaser is by no means restricted to these sorts of pseudo-cells in its handling of two-fold tNCS, and the tNCS vector can be in a general position.<br />
<br />
===Non-default tNCS correction===<br />
====Higher order tNCS====<br />
Frequently, tNCS does not associate 2 clusters of molecules in the asymmetric unit, but rather there are 3 or more (n) clusters of molecules associated by a series of vectors that are multiples of 1, 2, 3 ... (n-1) times a basic translation vector. Where n times the basic translation vector equates to (very close to) integer multiples of unit cell axes, the tNCS represents a pseudo-cell, and this case is known as commensurate modulation. <br />
<br />
Phaser attempts to automatically detect commensurate modulation. The peaks of the native Patterson are analyzed to find the n-fold relationship. The series will not generally have all peaks the same height. Lower peaks in the series represent relationships where the relative rotations between related molecules are larger. Missing peaks in the series may be below the default 20% of origin cut-off. This can be lowered with TNCS PATT PERCENT <x><br />
<br />
Phaser then sets TNCS NMOL <n> and the vector for the tNCS, and searches for ensembles in multiples of NMOL.<br />
<br />
When there are more than two molecules related by tNCS, Phaser does not refine the orientations between the molecules related by the tNCS.<br />
<br />
However, as for two-fold tNCS, Phaser is not restricted to these sorts of pseudo-cells and the basic tNCS vector can be in a general position, as can the number of copies.<br />
<br />
'''The automatic detection may not give the true tNCS relationship'''. For example, the true commensurate modulation may be a factor of the NMOL automatically detected by Phaser, or there may not be commensurate modulation at all, or commensurate modulation may not be found with the default Pattesron peak height cutoff. In difficult cases, please inspect the Patterson for peaks.<br />
<br />
====Complex tNCS====<br />
If there are many molecules in the asymmetric unit but they are not all related by tNCS, or there are sub-groups of molecules related by different tNCS vectors, then the modulations of the expected intensities due to the tNCS will be much less significant than the cases described above. '''In these cases it is possible that structure solution will be achieved without any tNCS correction factors being applied.''' Indeed, searching for all the copies as tNCS-related multiples when some molecules are not related by tNCS will cause structure solution to fail. To turn off the automatic detection and use of tNCS use the keyword TNCS USE OFF.<br />
<br />
If turning off the TNCS correction factors fails to give a solution, then a good approach is to proceed step-wise. Consider the highest native Patterson peak first and determine that nature of the tNCS associated with it. Use the appropriate correction factors to locate all the molecules with this tNCS. Then take the second independent native Patterson peak and apply the correction factors associated with it to find the second set of molecules, fixing the first, etc. Finally, turn TNCS off to find any orphan molecules.</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Keywords&diff=2408Keywords2017-07-21T12:14:05Z<p>Airlie: </p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
===Phaser Executable===<br />
<br />
The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the [[#MODE | MODE]] keyword. The different modes and the keywords relevant to each mode are described in [[Modes]].<br />
<br />
Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. However, some keywords are meaningful when entered multiple times. The order may or may not be important. <br />
<br />
*[[Image:User1.gif|link=]] [[#Basic Keywords | Basic Keywords]]<br />
<br />
*[[Image:Output.png|link=]] [[#Output Control Keywords | Output Control Keywords]]<br />
<br />
*[[Image:User2.gif|link=]] [[#Advanced Keywords |Advanced Keywords ]]<br />
<br />
*[[Image:Expert.gif|link=]] [[#Expert Keywords | Expert Keywords]]<br />
<br />
*[[Image:Developer.gif|link=]] [[#Developer Keywords | Developer Keywords]]<br />
<br />
<br />
===Python Interface===<br />
<br />
Phaser can be compiled as a python library. The mode is selected by calling the appropriate run-job. Input to the run-job is via input-objects, which are passed to the run-job. Setter function on the input objects are equivalent to the keywords for input to the phaser executable. The different modes and the keywords relevant to each mode are described in [[Modes]]. See [[Python Interface]] for details. <br />
<br />
The python interface uses standard python and cctbx/scitbx variable types.<br />
<br />
str string<br />
float double precision floating point<br />
Miller cctbx::miller::index<int> <br />
dvect3 scitbx::vec3<float> <br />
dmat33 scitbx::mat3<float> <br />
'''type'''_array scitbx::af::shared<'''type'''> arrays<br />
<br />
=Basic Keywords=<br />
==[[Image:User1.gif|link=]]ATOM== <br />
; ATOM CRYSTAL <XTALID> PDB <FILENAME><br />
: Definition of atom positions using a pdb file.<br />
; ATOM CRYSTAL <XTALID> HA <FILENAME><br />
: Definition of atom positions using a ha file (from RANTAN, MLPHARE etc.).<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> <br />
: Minimal definition of atom position. B-factor defaults to isotropic and Wilson B-factor. Use <TYPE>=TX for Ta6Br12 cluster and <TYPE>=XX for all other clusters. Scattering for cluster is spherically averaged. Coordinates of cluster compounds other than Ta6Br12 must be entered with CLUSTER keyword. Ta6Br12 coordinates are in phaser code and do not need to be given with CLUSTER keyword.<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> [ ISOB <ISOB> | ANOU <HH KK LL HK HL KL> | USTAR <HH KK LL HK HL KL>] FIXX [ON|OFF] FIXO [ON|OFF] FIXB [ON|OFF] BSWAP [ON|OFF] LABEL <SITE_NAME><br />
: Full definition of atom position including B-factor.<br />
;ATOM CHANGE BFACTOR WILSON [ON|OFF]<br />
: Reset all atomic B-factors to the Wilson B-factor.<br />
; ATOM CHANGE SCATTERER <SCATTERER><br />
:Reset all atomic scatterers to element (or cluster) type.<br />
setATOM_PDB(str <XTALID>,str <PDB FILENAME>)<br />
setATOM_IOTBX(str <XTALID>,iotbx::pdb::hierarchy::root <iotbx object>)<br />
setATOM_STR(str <XTALID>,str <pdb format string>)<br />
setATOM_HA(str <XTALID>,str <FILENAME>)<br />
addATOM(str <XTALID>,str <TYPE>,<br />
float <X>,float <Y>,float <Z>,float <OCC>)<br />
addATOM_FULL(str <XTALID>,str <TYPE>,bool <ORTH>,<br />
dvect3 <X Y Z>,float <OCC>,bool <ISO>,float <ISOB>,<br />
bool <ANOU>,dmat6 <HH KK LL HK HL KL>,<br />
bool <FIXX>,bool <FIXO>,bool <FIXB>,bool <SWAPB>,<br />
str <SITE_NAME>)<br />
setATOM_CHAN_BFAC_WILS(bool)<br />
setATOM_CHAN_SCAT(bool)<br />
setATOM_CHAN_SCAT_TYPE(str <TYPE>)<br />
<br />
==[[Image:User1.gif|link=]]CLUSTER== <br />
; CLUSTER PDB <PDBFILE><br />
: Sample coordinates for a cluster compound for experimental phasing. Clusters are specified with type XX. Ta6Br12 clusters do not need to have coordinates specified as the coordinates are in the phaser code. To use Ta6Br12 clusters, specify atomtypes/clusters as TX.<br />
setCLUS_PDB(str <PDBFILE>)<br />
addCLUS_PDB(str <ID>, str <PDBFILE>)<br />
<br />
==[[Image:User1.gif|link=]]COMPOSITION== <br />
; COMPOSITION BY [ <sup>1</sup>AVERAGE| <sup>2</sup>SOLVENT| <sup>3</sup>ASU ]<br />
: Alternative ways of defining composition<br />
: <sup>1</sup> AVERAGE solvent fraction for crystals (50%)<br />
: <sup>2</sup> Composition entered by solvent content.<br />
: <sup>3</sup> Explicit description of composition of ASU by sequence or molecular weight<br />
; <sup>2</sup>COMPOSITION PERCENTAGE <SOLVENT><br />
: Specified SOLVENT content<br />
; <sup>3</sup>COMPOSITION PROTEIN [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of protein in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION NUCLEIC [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of nucleic acid in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION ATOM <TYPE> NUMBER <NUM><br />
: Add NUM copies of an atom (usually a heavy atom) to the composition<br />
* Default: COMPOSITION BY ASU<br />
setCOMP_BY(str ["AVERAGE" | "SOLVENT" | "ASU" ])<br />
setCOMP_PERC(float <SOLVENT>)<br />
addCOMP_PROT_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_PROT_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_PROT_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_PROT_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_NUCL_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_NUCL_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_NUCL_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_NUCL_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_ATOM(str <TYPE>,float <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]CRYSTAL== <br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN Fpos =<F+> SIGFpos=<SIG+> Fneg=<F-> SIGFneg=<SIG-><br />
: Columns of MTZ file to read for this (anomalous) dataset<br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN F =<F> SIGF=<SIGF><br />
: Columns of MTZ file to read for this (non-anomalous) dataset. Used for LLG completion in SAD phasing when there is no anomalous signal (single atom MR protocol). Use LABIN for MR.<br />
setCRYS_ANOM_LABI(str <F+>,str <SIGF+>,str <F->,str <SIGF->) <br />
setCRYS_MEAN_LABI(str <F>,str <SIGF>)<br />
<br />
==[[Image:User1.gif|link=]]ENSEMBLE== <br />
; ENSEMBLE <MODLID> [PDB|CIF] <PDBFILE> [RMS <RMS><sup>1</sup> | ID <ID><sup>2</sup> | CARD ON<sup>3</sup>] ''CHAIN "<CHAIN>"<sup>4</sup> MODEL <NUM><sup>5</sup>''<br />
: The names of the PDB/CIF files used to build the ENSEMBLE, and either<br />
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
:: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file (e.g. "REMARK PHASER ENSEMBLE MODEL 1 ID 31.2") containing the superimposed models concatenated in the one file. This syntax enables simple automation of the use of ensembles. The pdb file can be non-standard because the atom list for the different models need not be the same.<br />
:: <sup>4</sup> CHAIN is selected from the pdb file. <br />
:: <sup>5</sup> MODEL number is selected from the pdb file.<br />
; ENSEMBLE <MODLID> HKLIN <MTZFILE> F=<F> PHI=<PHI> EXTENT <EX> <EY> <EZ> RMS <RMS> CENTRE <CX> <CY> <CZ> PROTEIN MW <PMW> NUCLEIC MW <NMW> ''CELL SCALE <SCALE>''<br />
: An ENSEMBLE defined from a map (via an mtz file). The molecular weight of the object the map represents is required for scaling. The effective RMS coordinate error is needed to judge how the map accuracy falls off with resolution. For density obtained from an EM image reconstruction, a good first guess would be to take the resolution where the FSC curve drops below 0.5 and divide by 3. The extent (difference between maximum and minimum x,y,z coordinates of region containing model density) is needed to determine reasonable rotation steps, and the centre is needed to carry out a proper interpolation of the molecular transform. The extent and the centre are both given in Ångstroms. The cell scale factor defaults to 1 and can be refined (for example, if the map is from electron microscopy when the cell scale may be unknown to within a few percent).<br />
; ENSEMBLE <MODLID> ATOM <TYPE> RMS <RMS><br />
: Define an ensemble as a single atom for single atom MR<br />
; ENSEMBLE <MODLID> HELIX <NUM> <br />
: Define an ensemble as a helix with NUM residues<br />
; ENSEMBLE <MODLID> HETATM [ON|OFF]<br />
: Use scattering from HETATM records in pdb file. See [[Molecular_Replacement#Coordinate_Editing | Coordinate Editing ]]<br />
; ENSEMBLE <MODLID> DISABLE CHECK [ON|OFF]<br />
: Toggle to disable checking of deviation between models in an ensemble. '''Use with extreme caution'''. Results of computations are not guaranteed to be sensible.<br />
; ENSEMBLE <MODLID> ESTIMATOR [OEFFNER | OEFFNERHI | OEFFNERLO | CHOTHIALESK ]<br />
: Define the estimator function for converting ID to RMS<br />
; ENSEMBLE <MODLID> PTGRP [COVERAGE | IDENTITY | RMSD | TOLANG | TOLSPC | EULER | SYMM ]<br />
: Define the pointgroup parameters <br />
; ENSEMBLE <MODLID> BINS [MIN <N>| MAX <M>| WIDTH <W> ]<br />
: Define the Fcalc reflection binning parameters <br />
; ENSEMBLE <MODLID> TRACE [PDB|CIF] <PDBFILE><br />
: Define the coordinates used for packing independent of the coordinates used for structure factor calculation<br />
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
:: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file <br />
; ENSEMBLE <MODLID> TRACE SAMPLING MIN <DIST> <br />
: Set the minimum distance for the sampling of packing grid<br />
; ENSEMBLE <MODLID> TRACE SAMPLING TARGET <NUM> <br />
: Set the target for the number of points to sample the smallest molecule to be packed<br />
; ENSEMBLE <MODLID> TRACE SAMPLING RANGE <NUM> <br />
: Target range (TARGET+/-RANGE) for search for hexgrid points in protein volume<br />
; ENSEMBLE <MODLID> TRACE SAMPLING USE [AUTO | ALL | CALPHA | HEXGRID ]<br />
: Sample trace coordinates using all atoms, C-alpha atoms, a hexagonal grid in the atomic volume or use an automatically determined choice<br />
; ENSEMBLE <MODLID> TRACE SAMPLING DISTANCE <DIST> <br />
: Set the distance for the sampling of the hexagonal grid explicitly and do not use TARGET to find default sampling distance<br />
; ENSEMBLE <MODLID> TRACE SAMPLING WANG <WANG> <br />
: Scale factor for the size of the Wang mask generated from an ensemble map<br />
; ENSEMBLE <MODLID> TRACE PDB <PDBFILE> <br />
: Use the given set of coordinates for packing rather than using the coordinates for structure factor calculation<br />
* Default: ENSEMBLE <MODLID> DISABLE CHECK OFF<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING MIN 1.0<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING TARGET 1000<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING RANGE 100<br />
addENSE_PDB_ID(str <MODLID>,str <FILE>,float <ID>) <br />
addENSE_PDB_RMS(str <MODLID>,str <FILE>,float <RMS>) <br />
setENSE_TRAC_SAMP_MIN(MODLID,float <MIN>)<br />
setENSE_TRAC_SAMP_TARG(MODLID,int <TARGET>)<br />
setENSE_TRAC_SAMP_RANG(MODLID,int <RANGE>)<br />
setENSE_TRAC_SAMP_USE(MODLID,str)<br />
setENSE_TRAC_SAMP_DIST(MODLID,float <DIST>)<br />
setENSE_TRAC_SAMP_WANG(MODLID,float <WANG>)r <FILE>,float <RMS>)<br />
addENSE_CARD(str <MODLID>,str <FILE>,bool)<br />
addENSE_MAP(str <MODLID>,str <MTZFILE>,str <F>,str <PHI>,dvect3 <EX EY EZ>,<br />
float <RMS>,dvect3 <CX CY CZ>,float <PMW>,float <NMW>,float <CELL>)<br />
setENSE_DISA_CHEC(bool)<br />
<br />
==[[Image:User1.gif|link=]]FIND==<br />
; FIND SCATTERER <ATOMTYPE><br />
: Phassade, type of scatterers to find<br />
; FIND NUMBER <NUMBER><br />
: Phassade, number of scatteres to find<br />
; FIND CLUSTER [ON|OFF]<br />
: Phassade, scatterer name is a cluster<br />
; FIND PEAK SELECT [PERCENT | SIGMA]<br />
: Phassade, peak selection method from Phassade FFT<br />
; FIND PEAK CUTOFF <CUTOFF><br />
: Phassade, peak selection method cutoff from Phassade FFT<br />
; FIND PURGE SELECT [PERCENT | SIGMA]<br />
: Phassade, purge selection method after all Phassade FFT<br />
; FIND PURGE CUTOFF <CUTOFF><br />
: Phassade, purge selection method cutoff after all Phassade FFT<br />
setFIND_SCAT(str <ATOMTYPE>)<br />
setFIND_NUMB(int <NUMBER>)<br />
setFIND_NUMB(int <NUMBER>)<br />
setFIND_CLUS(bool <CLUSTER>)<br />
setFIND_PEAK_SELE(str <SELECT>)<br />
setFIND_PEAK_CUTO(float <CUTOFF>)<br />
setFIND_PURG_SELE(str <SELECT>)<br />
setFIND_PURG_CUTO(float <CUTOFF>)<br />
<br />
==[[Image:User1.gif|link=]]HKLIN==<br />
; HKLIN <FILENAME><br />
: The mtz file containing the data<br />
setHKLI(str <FILENAME>)<br />
<br />
==[[Image:User1.gif|link=]]JOBS== <br />
; JOBS <NUM><br />
: Number of processors to use in parallelized sections of code<br />
* Default: JOBS 2<br />
setJOBS(int <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]LABIN== <br />
; LABIN F = <F> SIGF = <SIGF> <br />
: Columns in mtz file. F must be given. SIGF should be given but is optional<br />
; LABIN I = <nowiki><I></nowiki> SIGI = <SIGI> <br />
: Columns in mtz file. I must be given. SIGI should be given but is optional<br />
; LABIN FMAP = <PH> PHMAP = <PHMAP> <br />
: Columns in mtz file. FMAP/PHMAP are weighted coefficients for use in the Phased Translation Function.<br />
; LABIN FMAP = <PH> PHMAP = <PHMAP> FOM = <FOM><br />
: Columns in mtz file. FMAP/PHMAP are unweighted coefficients for use in the Phased Translation Function and FOM the figure of merit for weighting<br />
setLABI_F_SIGF(str <F>,str <SIGF>)<br />
setLABI_I_SIGI(str <nowiki><I></nowiki>,str <SIGI>)<br />
setLABI_PTF(str <FMAP>,str <PHMAP>,str <FOM>)<br />
<br />
''Data should be input to python run-jobs using one data_refl parameter''<br />
''This is extracted from the ResultMR_DAT object after a call to runMR_DAT''<br />
setREFL_DATA(data_ref)<br />
''Example:''<br />
i = InputMR_DAT()<br />
i.setHKLI("*.mtz")<br />
i.setLABI_F_SIGF("F","SIGF")<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputMR_LLG()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.setREFL_DATA(r.getDATA())<br />
''See also: '' [[Python Example Scripts]]<br />
<br />
''Alternatively, reflection arrays can be set using cctbx::af::shared<double>''<br />
setREFL_F_SIGF(float_array <F>,float_array <SIGF>)<br />
setREFL_I_SIGI(float_array <nowiki><I></nowiki>,float_array <SIGI>)<br />
setREFL_PTF(float_array <FMAP>,float_array <PHMAP>,float_array <FOM>)<br />
<br />
==[[Image:User1.gif|link=]]MODE==<br />
; MODE [ ANO | CCA | SCEDS | NMAXYZ | NCS | MR_ELLG | MR_AUTO | MR_GYRE | MR_ATOM | MR_ROT | MR_TRA | MR_RNP | | MR_OCC | MR_PAK | EP_AUTO | EP_SAD]<br />
: The mode of operation of Phaser. The different modes are described in a separate page on [[Keyword Modes]]<br />
ResultANO r = runANO(InputANO)<br />
ResultCCA r = runCCA(InputCCA)<br />
ResultNMA r = runSCEDS(InputNMA)<br />
ResultNMA r = runNMAXYZ(InputNMA)<br />
ResultNCS r = runNCS(InputNCS)<br />
ResultELLG r = runMR_ELLG(InputMR_ELLG)<br />
ResultMR r = runMR_AUTO(InputMR_AUTO)<br />
ResultEP r = runMR_ATOM(InputMR_ATOM)<br />
ResulrMR_RF r = runMR_FRF(InputMR_FRF)<br />
ResultMR_TF r = runMR_FTF(InputMR_FTF)<br />
ResultMR r = runMR_RNP(InputMR_RNP)<br />
ResultGYRE r = runMR_GYRE(InputMR_RNP)<br />
ResultMR r = runMR_OCC(InputMR_OCC)<br />
ResultMR r = runMR_PAK(InputMR_PAK)<br />
ResultEP r = runEP_AUTO(InputEP_AUTO)<br />
ResultEP_SAD r = runEP_SAD(InputEP_SAD)<br />
<br />
==[[Image:User1.gif|link=]]PARTIAL== <br />
; PARTIAL PDB <PDBFILE> [RMSIDENTITY] <RMS_ID><br />
: The partial structure for MR-SAD substructure completion. Note that this must already be correctly placed, as the experimental phasing module will not carry out molecular replacement.<br />
; PARTIAL HKLIN <MTZFILE> [RMS|IDENTITY] <RMS_ID><br />
: The partial electron density for MR-SAD substructure completion.<br />
; PARTIAL LABIN FC=<FC> PHIC=<PHIC><br />
: Column labels for partial electron density for MR-SAD substructure completion.<br />
setPART_PDB(str <PDBFILE>)<br />
setPART_HKLI(str <MTZFILE>) <br />
setPART_LABI_FC(str <FC>)<br />
setPART_LABI_PHIC(str <PHIC>) <br />
setPART_VARI(str ["ID"|"RMS"])<br />
setPART_DEVI(float <RMS_ID>)<br />
<br />
==[[Image:User1.gif|link=]]SEARCH==<br />
; SEARCH ENSEMBLE <MODLID> ''{OR ENSEMBLE <MODLID>}… NUMBER <NUM><sup>*</sup>''<br />
: The ENSEMBLE to be searched for in a rotation search or an automatic search. When multiple ensembles are given using the OR keyword, the search is performed for each ENSEMBLE in turn. When the keyword is entered multiple times, each SEARCH keyword refers to a new component of the structure. If the component is present multiple times the sub-keyword NUMber can be used (rather than entering the same SEARCH keyword NUMber times).<br />
: <sup>*</sup>For automatic determination of search number use NUMBER 0. If the composition is entered, the maximum number will be that defined by the composition, otherwise the maximum number will fill the asymmetric unit to a minimum solvent content of 20%. Searches for new components will continue until the TFZ score is above 8, and terminate if the TFZ score drops below 8 before the placement of the maximum number of components.<br />
; SEARCH METHOD [FULL|FAST]<br />
: Search using the [[Modes#Modes |full search]] or [[Modes#Modes | fast search]] algorithms.<br />
; SEARCH ORDER AUTO [ON|OFF]<br />
: Search in the "best" order as estimated using estimated rms deviation and completeness of models.<br />
; SEARCH PRUNE [ON|OFF]<br />
: For high TFZ solutions that fail the packing test, carry out a sliding-window occupancy refinement and prune residues that refine to low occupancy, in an effort to resolve packing clashes. If this flag is set to true, the flag for keeping high tfz score solutions (see [[#PACK | PACK]]) that don't pack is also set to true (PACK KEEP HIGH TFZ ON).<br />
; SEARCH AMALGAMATE USE [ON|OFF]<br />
: For multiple high TFZ solutions, enable amalgamation into a single solution<br />
; SEARCH BFACTOR <BFAC><br />
: B-factor applied to search molecule (or atom).<br />
; SEARCH OFACTOR <OFAC><br />
: Occupancy factor applied to search molecule (or atom).<br />
* Default: SEARCH METHOD FAST<br />
* Default: SEARCH ORDER AUTO ON<br />
* Default: SEARCH PRUNE ON<br />
* Default: SEARCH AMALGAMATE USE ON<br />
* Default: SEARCH BFACTOR 0<br />
* Default: SEARCH OFACTOR 1<br />
addSEAR_ENSE_NUM(str <MODLID>,int <NUM>) <br />
addSEAR_ENSE_OR_ENSE_NUM(string_array <MODLIDS>,int <NUM>) <br />
setSEAR_METH(str [ "FULL" | "FAST" ])<br />
setSEAR_ORDE_AUTO(bool)<br />
setSEAR_PRUN(bool <PRUNE>)<br />
setSEAR_AMAL_USE(bool <AMAL>)<br />
setSEAR_BFAC(float <BFAC>)<br />
setSEAR_OFAC(float <OFAC>)<br />
<br />
==[[Image:User1.gif|link=]]SGALTERNATIVE==<br />
; SGALTERNATIVE SELECT [<sup>1</sup>ALL| <sup>2</sup>HAND| <sup>3</sup>LIST| <sup>4</sup>NONE]<br />
: Selection of alternative space groups to test in translation functions i.e. those that are in same laue group as that given in [[#SPACEGROUP | SPACEGROUP]]<br />
: <sup>1</sup> Test all possible space groups, <br />
: <sup>2</sup> Test the given space group and its enantiomorph.<br />
: <sup>3</sup> Test the space groups listed with SGALTERNATIVE TEST <SG>.<br />
: <sup>4</sup> Do not test alternative space groups.<br />
; SGALTERNATIVE TEST <SG><br />
: Alternative space groups to test. Multiple test space groups can be entered.<br />
* Default: SGALTERNATIVE SELECT HAND<br />
setSGAL_SELE(str [ "ALL" | "HAND" | "LIST" | "NONE" ]) <br />
addSGAL_TEST(str <SG>)<br />
<br />
==[[Image:User1.gif|link=]]SOLUTION==<br />
; SOLUTION SET <ANNOTATION><br />
: Start new set of solutions <br />
; SOLUTION TEMPLATE <ANNOTATION><br />
: Specifies a template solution against which other solutions in this run will be compared. Given in place of SOLUTION SET. Template rotation and translations given by subsequent SOLUTION 6DIM cards as per SOLUTION SETS.<br />
; SOLUTION 6DIM ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> [ORTH|FRAC] <X> <Y> <Z> ''FIXR [ON|OFF] FIXT [ON|OFF] FIXB [ON|OFF] BFAC <BFAC> MULT <MULT>''<br />
: This keyword is repeated for each known position and orientation of an ENSEMBLE MODLID. A B G are the Euler angles (z-y-z convention) and X Y Z are the translation elements, expressed either in orthogonal Angstroms (ORTH) or fractions of a cell edge (FRAC). The input ensemble is transformed by a rotation around the origin of the coordinate system, followed by a translation. BFAC default to 0, MULT (for multiplicity) defaults to 1.<br />
; SOLUTION ENSEMBLE <MODLID> VRMS DELTA <DELTA> RMSD <RMSD><br />
: Refined RMS variance terms for pdb files (or map) in ensemble MODLID. RMSD is the input RMSD of the job that produced the sol file, DELTA is the shift with respect to this RMSD. If given as part of a solution, these values overwrite the values used for input in the ENSEMBLE keyword (if refined).<br />
; SOLUTION ENSEMBLE <MODLID> CELL SCALE <SCALE><br />
: Refined cell scale factor. Only applicable to ensembles that are maps<br />
; SOLUTION TRIAL ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> RF <RF> RFZ <RFZ><br />
: Rotation List for translation function<br />
; SOLUTION ORIGIN ENSEMBLE <MODLID><br />
: Create solution for ensemble MODLID at the origin<br />
; SOLUTION SPACEGROUP <SG><br />
: Space Group of the solution (if alternative spacegroups searched)<br />
; SOLUTION RESOLUTION <HIRES><br />
: High resolution limit of data used to find/refine this solution<br />
; SOLUTION PACKS <PACKS><br />
: Flag for whether solution has been retained despite failing packing test, due to having high TFZ<br />
setSOLU(mr_solution <SOL>) <br />
addSOLU_SET(str <ANNOTATION>) <br />
addSOLU_TEMPLATE(str <ANNOTATION>) <br />
addSOLU_6DIM_ENSE(str <MODLID>,dvect3 <A B C>,bool <FRAC>,dvect3 <X Y Z>,<br />
float <BFAC>,bool <FIXR>,bool <FIXT>,bool <FIXB>,int <MULT>, 1.0) <br />
addSOLU_ENSE_DRMS(str <MODLID>, float <DRMS>) <br />
addSOLU_ENSE_CELL(str <MODLID>, float <SCALE>)<br />
addSOLU_TRIAL_ENSE(string <MODLID>,dvect3 <A B C>,float <RF>, float <RFZ>)<br />
addSOLU_ORIG_ENSE(string <MODLID>)<br />
setSOLU_SPAC(str <SG>)<br />
setSOLU_RESO(float <HIRES>)<br />
setSOLU_PACK(bool <PACKS>)<br />
<br />
==[[Image:User1.gif|link=]]SPACEGROUP==<br />
; SPACEGROUP <SG><br />
: Space group may be altered from the one on the MTZ file to a space group in the same point group. The space group can be entered in one of three ways<br />
#The Hermann-Mauguin symbol e.g. P212121 or P 21 21 21 (with or without spaces)<br />
#The international tables number, which gives standard setting e.g. 19 <br />
#The Hall symbols e.g. P 2ac 2ab<br />
: '''The space group can also be a subgroup of the merged space group'''. For example, P1 is always allowed. The reflections will be expanded to the symmetry of the given subgroup. This is only a valid approach when the true symmetry is the symmetry of the subgroup and perfect twinning causes the data to merge "perfectly" in the higher symmetry. <br />
:'''A list of the allowed space groups in the same point group as the given space group (or space group read from MTZ file) and allowed subgroups of these is given in the Cell Content Analysis logfile.'''<br />
* Default: Read from MTZ file<br />
setSPAC_NUM(int <NUM>)<br />
setSPAC_NAME(string <HM>)<br />
setSPAC_HALL(string <HALL>)<br />
<br />
==[[Image:User1.gif|link=]]WAVELENGTH== <br />
; WAVELENGTH <LAMBDA> <br />
: The wavelengh at which the SAD dataset was collected<br />
setWAVE(float <LAMBDA>)<br />
<br><br />
<br><br />
<br />
=Output Control Keywords=<br />
==[[Image:Output.png|link=]]DEBUG== <br />
; DEBUG [ON|OFF]<br />
: Extra verbose output for debugging<br />
* Default: DEBUG OFF<br />
setDEBU(bool) <br />
<br />
==[[Image:Output.png|link=]]EIGEN==<br />
; EIGEN WRITE [ON|OFF]<br />
; EIGEN READ <EIGENFILE><br />
: Read or write a file containing the eigenvectors and eigenvalues. If reading, the eigenvalues and eigenvectors of the Hessian are read from the file generated by a previous run, rather than calculated. This option must be used with the job that generated the eigenfile and the job reading the eigenfile must have identical input for the ENM parameters. Use WRITE to control whether or not the eigenfile is written when not using the READ mode.<br />
* Default: EIGEN WRITE ON<br />
setEIGE_WRIT(bool)<br />
setEIGE_READ(str <EIGENFILE>)<br />
<br />
==[[Image:Output.png|link=]]HKLOUT== <br />
; HKLOUT [ON|OFF]<br />
: Flags for output of an mtz file containing the phasing information<br />
* Default: HKLOUT ON<br />
setHKLO(bool) <br />
<br />
==[[Image:Output.png|link=]]KEYWORDS== <br />
; KEYWORDS [ON|OFF]<br />
: Write output Phaser .sol file (.rlist file for rotation function)<br />
* Default: KEYWORDS ON<br />
setKEYW(bool)<br />
<br />
==[[Image:Output.gif|link=]]LLGMAPS==<br />
; LLGMAPS [ON|OFF]<br />
: Write log-likelihood gradient map coefficients to MTZ file<br />
* Default: LLGMAPS OFF<br />
setLLGM(bool <True|False>)<br />
<br />
==[[Image:Output.png|link=]]MUTE== <br />
; MUTE [ON|OFF]<br />
: Toggle for running in silent/mute mode, where no logfile is written to ''standard output''.<br />
* Default: MUTE OFF<br />
setMUTE(bool) <br />
<br />
==[[Image:Output.png|link=]]KILL== <br />
; KILL TIME [MINS]<br />
: Kill Phaser after MINS minutes of CPU have elapsed, provided parallel section is complete<br />
; KILL FILE [FILENAME]<br />
: Kill Phaser if file FILENAME is present, provided parallel section is complete<br />
* Default: KILL TIME 0 ''Phaser runs to completion''<br />
* Detaulf: KILL FILE "" ''Phaser runs to completion''<br />
setKILL_TIME(float) <br />
setKILL_FILE(string)<br />
<br />
==[[Image:Output.png|link=]]OUTPUT== <br />
; OUTPUT LEVEL [SILENT|CONCISE|SUMMARY|LOGFILE|VERBOSE|DEBUG]<br />
: Output level for logfile<br />
; OUTPUT LEVEL [0|1|2|3|4|5]<br />
: Output level for logfile (equivalent to keyword level setting)<br />
* Default: OUTPUT LEVEL LOGFILE<br />
setOUTP_LEVE(string)<br />
setOUTP(enum)<br />
<br />
==[[Image:Output.png|link=]]TITLE==<br />
; TITLE <TITLE><br />
: Title for job<br />
* Default: TITLE [no title given]<br />
setTITL(str <TITLE>)<br />
<br />
==[[Image:Output.png|link=]]TOPFILES== <br />
; TOPFILES <NUM><br />
: Number of top pdbfiles or mtzfiles to write to output.<br />
* Default: TOPFILES 1<br />
setTOPF(int <NUM>) <br />
<br />
==[[Image:Output.png|link=]]ROOT== <br />
; ROOT <FILEROOT><br />
: Root filename for output files (e.g. FILEROOT.log)<br />
* Default: ROOT PHASER<br />
setROOT(string <FILEROOT>)<br />
<br />
==[[Image:Output.png|link=]]VERBOSE== <br />
; VERBOSE [ON|OFF] <br />
: Toggle to send verbose output to log file.<br />
* Default: VERBOSE OFF<br />
setVERB(bool) <br />
<br />
==[[Image:Output.png|link=]]XYZOUT== <br />
; XYZOUT [ON|OFF] ''ENSEMBLE [ON|OFF]<sup>1</sup> PACKING [ON|OFF]<sup>2</sup>''<br />
: Toggle for output coordinate files. <br />
::<sup>1</sup> If the optional ENSEMBLE keyword is ON, then each placed ensemble is written to its own pdb file. The files are named FILEROOT.#.#.pdb with the first # being the solution number and the second # being the number of the placed ensemble (representing a SOLU 6DIM entry in the .sol file). <br />
::<sup>2</sup> If the optional PACKING keyword is ON, then the hexagonal grid used for the packing analysis is output to its own pdb file FILEROOT.pak.pdb<br />
* Default: XYZOUT OFF (Rotation functions)<br />
* Default: XYZOUT ON ENSEMBLE OFF (all other relevant modes)<br />
* Default: XYZOUT ON PACKING OFF (all other relevant modes)<br />
setXYZO(bool) <br />
setXYZO_ENSE(bool)<br />
setXYZO_PACK(bool)<br />
<br><br />
<br><br />
<br />
=Advanced Keywords=<br />
==[[Image:User2.gif|link=]]ELLG==<br />
([[Molecular_Replacement#Should_Phaser_Solve_It.3F|explained here]])<br />
; ELLG TARGET <TARGET><br />
: Target value for expected LLG for determining resolution limits and search order<br />
<!--; ELLG HIRES <HIRES> Internal control only--><br />
* Default: ELLG TARGET 225<br />
setELLG_TARG(float <TARGET>)<br />
<br />
==[[Image:User2.gif|link=]]FORMFACTORS==<br />
; FORMFACTORS [XRAY | ELECTRON | NEUTRON]<br />
: Use scattering factors from x-ray, electron or neutrons<br />
* Default: FORMFACTORS XRAY<br />
setFORM(string XRAY)<br />
<br />
==[[Image:User2.gif|link=]]HAND==<br />
; HAND [ <sup>1</sup>ON| <sup>2</sup>OFF| <sup>3</sup>BOTH]<br />
: Hand of heavy atoms for experimental phasing<br />
: <sup>1</sup>Phase using the other hand of heavy atoms <br />
: <sup>2</sup>Phase using given hand of heavy atoms <br />
: <sup>3</sup>Phase using both hands of heavy atoms<br />
* Default: HAND BOTH<br />
setHAND(str [ "OFF" | "ON" | "BOTH" ])<br />
<br />
==[[Image:User2.gif|link=]]LLGCOMPLETE==<br />
; LLGCOMPLETE COMPLETE [ON|OFF]<br />
: Toggle for structure completion by log-likelihood gradient maps<br />
; LLGCOMPLETE SCATTERER <TYPE> <br />
: Atom/Cluster type(s) to be used for log-likelihood gradient completion. If more than one element is entered for log-likelihood gradient completion, the atom type that gives the highest Z-score for each peak is selected. Type = "RX" is a purely real scatterer and type="AX" is purely anomalous scatterer<br />
; LLGCOMPLETE REAL ON<br />
: Use a purely real scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER RX)<br />
; LLGCOMPLETE ANOMALOUS ON<br />
: Use a purely anomalous scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER AX)<br />
; LLGCOMPLETE CLASH <CLASH> <br />
: Minimum distance between atoms in log-likelihood gradient maps and also the distance used for determining anisotropy of atoms (default determined by resolution, flagged by CLASH=0)<br />
; LLGCOMPLETE SIGMA <Z><br />
: Z-score (sigma) for accepting peaks as new atoms in log-likelihood gradient maps<br />
; LLGCOMPLETE NCYC <NMAX><br />
: Maximum number of cycles of log-likelihood gradient structure completion. By default, NMAX is 50, but this limit should never be reached, because all features in the log-likelihood gradient maps should be assigned well before 50 cycles are finished. This keyword should be used to reduce the number of cycles to 1 or 2.<br />
; LLGCOMPLETE METHOD [IMAGINARY|ATOMTYPE]<br />
: Pick peaks from the imaginary map only or from all the completion atomtype maps.<br />
* Default: LLGCOMPLETE COMPLETE OFF<br />
* Default: LLGCOMPLETE CLASH 0<br />
* Default: LLGCOMPLETE SIGMA 6<br />
* Default: LLGComplete NCYC 50<br />
* Default: LLGComplete METHOD ATOMTYPE<br />
setLLGC_COMP(bool <True|False>) <br />
setLLGC_CLAS(float <CLASH>) <br />
setLLGC_SIGM(float <Z>) <br />
setLLGC_NCYC(int <NMAX>)<br />
setLLGC_METH(str ["IMAGINARY"|"ATOMTYPE"])<br />
<br />
==[[Image:User2.gif|link=]]NMA== <br />
; NMA MODE <M1> ''{MODE <M2>…}'' <br />
: The MODE keyword gives the mode along which to perturb the structure. If multiple modes are entered, the structure is perturbed along all the modes AND combinations of the modes given. There is no limit on the number of modes that can be entered, but the number of pdb files explodes combinatorially. The first 6 modes are the pure rotation and translation modes and do not lead to perturbation of the structure. If the number M is less than 7 then M is interpreted as the first M modes starting at 7, so for example, MODE 5 would give modes 7 8 9 10 11.<br />
; NMA COMBINATION <NMAX><br />
: Controls how many modes are present in any combination.<br />
* Default: NMA MODE 5<br />
* Default: NMA COMBINATION 2<br />
addNMA_MODE(int <MODE>) <br />
setNMA_COMB(int <NMAX>)<br />
<br />
==[[Image:User2.gif|link=]]PACK==<br />
; PACK SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>ALL ]<br />
: <sup>1</sup>Allow up to the PERCENT of sampling points to clash, considering only pairwise clashes <br />
: <sup>2</sup>Allow all solutions (no packing test)<br />
; PACK CUTOFF <PERCENT> <br />
: Limit on total number (or percent) of clashes <br />
; PACK QUICK [ON|OFF]<br />
: Packing check stops when ALLOWED_CLASHES or MAX_CLASHES is reached. However, all clashes are found when the solution has a high Z-score (see [[#ZSCORE | ZSCORE]]).<br />
; PACK COMPACT [ON|OFF]<br />
: Pack ensembles into a compact association (minimize distances between centres of mass for the addition of each component in a solution).<br />
; PACK KEEP HIGH TFZ [ON|OFF]<br />
: Solutions with high tfz (see [[#ZSCORE | ZSCORE]]) but that fail to pack are retained in the solution list. Set to true if SEARCH PRUNE ON (see [[#SEARCH | SEARCH]])<br />
* Default: PACK SELECT PERCENT<br />
* Default: PACK CUTOFF 10<br />
* Default: PACK COMPACT ON<br />
* Default: PACK QUICK ON<br />
* Default: PACK KEEP HIGH TFZ OFF<br />
* Default: PACK CONSERVATION DISTANCE 1,5<br />
setPACK_SELE(str ["PERCENT"|"ALL"]) <br />
setPACK_CUTO(float <ALLOWED_CLASHES>)<br />
setPACK_QUIC(bool)<br />
setPACK_KEEP_HIGH_TFZ(bool)<br />
setPACK_COMP(bool)<br />
<br />
==[[Image:User2.gif|link=]]PEAKS==<br />
; PEAKS TRA SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL] <br />
; PEAKS ROT SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL]<br />
: Peaks for individual rotation functions (ROT) or individual translation functions (TRA) satisfying selection criteria are saved. To be used for subsequent steps, peaks must also satisfy the overall [[#PURGE | PURGE]] selection criteria, so it will usually be appropriate to set only the PURGE criteria (which over-ride the defaults for the PEAKS criteria if not explicitly set). See [[Molecular_Replacement#How_to_Select_Peaks | How to Select Peaks]]<br />
: <sup>1</sup> Select peaks by taking all peaks over CUTOFF percent of the difference between the top peak and the mean value.<br />
: <sup>2</sup> Select peaks by taking all peaks with a Z-score greater than CUTOFF.<br />
: <sup>3</sup> Select peaks by taking top CUTOFF.<br />
: <sup>4</sup> Select all peaks.<br />
; PEAKS ROT CUTOFF <CUTOFF><br />
; PEAKS TRA CUTOFF <CUTOFF><br />
: Cutoff value for the rotation function (ROT) or translation function (TRA) peak selection criteria.<br />
: If selection is by percent and [[#PURGE | PURGE PERCENT]] is changed from the default, then the PEAKS percent value is set to the lower PURGE percent value.<br />
; PEAKS ROT CLUSTER [ON|OFF] <br />
; PEAKS TRA CLUSTER [ON|OFF]<br />
: Toggle selects clustered or unclustered peaks for rotation function (ROT) or translation function (TRA).<br />
; PEAKS ROT DOWN [PERCENT] <br />
: [[#SEARCH | SEARCH METHOD FAST]] only. Percentage to reduce rotation function cutoff if there is no TFZ over the zscore cutoff that determines a true solution (see [[#ZSCORE | ZSCORE]]) in first search.<br />
* Default: PEAKS ROT SELECT PERCENT<br />
* Default: PEAKS TRA SELECT PERCENT<br />
* Default: PEAKS ROT CUTOFF 75<br />
* Default: PEAKS TRA CUTOFF 75<br />
* Default: PEAKS ROT CLUSTER ON<br />
* Default: PEAKS TRA CLUSTER ON<br />
setPEAK_ROTA_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"]) <br />
setPEAK_TRAN_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"])<br />
setPEAK_ROTA_CUTO(float <CUTOFF>)<br />
setPEAK_TRAN_CUTO(float <CUTOFF>) <br />
setPEAK_ROTA_CLUS(bool <CLUSTER>) <br />
setPEAK_TRAN_CLUS(bool <CLUSTER>)<br />
setPEAK_ROTA_DOWN(float <PERCENT>)<br />
<br />
==[[Image:User2.gif|link=]]PERMUTATIONS== <br />
; PERMUTATIONS [ON|OFF]<br />
: Only relevant to [[#SEARCH | SEARCH METHOD FULL]]. Toggle for whether the order of the search set is to be permuted.<br />
* Default: PERMUTATIONS OFF<br />
setPERM(bool <PERMUTATIONS>)<br />
<br />
==[[Image:User2.gif|link=]]PERTURB== <br />
; PERTURB RMS STEP <RMS><br />
: Increment in rms Ångstroms between pdb files to be written. <br />
; PERTURB RMS MAX <MAXRMS><br />
: The structure will be perturbed along each mode until the MAXRMS deviation has been reached.<br />
; PERTURB RMS DIRECTION [FORWARD|BACKWARD|TOFRO] <br />
: The structure is perturbed either forwards or backwards or to-and-fro (FORWARD|BACKWARD|TOFRO) along the eigenvectors of the modes specified.<br />
; PERTURB INCREMENT [RMS| DQ] <br />
: Perturb the structure by rms devitations along the modes, or by set dq increments<br />
; PERTURB DQ <DQ1> ''{DQ <DQ2>…}''<br />
: Alternatively, the DQ factors (as used by the Elnemo server (K. Suhre & Y-H. Sanejouand, NAR 2004 vol 32) ) by which to perturb the atoms along the eigenvectors can be entered directly.<br />
* Default: PERTURB INCREMENT RMS<br />
* Default: PERTURB RMS STEP 0.2<br />
* Default: PERTURB RMS MAXRMS 0.3<br />
* Default: PERTURB RMS DIRECTION TOFRO<br />
setPERT_INCR(str [ "RMS" | "DQ" ])<br />
setPERT_RMS_MAXI(float <MAX>)<br />
setPERT_RMS_DIRE(str [ "FORWARDS" | "BACKWARDS" | "TOFRO" ]) <br />
addPERT_DQ(float <DQ>)<br />
<br />
==[[Image:User2.gif|link=]]PURGE== <br />
; PURGE ROT ENABLE [ON|OFF]<sup>1</sup><br />
; PURGE ROT PERCENT <PERC><sup>2</sup><br />
; PURGE ROT NUMBER <NUM><sup>3</sup><br />
: Purging criteria for rotation function (RF), where PERCENT and NUMBER are alternative selection criteria (''OR'' criteria)<br />
::<sup>1</sup> Toggle for whether to purge the solution list from the RF according to the top solution found. If there are a number of RF searches with different partial solution backgrounds, the PURGE is applied to the total list of peaks. If there is one clearly significant RF solution from one of the backgrounds it acts to purge all the less significant solutions. If there is only one RF (a single partial solution background) the PURGE gives no additional selection over and above the PEAKS command. <br />
::<sup>2</sup> [[Molecular_Replacement#How_to_Select_Peaks | Selection by percent]]. PERC is percentage of the top peak, where the value of the top peak is defined as 100% and the value of the mean is defined as 0%. Note that this criterion is applied subsequent to any selection criteria applied through the [[#PEAKS | PEAKS]] command. If the [[#PEAKS | PEAKS]] selection is by percent, then the percent cutoff given in the PURGE command over-rides that for [[#PEAKS | PEAKS]], so as to rationalize results in the case of only a single RF (single partial solution background.)<br />
::<sup>3</sup> NUM is the number of solutions to retain in purging. If NUMBER is given (non-zero) it overrides the PERCENT option. NUMBER given as zero is the flag for not applying this criterion.<br />
; PURGE TRA ENABLE [ON|OFF]<br />
; PURGE TRA PERCENT <PERC><br />
; PURGE TRA NUMBER <NUM><br />
: As above, but for translation function<br />
; PURGE RNP ENABLE [ON|OFF]<br />
; PURGE RNP PERCENT <PERC><br />
; PURGE RNP NUMBER <NUM><br />
: As above but for refinement, but with the important distinction that PERCENT and NUMBER are concurrent selection criteria (''AND'' criteria)<br />
* Default: PURGE ROT ENABLE ON <br />
* Default: PURGE ROT PERC 75<br />
* Default: PURGE ROT NUM 0<br />
* Default: PURGE TRA ENABLE ON<br />
* Default: PURGE TRA PERC 75<br />
* Default: PURGE TRA NUM 0<br />
* Default: PURGE RNP ENABLE ON<br />
* Default: PURGE RNP PERC 75<br />
* Default: PURGE RNP NUM 0<br />
setPURG_ROTA_ENAB(bool <ENABLE>)<br />
setPURG_TRAN_ENAB(bool <ENABLE>) <br />
setPURG_RNP_ENAB(bool <ENABLE>)<br />
setPURG_ROTA_PERC(float <PERC>) <br />
setPURG_TRAN_PERC(float <PERC>) <br />
setPURG_RNP_PERC(float <PERC>)<br />
setPURG_ROTA_NUMB(float <NUM>) <br />
setPURG_TRAN_NUMB(float <NUM>)<br />
setPURG_TRAN_NUMB(float <NUM>)<br />
setPURG_RNP_NUMB(float <NUM>)<br />
<br />
==[[Image:User2.gif|link=]]RESOLUTION== <br />
; RESOLUTION HIGH <HIRES> <br />
: High resolution limit in Ångstroms. <br />
; RESOLUTION LOW <LORES><br />
: Low resolution limit in Ångstroms.<br />
; RESOLUTION AUTO HIGH <HIRES> <br />
: High resolution limit in Ångstroms for final high resolution refinement in MR_AUTO mode.<br />
* Default for molecular replacement: Set by [[#ELLG | ELLG TARGET]] for structure solution, final refinement uses all data<br />
* Default for experimental phasing: All data used<br />
setRESO_HIGH(float <HIRES>) <br />
setRESO_LOW(float <LORES>)<br />
setRESO_AUTO_HIGH(float <HIRES>) <br />
setRESO(float <HIRES>,float <LORES>)<br />
<br />
==[[Image:User2.gif|link=]]ROTATE== <br />
; ROTATE VOLUME FULL<br />
: Sample all unique angles <br />
; ROTATE VOLUME AROUND EULER <A> <nowiki><B></nowiki> <C> RANGE <RANGE> <br />
: Restrict the search to the region of +/- RANGE degrees around orientation given by EULER<br />
setROTA_VOLU(string ["FULL"|"AROUND"|) <br />
setROTA_EULE(dvect3 <A B C>) <br />
setROTA_RANG(float <RANGE>)<br />
<br />
==[[Image:User2.gif|link=]]SCATTERING==<br />
; SCATTERING TYPE <TYPE> FP=<FP> FDP=<FDP> FIX [ON|OFF|EDGE]<br />
: Measured scattering factors for a given atom type, from a fluorescence scan. FIX EDGE (default) fixes the fdp value if it is away from an edge, but refines it if it is close to an edge, while FIX ON or FIX OFF does not depend on proximity of edge.<br />
; SCATTERING RESTRAINT [ON|OFF]<br />
: use Fdp restraints<br />
; SCATTERING SIGMA <SIGMA><br />
: Fdp restraint sigma used is SIGMA multiplied by initial fdp value<br />
* Default: SCATTERING SIGMA 0.2<br />
* Default: SCATTERING RESTRAINT ON<br />
addSCAT(str <TYPE>,float <FP>,float <FDP, string <FIXFDP>) <br />
setSCAT_REST(bool) <br />
setSCAT_SIGM(float <SIGMA>)<br />
<br />
==[[Image:User2.gif|link=]]SCEDS== <br />
; SCEDS NDOM <NDOM><br />
:Number of domains into which to split the protein<br />
; SCEDS WEIGHT SPHERICITY <WS><br />
: Weight factor for the the Density Test in the SCED Score. The Sphericity Test scores boundaries that divide the protein into more spherical domains more highly.<br />
; SCEDS WEIGHT CONTINUITY <WC><br />
: Weight factor for the the Continuity Test in the SCED Score. The Continuity Test scores boundaries that divide the protein into domains contigous in sequence more highly. <br />
; SCEDS WEIGHT EQUALITY <WE><br />
: Weight factor for the the Equality Test in the SCED Score. The Equality Test scores boundaries that divide the protein more equally more highly.<br />
; SCEDS WEIGHT DENSITY <WD><br />
: Weight factor for the the Equality Test in the SCED Score. The Density Test scores boundaries that divide the protein into domains more densely packed with atoms more highly. <br />
* Default: SCEDS NDOM 2<br />
* Default: SCEDS WEIGHT EQUALITY 1<br />
* Default: SCEDS WEIGHT SPHERICITY 4 <br />
* Default: SCEDS WEIGHT DENSITY 1<br />
* Default: SCEDS WEIGHT CONTINUITY 0<br />
setSCED_NDOM(int <NDOM>) <br />
setSCED_WEIG_SPHE(float <WS>) <br />
setSCED_WEIG_CONT(float <WC>)<br />
setSCED_WEIG_EQUA(float <WE>) <br />
setSCED_WEIG_DENS(float <WD>)<br />
<br />
==[[Image:User2.gif|link=]]TARGET==<br />
; TARGET ROT [FAST | BRUTE]<br />
: Target function for fast rotation searches (2). BRUTE searches all angles on a grid with the full rotation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these rotations with the full rotation likelihood target.<br />
; TARGET TRA [FAST | BRUTE | PHASED]<br />
: Target function for fast translation searches (3). BRUTE searches all positions on a grid with the full translation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these positions with the full translation likelihood target. PHASED selects the "phased translation function", for which a LABIN command should also be given, specifying FMAP, PHMAP and (optionally) FOM.<br />
* Default: TARGET ROT FAST<br />
* Default: TARGET TRA FAST<br />
setTARG_ROTA(str ["FAST"|"BRUTE"])<br />
setTARG_TRAN(str ["FAST"|"BRUTE"|"PHASED"])<br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS NMOL <NMOL><br />
: Number of molecules/molecular assemblies related by single TNCS vector (usually only 2). If the TNCS is a pseudo-tripling of the cell then NMOL=3, a pseudo-quadrupling then NMOL=4 etc.<br />
* Default: TNCS NMOL 2<br />
setTNCS_NMOL(int <NMOL>)<br />
<br><br />
<br />
==[[Image:User2.gif|link=]]TRANSLATION== <br />
; TRANSLATION VOLUME [ <sup>1</sup>FULL | <sup>2</sup>REGION | <sup>3</sup>LINE | <sup>4</sup>AROUND ])<br />
: Search volume for brute force translation function.<br />
: <sup>1</sup> Cheshire cell or Primitive cell volume. <br />
: <sup>2</sup> Search region.<br />
: <sup>3</sup> Search along line. <br />
: <sup>4</sup> Search around a point.<br />
; <sup>1 2 3</sup>TRANSLATION START <X Y Z> <br />
; <sup>1 2 3</sup>TRANSLATION END <X Y Z><br />
: Search within region or line bounded by START and END.<br />
; <sup>4</sup>TRANSLATION POINT <X Y Z><br />
; <sup>4</sup>TRANSLATION RANGE <RANGE><br />
: Search within +/- RANGE Ångstroms (not fractional coordinates, even if the search point is given as fractional coordinates) of a point <X Y Z>.<br />
; TRANSLATION [ORTH | FRAC]<br />
: Coordinates are given in orthogonal or fractional values.<br />
; TRANSLATION PACKING USE [ON | OFF]<br />
: Top translation function peak will be testes for packing.<br />
; TRANSLATION PACKING CUTOFF <PERC><br />
: Percent pairwise packing used for packing function test of top TF peak. Equivalent to PACK CUTOFF <PERC> for packing function. <br />
; TRANSLATION PACKING NUM <NUM><br />
: Number of translation function peaks to test for packing before bailing out of packing test. Set to 0 to pack all translation function peaks (slow for large packing volumes). <br />
* Default: TRANSLATION VOLUME FULL<br />
* Default: TRANSLATION PACK CUTOFF 50<br />
* Default: TRANSLATION PACK NUM 0 (helices - all packing checked)<br />
* Default: TRANSLATION PACK NUM 500 (non-helices)<br />
setTRAN_VOLU(string ["FULL"|"REGION"|"LINE"|"AROUND"])<br />
setTRAN_START(dvect <START>)<br />
setTRAN_END(dvect <END>)<br />
setTRAN_POINT(dvect <POINT>)<br />
setTRAN_RANGE(float <RANGE>)<br />
setTRAN_FRAC(bool <True=FRAC False=ORTH>)<br />
setTRAN_PACK_USE(bool)<br />
setTRAN_PACK_CUTO(float)<br />
<br />
==[[Image:User2.gif|link=]]ZSCORE== <br />
; ZSCORE USE [ON|OFF]<br />
: Use the TFZ tests. Only applicable with [[#SEARCH | SEARCH METHOD FAST]]. (Note Phaser-2.4.0 and below use "ZSCORE SOLVED 0" to turn off the TFZ tests)<br />
; ZSCORE SOLVED <ZSCORE_SOLVED><br />
: Set the minimum TFZ that indicates a definite solution for amalgamating solutions in FAST search method. <br />
;ZSCORE STOP [ON|OFF]<br />
: Stop adding components beyond point where TFZ is below cutoff when adding multiple components in FAST mode. However, FAST mode will always add one component even if TFZ is below cutoff, or two components if starting search with no components input (no input solution).<br />
; ZSCORE HALF [ON|OFF]<br />
: Set the TFZ for amalgamating solutions in the FAST search method to the maximum of ZSCORE_SOLVED and half the maximum TFZ, to accommodate cases of partially correct solutions in very high TFZ cases (e.g. TFZ > 16)<br />
* Default: ZSCORE USE ON<br />
* Default: ZSCORE SOLVED 8<br />
* Default: ZSCORE HALF ON<br />
* Default: ZSCORE STOP ON<br />
setZSCO_USE(bool <True=ON False=OFF>)<br />
setZSCO_SOLV(floatType ZSCORE_SOLVED)<br />
setZSCO_HALF(bool <True=ON False=OFF>)<br />
setZSCO_STOP(bool <True=ON False=OFF>)<br />
<br><br />
<br><br />
<br />
=Expert Keywords=<br />
<br />
==[[Image:Expert.gif|link=]]MACANO== <br />
; MACANO PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for the refinement of SigmaN in the anisotropy correction<br />
; MACANO ANISO [ON|OFF] BINS [ON|OFF] SOLK [ON|OFF] SOLB [ON|OFF] ''{NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}''<br />
: Macrocycle for the custom refinement of SigmaN in the anisotropy correction. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACANO PROTOCOL DEFAULT<br />
setMACA_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACA(bool <ANISO>,bool <BINS>,bool <SOLK>,bool <SOLB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACMR== <br />
; MACMR PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACMR ROT [ON|OFF] TRA [ON|OFF] BFAC [ON|OFF] VRMS [ON|OFF] ''CELL [ON|OFF] LAST [ON|OFF] NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of molecular replacement solutions. Macrocycles are performed in the order in which they are entered. For description of VRMS see the [[FAQ]]. CELL is the scale factor for the unit cell for maps (EM maps). LAST is a flag that refines the parameters for the last component of a solution only, fixing all the others.<br />
; MACMR CHAINS [ON|OFF]<br />
: Split the ensembles into chains for refinement<br />
: Not possible as part of an automated mode<br />
* Default: MACMR PROTOCOL DEFAULT<br />
* Default: MACMR CHAINS OFF<br />
setMACM_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACM(bool <ROT>,bool <TRA>,bool <BFAC>,bool <VRMS>,bool <CELL>,bool <LAST>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
setMACM_CHAI(bool])<br />
<br />
==[[Image:Expert.gif|link=]]MACOCC== <br />
; MACOCC PROTOCOL [ DEFAULT | CUSTOM | OFF | ALL ]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACOCC NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of occupancy for solutions. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACOCC PROTOCOL DEFAULT<br />
setMACO_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACO(int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACGYRE== <br />
; MACGYRE PROTOCOL [ DEFAULT | CUSTOM | OFF | ALL ]<br />
: Protocol for refinement of gyre rotations<br />
; MACGYRE ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] ''ANCHOR [ON|OFF] SIGROT <SIGR> SIGTRA <SIGT> NCYCLE <NCYC> MINIMIZER [ BFGS | NEWTON | DESCENT ]''<br />
: Macrocycle for custom refinement of gyre refinement for solutions. Macrocycles are performed in the order in which they are entered.<br />
; MACGYRE SIGROT <SIGROT> <br />
; MACGYRE SIGTRA <SIGTRA> <br />
; MACGYRE ANCHOR [ON|OFF]<br />
: Override default values for harmonic restraints for rotation and translation refinement, and whether or not to anchor one fragment (no translation) for all macrocycles<br />
* Default: MACGYRE PROTOCOL DEFAULT<br />
setMACG_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACG(bool <REF>,bool <REF>, bool <REF>)<br />
addMACG_FULL(bool <REF>,bool <REF>,bool<REF>,bool <ANCHOR>,float <SIGROT>,float <SIGTRA>,int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
setMACG_SIGR(bool <SIGROT>)<br />
setMACG_SIGT(bool <SIGTRA>)<br />
setMACG_ANCH(bool <ANCHOR>)<br />
<br />
==[[Image:Expert.gif|link=]]MACSAD== <br />
; MACSAD PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for SAD refinement.<br />
:''n.b. PROTOCOL ALL will crash phaser and is only useful for debugging - see code for details''<br />
; MACSAD XYZ [ON|OFF] OCC [ON|OFF] BFAC [ON|OFF] FDP [ON|OFF] SA [ON|OFF] SB [ON|OFF] SP [ON|OFF] SD [ON|OFF] ''{PK [ON|OFF]} {PB [ON|OFF]} {NCYCLE <NCYC>} MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for SAD refinement. Macrocycles are performed in the order in which they are entered.<br />
*Default: MACSAD PROTOCOL DEFAULT<br />
setMACS_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACS(<br />
bool <XYZ>,bool <OCC>,bool <BFAC>,bool <FDP><br />
bool <SA>,bool <SB>,bool <SP>,bool <SD>,<br />
bool <PK>, bool <PB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACTNCS== <br />
; MACTNCS PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for pseudo-translational NCS refinement.<br />
; MACTNCS ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] ''NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for pseudo-translational NCS refinement. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACTNCS PROTOCOL DEFAULT<br />
setMACT_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACT(bool <ROT>,bool <TRA>,bool <VRMS>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]OCCUPANCY== <br />
; OCCUPANCY WINDOW ELLG <ELLG><br />
: Target eLLG for determining number of residues in window for occupancy refinement. The number of residues in a window will be an odd number. Occupancy refinement will be done for each offset of the refinement window.<br />
; OCCUPANCY WINDOW NRES <NRES><br />
: As an alternative to using the eLLG to define the number of residues in window for occupancy refinement, the number may be input directly. NRES must be an odd number.<br />
; OCCUPANCY WINDOW MAX <NRES><br />
: Maximum number of residues in an occupancy window (determined either by ellg or given as NRES) for which occupancy is refined. Prevents the refinement windows from spanning non-local regions of space.<br />
; OCCUPANCY MIN <MINOCC> MAX <MAXOCC><br />
: Minimum and maximum values of occupancy during refinement.<br />
; OCCUPANCY MERGE [ON/OFF]<br />
: Merge refined occupancies from different window offsets to give final occupancies per residue. If OFF, occupancies from a single window offset will be used, selected using OCCUPANCY OFFSET <N><br />
; OCCUPANCY FRAC <FRAC><br />
: Minimum fraction of the protein for which the occupancy may be set to zero.<br />
; OCCUPANCY OFFSET <N><br />
: If OCCUPANCY MERGE OFF, then <N> defines the single window offset from which final occupancies will be taken<br />
* Default: OCCUPANCY WINDOW ELLG 5<br />
* Default: OCCUPANCY WINDOW MAX 111<br />
* Default: OCCUPANCY MIN 0.01 MAX 1<br />
* Default: OCCUPANCY NCYCLES 1<br />
* Default: OCCUPANCY MERGE ON<br />
* Default: OCCUPANCY FRAC 0.5<br />
* Default: OCCUPANCY OFFSET 0<br />
setOCCU_WIND_ELLG(float <ELLG>)<br />
setOCCU_WIND_NRES(int <NRES>)<br />
setOCCU_WIND_MAX(int <NRES>)<br />
setOCCU_MIN(float <MIN>)<br />
setOCCU_MAX(float <MAX>)<br />
setOCCU_MERG(float <FRAC>)<br />
setOCCU_FRAC(bool)<br />
setOCCU_OFFS(int <N>)<br />
<br />
==[[Image:Expert.gif|link=]]RESCORE== <br />
; RESCORE ROT [ON|OFF]<br />
; RESCORE TRA [ON|OFF]<br />
: Toggle for rescoring of fast rotation function (ROT) or fast translation function (TRA) search peaks. <br />
* Default: RESCORE ROT ON<br />
* Default: RESCORE TRA ON|OFF will depend on whether phaser is running in the mode [[#MODE | MODE MR_AUTO]] with [[#SEARCH | SEARCH METHOD FAST]] or with [[#SEARCH | SEARCH METHOD FULL]], or running the translation function separately [[#MODE | MODE MR_FTF]]. For [[#SEARCH | SEARCH METHOD FAST]] the default also depends on whether or not the expected LLG target [[#ELLG | ELLG TARGET <TARGET>]] value is reached.<br />
setRESC_ROTA(bool)<br />
setRESC_TRAN(bool)<br />
<br />
==[[Image:Expert.gif|link=]]RFACTOR== <br />
; RFACTOR USE [ON|OFF]<br />
: For cases of searching for one ensemble when there is one ensemble in the asymmetric unit, the R-factor for the ensemble at the orientation and position in the input is calculated. If this value is low then MR is not performed in the MR_AUTO job in FAST search mode. Instead, rigid body refinement is performed before exiting. Note that the same R-factor test and cutoff is used for judging success in single-atom molecular replacement (MR_ATOM mode).<br />
; RFACTOR CUTOFF <VALUE><br />
: Rfactor in percent used as cutoff for deciding whether or not the R-factor indicates that MR is not necessary.<br />
* Default: RFACTOR USE ON CUTOFF 35<br />
setRFAC_USE(bool)<br />
setRFAC_CUTO(float <PERCENT>)<br />
<br />
==[[Image:Expert.gif|link=]]SAMPLING==<br />
; SAMPLING ROT <SAMP><br />
; SAMPLING TRA <SAMP><br />
: Sampling of search given in degrees for a rotation search and Ångstroms for a translation search. Sampling for rotation search depends on the mean radius of the Ensemble and the high resolution limit (dmin) of the search.<br />
* Default: SAMP = 2*atan(dmin/(4*meanRadius)) (ROTATION FUNCTION)<br />
* Default: SAMP = dmin/5; (BRUTE TRANSLATION FUNCTION)<br />
* Default: SAMP = dmin/4; (FAST TRANSLATION FUNCTION)<br />
setSAMP_ROTA(float <SAMP>)<br />
setSAMP_TRAN(float <SAMP>)<br />
<br><br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS USE [ON|OFF]<br />
: Use TNCS if present: apply TNCS corrections. (Note: was TNCS IGNORE [ON|OFF] in Phaser-2.4.0)<br />
; TNCS RLIST ADD [ON | OFF]<br />
: Supplement the rotation list used in the translation function with rotations already present in the list of known solutions. New molecules in the same orientation as those in the known search (as occurs with translational ncs) may not have peaks associated with them from the rotation function because the known molecules mask the presence of the ones not yet found. <br />
; TNCS PATT HIRES <hires><br />
: High resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT LORES <lores><br />
: Low resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT PERCENT <percent><br />
: Percent of origin Patterson peak that qualifies as a TNCS vector<br />
; TNCS PATT DISTANCE <distance><br />
: Minimum distance of Patterson peak from origin that qualifies as a TNCS vector<br />
; TNCS TRANSLATION PERTURB [ON | OFF]<br />
: If the TNCS translation vector is on a special position, perturb the vector from the special position before refinement<br />
; TNCS ROTATION RANGE <angle><br />
: Maximum deviation from initial rotation from which to look for rotational deviation. Default uses internally determined value based on resolution of data and size of G-function effective molecular radius. Value of 0 turns rotational refinement off.<br />
; TNCS ROTATION SAMPLING <sampling><br />
: Sampling for rotation search. Default uses internally determined value based on resolution of data and size of G-function effective molecular radius. Value of 0 turns rotational refinement off.<br />
* Default: TNCS USE ON<br />
* Default: TNCS RLIST ADD ON<br />
* Default: TNCS PATT HIRES 5<br />
* Default: TNCS PATT LORES 10<br />
* Default: TNCS PATT PERCENT 20<br />
* Default: TNCS PATT DISTANCE 15 <br />
* Default: TNCS TRANSLATION PERTURB ON<br />
setTNCS_USE(bool)<br />
setTNCS_RLIS_ADD(bool)<br />
setTNCS_PATT_HIRE(float <HIRES>)<br />
setTNCS_PATT_LORE(float <LORES>) <br />
setTNCS_PATT_PERC(float <PERCENT>) <br />
setTNCS_PATT_DIST(float <DISTANCE>)<br />
setTNCS_TRAN_PERT(bool)<br />
setTNCS_ROTA_RANG(float <RANGE>) <br />
setTNCS_ROTA_SAMP(float <SAMPLING>) <br />
<br><br />
<br><br />
<br />
=Developer Keywords=<br />
==[[Image:Developer.gif|link=]]BINS== <br />
; BINS DATA [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the data.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections<br />
; BINS ENSE [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the calaculated structure factos for the ensembles.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections<br />
* Default: BINS DATA MIN 6 MAX 50 WIDTH 500 <br />
* Default: BINS ENSE MIN 6 MAX 1000 WIDTH 1000 <br />
setBINS_DATA_MINI(float <L>)<br />
setBINS_DATA_MAXI(float <H>)<br />
setBINS_DATA_WIDT(float <W>)<br />
setBINS_ENSE_MINI(float <L>)<br />
setBINS_ENSE_MAXI(float <H>)<br />
setBINS_ENSE_WIDT(float <W>)<br />
<br />
==[[Image:Developer.gif|link=]]BFACTOR==<br />
; BFACTOR WILSON RESTRAINT [ON|OFF]<br />
: Toggle to use the Wilson restraint on the isotropic component of the atomic B-factors in SAD phasing.<br />
; BFACTOR SPHERICITY RESTRAINT [ON|OFF] <br />
: Toggle to use the sphericity restraint on the anisotropic B-factors in SAD phasing<br />
; BFACTOR REFINE RESTRAINT [ON|OFF] <br />
: Toggle to use the restraint to zero for the molecular B-factor in molecular replacement.<br />
; BFACTOR WILSON SIGMA <SIGMA><br />
: The sigma of the Wilson restraint.<br />
; BFACTOR SPHERICITY SIGMA <SIGMA><br />
: The sigma of the sphericity restraint.<br />
; BFACTOR REFINE SIGMA <SIGMA><br />
: The sigma of the restraint to zero for the molecular B-factor in molecular replacement.<br />
* Default: BFACTOR WILSON RESTRAINT ON <br />
* Default: BFACTOR SPHERICITY RESTRAINT ON <br />
* Default: BFACTOR REFINE RESTRAINT ON <br />
* Default: BFACTOR WILSON SIGMA 5<br />
* Default: BFACTOR SPHERICITY SIGMA 5<br />
* Default: BFACTOR REFINE SIGMA 6<br />
setBFAC_WILS_REST(bool <True|False>)<br />
setBFAC_SPHE_REST(bool <True|False>)<br />
setBFAC_REFI_REST(bool <True|False>) <br />
setBFAC_WILS_SIGM(float <SIGMA>) <br />
setBFAC_SPHE_SIGM(float <SIGMA>) <br />
setBFAC_REFI_SIGM(float <SIGMA>)<br />
<br />
==[[Image:Developer.gif|link=]]BOXSCALE==<br />
; BOXSCALE <BOXSCALE><br />
: Scale for box for calculating structure factors. The ensembles are put in a box equal to (extent of molecule)*BOXSCALE<br />
* Default: BOXSCALE 4<br />
setBOXS<float <BOXSCALE>)<br />
<br />
==[[Image:Developer.gif|link=]]CELL==<br />
; <span style="color:darkorange">Python Only</span> <br />
: Unit cell dimensions<br />
* Default: Cell read from MTZ file<br />
setCELL(float <A>,float <nowiki><B></nowiki>,float <C>,float <ALPHA>,float <BETA>,float <GAMMA>)<br />
setCELL6(float_array <A B C ALPHA BETA GAMMA>)<br />
<br />
==[[Image:Developer.gif|link=]]COMPOSITION== <br />
; COMPOSITION MIN SOLVENT <PERC><br />
: Minimum solvent to give maximum asu packing volume for automated search copy determination (NUM 0)<br />
* Default: COMPOSITION MIN SOLVENT 0.2<br />
setCOMP_MIN_SOLV(float)<br />
<br />
==[[Image:Developer.gif|link=]]DDM== <br />
; DDM SLIDER <VAL> <br />
: The SLIDER window width is used to smooth the Difference Distance Matrix. <br />
; DDM DISTANCE MIN <VAL> MAX <VAL> STEP <VAL><br />
: The range and step interval, as the fraction of the difference between the lowest and highest DDM values used to step.<br />
; DDM SEPARATION MIN <VAL> MAX <VAL><br />
: Through space separation in Angstroms used.<br />
; DDM SEQUENCE MIN <VAL> MAX <VAL><br />
: The range of sequence separations between matrix pairs.<br />
; DDM JOIN MIN <VAL> MAX <VAL><br />
: The range of lengths of the sequences to join if domain segments are discontinuous in percentages of the polypeptide chain.<br />
* Default: DDM SLIDER 0<br />
* Default: DDM DISTANCE MIN 1 MAX 5 STEP 50<br />
* Default: DDM SEPARATION MIN 7 MAX 14<br />
* Default: DDM SEQUENCE MIN 0 MAX 1<br />
* Default: DDM JOIN MIN 2 MAX 12<br />
setDDM_SLID(int <VAL>) <br />
setDDM_DIST_STEP(int <VAL>) <br />
setDDM_DIST_MINI(int <VAL>) <br />
setDDM_DIST_MAXI(int <VAL>) <br />
setDDM_SEPA_MINI(float <VAL>) <br />
setDDM_SEPA_MAXI(float <VAL>)<br />
setDDM_JOIN_MINI(int <VAL>) <br />
setDDM_JOIN_MAXI(int <VAL>) <br />
setDDM_SEQU_MINI(int <VAL>) <br />
setDDM_SEQU_MAXI(int <VAL>)<br />
<br />
==[[Image:Developer.gif|link=]]ENM== <br />
; ENM OSCILLATORS [ <sup>1</sup>RTB | <sup>2</sup>ALL ] <br />
: Define the way the atoms are used for the elastic network model.<br />
: <sup>1</sup>Use the rotation-translation block method.<br />
: <sup>2</sup>Use all atoms to determine the modes (only for use on very small molecules, less than 250 atoms). <br />
; ENM MAXBLOCKS <MAXBLOCKS><br />
: MAXBLOCKS is the number of rotation-translation blocks for the RTB analysis.<br />
; ENM NRES <NRES><br />
: For the RTB analysis, by default NRES=0 and then it is calculated so that it is as small as it can be without reaching MAXBlocks. <br />
; ENM RADIUS <RADIUS><br />
: Elastic Network Model interaction radius (Angstroms)<br />
; ENM FORCE <FORCE><br />
: Elastic Network Model force constant<br />
* Default: ENM OSCILLATORS RTB MAXBLOCKS 250 NRES 0 RADIUS 5 FORCE 1<br />
setENM_OSCI(str ["RTB"|"CA"|"ALL"])<br />
setENM_RTB_MAXB(float <MAXB>)<br />
setENM_RTB_NRES(float <NRES>) <br />
setENM_RADI(float <RADIUS>) <br />
setENM_FORC(float <FORCE>)<br />
<br />
==[[Image:Developer.gif|link=]]NORMALIZATION==<br />
; <span style="color:darkorange">Scripting Only</span><br />
; NORM EPSFAC WRITE <FILENAME><br />
: The normalization factors that correct for anisotropy in the data are written to BINARY file FILENAME<br />
; NORM EPSFAC READ <FILENAME><br />
: The normalization factors that correct for anisotropy in the data are read from BINARY file FILENAME. Further refinement is automatically turned off.<br />
; <span style="color:darkorange">Python Only</span><br />
The normalization factors that correct for anisotropy in the data, extracted from ResultANO object with getSigmaN(). Anisotropy should subsequently be turned off with setMACA_PROT("OFF").<br />
setNORM_DATA(data_norm <SIGMAN>)<br />
<br />
==[[Image:Developer.gif|link=]]OUTLIER==<br />
; OUTLIER REJECT [ON|OFF]<br />
: Reject low probability data outliers<br />
; OUTLIER PROB <PROB><br />
: Cutoff for rejection of low probablity outliers<br />
* Default: OUTLIER REJECT ON PROB 0.000001<br />
setOUTL_REJE(bool) <br />
setOUTL_PROB(float <PROB>)<br />
<br />
==[[Image:Developer.gif|link=]]PTGROUP== <br />
; PTGROUP COVERAGE <COVERAGE><br />
: Percentage coverage for two sequences to be considered in same pointgroup<br />
; PTGROUP IDENTITY <IDENTITY><br />
: Percentage identity for two sequences to be considered in same pointgroup<br />
; PTGROUP RMSD <RMSD><br />
: Percentage rmsd for two models to be considered in same pointgroup<br />
; PTGROUP TOLERANCE ANGULAR <ANG><br />
: Angular tolerance for pointgroup<br />
; PTGROUP TOLERANCE SPATIAL <DIST><br />
: Spatial tolerance for pointgroup<br />
setPTGR_COVE(float <COVERAGE>) <br />
setPTGR_IDEN(float <IDENTITY>) <br />
setPTGR_RMSD(float <RMSD>) <br />
setPTGR_TOLE_ANGU(float <ANG>) <br />
setPTGR_TOLE_SPAT(float <DIST>)<br />
<br />
==[[Image:Developer.gif|link=]]RESHARPEN== <br />
; RESHARPEN PERCENTAGE <PERC><br />
: Perecentage of the B-factor in the direction of lowest fall-off (in anisotropic data) to add back into the structure factors F_ISO and FWT and FDELWT so as to sharpen the electron density maps<br />
* Default: RESHARPEN PERCENT 100<br />
setRESH_PERC(float <PERCENT>)<br />
<br />
==[[Image:Developer.gif|link=]]SOLPARAMETERS==<br />
; SOLPARAMETERS SIGA FSOL <FSOL> BSOL <BSOL> MIN <MINSIGA><br />
: Babinet solvent parameters for Sigma(A) curves. MINSIGA is the minimum SIGA for Babinet solvent term (low resolution only). The solvent term in the Sigma(A) curve is given by <BR>max(1 - FSOL*exp(-BSOL/(4d^2)),MINSIGA).<br />
; SOLPARAMETERS BULK USE [ON|OFF]<br />
: Toggle for use of solvent mask scaling parameters for ensemble structure factors, applied to Fmask.<br />
; SOLPARAMETERS BULK FSOL <FSOL> BSOL <BSOL> <br />
: Solvent mask scaling parameters for ensemble structure factors, applied to Fmask.<br />
* Default: SOLPARAMETERS SIGA FSOL 1.05 BSOL 501 MIN 0.1<br />
* Default: SOLPARAMETERS SIGA RESTRAINT ON<br />
* Default: SOLPARAMETERS BULK USE OFF<br />
* Default: SOLPARAMETERS BULK FSOL 0.35 BSOL 45<br />
setSOLP_SIGA_FSOL(float <FSOL>) <br />
setSOLP_SIGA_BSOL(float <BSOL>)<br />
setSOLP_SIGA_MIN(float <MINSIGA>)<br />
setSOLP_BULK_USE(bool)<br />
setSOLP_BULK_FSOL(float <FSOL>) <br />
setSOLP_BULK_BSOL(float <BSOL>)<br />
<br />
==[[Image:Developer.gif|link=]]TARGET== <br />
; TARGET ROT FAST TYPE [LERF1 | CROWTHER]<br />
: Target function type for fast rotation searches<br />
; TARGET TRA FAST TYPE [LETF1 | LETF2 | CORRELATION]<br />
: Target function type for fast translation searches<br />
setTARG_ROTA_TYPE(string TYPE)<br />
setTARG_TRAN_TYPE(string TYPE)<br />
<br />
==[[Image:Developer.gif|link=]]TNCS==<br />
; TNCS ROTATION ANGLE <A> <nowiki><B></nowiki> <C><br />
: Input rotational difference between molecules related by the pseudo-translational symmetry vector, specified as rotations in degrees about x, y and z axes. Central value for grid search (RANGE > 0).<br />
; TNCS ROTATION RANGE <A><br />
: Range of angular difference in rotation angles to explore around central angle.<br />
; TNCS ROTATION SAMPLING <A><br />
: Sampling step for rotational grid search.<br />
; TNCS TRA VECTOR <x y z> <br />
: Input pseudo-translational symmetry vector (fractional coordinates). By default the translation is determined from the Patterson.<br />
; TNCS VARIANCE RMSD <num><br />
: Input estimated rms deviation between pseudo-translational symmetry vector related molecules.<br />
; TNCS VARIANCE FRAC <num><br />
: Input estimated fraction of cell content that obeys pseudo-translational symmetry.<br />
; TNCS LINK RESTRAINT [ON | OFF]<br />
: Link the occupancy of atoms related by TNCS in SAD phasing<br />
; TNCS LINK SIGMA <sigma><br />
: Sigma of link restraint of the occupancy of atoms related by TNCS in SAD phasing<br />
* Default: TNCS ROTATION ANGLE 0 0 0<br />
* Default: TNCS ROTATION RANGE -999 (determine from structure size and resolution)<br />
* Default: TNCS ROTATION SAMPLING -999 (determine from structure size and resolution)<br />
* Default: TNCS TRANSLATION VECTOR determined from position of Patterson peak<br />
* Default: TNCS VARIANCE RMSD 0.4 <br />
* Default: TNCS VARIANCE FRAC 1 <br />
* Default: TNCS LINK RESTRAINT ON<br />
* Default: TNCS LINK SIGMA 0.1<br />
setTNCS_ROTA_ANGL(dvect3 <A B C>) <br />
setTNCS_TRAN_VECT(dvect3 <X Y Z>) <br />
setTNCS_VARI_RMSD(float <RMSD>) <br />
setTNCS_VARI_FRAC(float <FRAC>)<br />
setTNCS_LINK_REST(bool)<br />
setTNCS_LINK_SIGM(float <SIGMA>)<br />
; <span style="color:darkorange">Scripting Only</span><br />
; TNCS EPSFAC WRITE <FILENAME><br />
: The normalization factors that correct for tNCS in the data are written to BINARY file FILENAME<br />
; TNCS EPSFAC READ <FILENAME><br />
: The normalization factors that correct for tNCS in the data are read from BINARY file FILENAME. Further refinement is automatically turned off.<br />
; <span style="color:darkorange">Python Only</span><br />
The normalization factors that correct for tNCS in the data, extracted from ResultNCS object with getPtNcs(). tNCS refinement should subsequently be turned off with setMACT_PROT("OFF").<br />
setTNCS(data_tncs <PTNCS>)<br />
<br />
==[[Image:Developer.gif|link=]]TRANSLATION== <br />
; TRANSLATION MAPS [ON | OFF]<br />
: Output maps of fast translation function FSS scoring functions<br />
: Maps take the names <ROOT>.<ensemble>.k.e.map where k is the Known backgound number and e is the Euler angle number for that known background<br />
* Default: TRANSLATION MAPS OFF<br />
setTRAN_MAPS(bool)</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Keywords&diff=2406Keywords2017-02-09T15:07:19Z<p>Airlie: /* link=FIND */ start phassade documentation</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
===Phaser Executable===<br />
<br />
The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the [[#MODE | MODE]] keyword. The different modes and the keywords relevant to each mode are described in [[Modes]].<br />
<br />
Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. However, some keywords are meaningful when entered multiple times. The order may or may not be important. <br />
<br />
*[[Image:User1.gif|link=]] [[#Basic Keywords | Basic Keywords]]<br />
<br />
*[[Image:Output.png|link=]] [[#Output Control Keywords | Output Control Keywords]]<br />
<br />
*[[Image:User2.gif|link=]] [[#Advanced Keywords |Advanced Keywords ]]<br />
<br />
*[[Image:Expert.gif|link=]] [[#Expert Keywords | Expert Keywords]]<br />
<br />
*[[Image:Developer.gif|link=]] [[#Developer Keywords | Developer Keywords]]<br />
<br />
<br />
===Python Interface===<br />
<br />
Phaser can be compiled as a python library. The mode is selected by calling the appropriate run-job. Input to the run-job is via input-objects, which are passed to the run-job. Setter function on the input objects are equivalent to the keywords for input to the phaser executable. The different modes and the keywords relevant to each mode are described in [[Modes]]. See [[Python Interface]] for details. <br />
<br />
The python interface uses standard python and cctbx/scitbx variable types.<br />
<br />
str string<br />
float double precision floating point<br />
Miller cctbx::miller::index<int> <br />
dvect3 scitbx::vec3<float> <br />
dmat33 scitbx::mat3<float> <br />
'''type'''_array scitbx::af::shared<'''type'''> arrays<br />
<br />
=Basic Keywords=<br />
==[[Image:User1.gif|link=]]ATOM== <br />
; ATOM CRYSTAL <XTALID> PDB <FILENAME><br />
: Definition of atom positions using a pdb file.<br />
; ATOM CRYSTAL <XTALID> HA <FILENAME><br />
: Definition of atom positions using a ha file (from RANTAN, MLPHARE etc.).<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> <br />
: Minimal definition of atom position. B-factor defaults to isotropic and Wilson B-factor. Use <TYPE>=TX for Ta6Br12 cluster and <TYPE>=XX for all other clusters. Scattering for cluster is spherically averaged. Coordinates of cluster compounds other than Ta6Br12 must be entered with CLUSTER keyword. Ta6Br12 coordinates are in phaser code and do not need to be given with CLUSTER keyword.<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> [ ISOB <ISOB> | ANOU <HH KK LL HK HL KL> | USTAR <HH KK LL HK HL KL>] FIXX [ON|OFF] FIXO [ON|OFF] FIXB [ON|OFF] BSWAP [ON|OFF] LABEL <SITE_NAME><br />
: Full definition of atom position including B-factor.<br />
;ATOM CHANGE BFACTOR WILSON [ON|OFF]<br />
: Reset all atomic B-factors to the Wilson B-factor.<br />
; ATOM CHANGE SCATTERER <SCATTERER><br />
:Reset all atomic scatterers to element (or cluster) type.<br />
setATOM_PDB(str <XTALID>,str <PDB FILENAME>)<br />
setATOM_IOTBX(str <XTALID>,iotbx::pdb::hierarchy::root <iotbx object>)<br />
setATOM_STR(str <XTALID>,str <pdb format string>)<br />
setATOM_HA(str <XTALID>,str <FILENAME>)<br />
addATOM(str <XTALID>,str <TYPE>,<br />
float <X>,float <Y>,float <Z>,float <OCC>)<br />
addATOM_FULL(str <XTALID>,str <TYPE>,bool <ORTH>,<br />
dvect3 <X Y Z>,float <OCC>,bool <ISO>,float <ISOB>,<br />
bool <ANOU>,dmat6 <HH KK LL HK HL KL>,<br />
bool <FIXX>,bool <FIXO>,bool <FIXB>,bool <SWAPB>,<br />
str <SITE_NAME>)<br />
setATOM_CHAN_BFAC_WILS(bool)<br />
setATOM_CHAN_SCAT(bool)<br />
setATOM_CHAN_SCAT_TYPE(str <TYPE>)<br />
<br />
==[[Image:User1.gif|link=]]CLUSTER== <br />
; CLUSTER PDB <PDBFILE><br />
: Sample coordinates for a cluster compound for experimental phasing. Clusters are specified with type XX. Ta6Br12 clusters do not need to have coordinates specified as the coordinates are in the phaser code. To use Ta6Br12 clusters, specify atomtypes/clusters as TX.<br />
setCLUS_PDB(str <PDBFILE>)<br />
addCLUS_PDB(str <ID>, str <PDBFILE>)<br />
<br />
==[[Image:User1.gif|link=]]COMPOSITION== <br />
; COMPOSITION BY [ <sup>1</sup>AVERAGE| <sup>2</sup>SOLVENT| <sup>3</sup>ASU ]<br />
: Alternative ways of defining composition<br />
: <sup>1</sup> AVERAGE solvent fraction for crystals (50%)<br />
: <sup>2</sup> Composition entered by solvent content.<br />
: <sup>3</sup> Explicit description of composition of ASU by sequence or molecular weight<br />
; <sup>2</sup>COMPOSITION PERCENTAGE <SOLVENT><br />
: Specified SOLVENT content<br />
; <sup>3</sup>COMPOSITION PROTEIN [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of protein in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION NUCLEIC [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of nucleic acid in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION ATOM <TYPE> NUMBER <NUM><br />
: Add NUM copies of an atom (usually a heavy atom) to the composition<br />
* Default: COMPOSITION BY ASU<br />
setCOMP_BY(str ["AVERAGE" | "SOLVENT" | "ASU" ])<br />
setCOMP_PERC(float <SOLVENT>)<br />
addCOMP_PROT_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_PROT_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_PROT_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_PROT_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_NUCL_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_NUCL_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_NUCL_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_NUCL_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_ATOM(str <TYPE>,float <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]CRYSTAL== <br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN Fpos =<F+> SIGFpos=<SIG+> Fneg=<F-> SIGFneg=<SIG-><br />
: Columns of MTZ file to read for this (anomalous) dataset<br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN F =<F> SIGF=<SIGF><br />
: Columns of MTZ file to read for this (non-anomalous) dataset. Used for LLG completion in SAD phasing when there is no anomalous signal (single atom MR protocol). Use LABIN for MR.<br />
setCRYS_ANOM_LABI(str <F+>,str <SIGF+>,str <F->,str <SIGF->) <br />
setCRYS_MEAN_LABI(str <F>,str <SIGF>)<br />
<br />
==[[Image:User1.gif|link=]]ENSEMBLE== <br />
; ENSEMBLE <MODLID> [PDB|CIF] <PDBFILE> [RMS <RMS><sup>1</sup> | ID <ID><sup>2</sup> | CARD ON<sup>3</sup>] ''CHAIN "<CHAIN>"<sup>4</sup> MODEL <NUM><sup>5</sup>''<br />
: The names of the PDB/CIF files used to build the ENSEMBLE, and either<br />
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
:: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file (e.g. "REMARK PHASER ENSEMBLE MODEL 1 ID 31.2") containing the superimposed models concatenated in the one file. This syntax enables simple automation of the use of ensembles. The pdb file can be non-standard because the atom list for the different models need not be the same.<br />
:: <sup>4</sup> CHAIN is selected from the pdb file. <br />
:: <sup>5</sup> MODEL number is selected from the pdb file.<br />
; ENSEMBLE <MODLID> HKLIN <MTZFILE> F=<F> PHI=<PHI> EXTENT <EX> <EY> <EZ> RMS <RMS> CENTRE <CX> <CY> <CZ> PROTEIN MW <PMW> NUCLEIC MW <NMW> ''CELL SCALE <SCALE>''<br />
: An ENSEMBLE defined from a map (via an mtz file). The molecular weight of the object the map represents is required for scaling. The effective RMS coordinate error is needed to judge how the map accuracy falls off with resolution. For density obtained from an EM image reconstruction, a good first guess would be to take the resolution where the FSC curve drops below 0.5 and divide by 3. The extent (difference between maximum and minimum x,y,z coordinates of region containing model density) is needed to determine reasonable rotation steps, and the centre is needed to carry out a proper interpolation of the molecular transform. The extent and the centre are both given in Ångstroms. The cell scale factor defaults to 1 and can be refined (for example, if the map is from electron microscopy when the cell scale may be unknown to within a few percent).<br />
; ENSEMBLE <MODLID> ATOM <TYPE> RMS <RMS><br />
: Define an ensemble as a single atom for single atom MR<br />
; ENSEMBLE <MODLID> HELIX <NUM> <br />
: Define an ensemble as a helix with NUM residues<br />
; ENSEMBLE <MODLID> HETATM [ON|OFF]<br />
: Use scattering from HETATM records in pdb file. See [[Molecular_Replacement#Coordinate_Editing | Coordinate Editing ]]<br />
; ENSEMBLE <MODLID> DISABLE CHECK [ON|OFF]<br />
: Toggle to disable checking of deviation between models in an ensemble. '''Use with extreme caution'''. Results of computations are not guaranteed to be sensible.<br />
; ENSEMBLE <MODLID> ESTIMATOR [OEFFNER | OEFFNERHI | OEFFNERLO | CHOTHIALESK ]<br />
: Define the estimator function for converting ID to RMS<br />
; ENSEMBLE <MODLID> PTGRP [COVERAGE | IDENTITY | RMSD | TOLANG | TOLSPC | EULER | SYMM ]<br />
: Define the pointgroup parameters <br />
; ENSEMBLE <MODLID> BINS [MIN <N>| MAX <M>| WIDTH <W> ]<br />
: Define the Fcalc reflection binning parameters <br />
; ENSEMBLE <MODLID> TRACE [PDB|CIF] <PDBFILE><br />
: Define the coordinates used for packing independent of the coordinates used for structure factor calculation<br />
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
:: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file <br />
; ENSEMBLE <MODLID> TRACE SAMPLING MIN <DIST> <br />
: Set the minimum distance for the sampling of packing grid<br />
; ENSEMBLE <MODLID> TRACE SAMPLING TARGET <NUM> <br />
: Set the target for the number of points to sample the smallest molecule to be packed<br />
; ENSEMBLE <MODLID> TRACE SAMPLING RANGE <NUM> <br />
: Target range (TARGET+/-RANGE) for search for hexgrid points in protein volume<br />
; ENSEMBLE <MODLID> TRACE SAMPLING USE [AUTO | ALL | CALPHA | HEXGRID ]<br />
: Sample trace coordinates using all atoms, C-alpha atoms, a hexagonal grid in the atomic volume or use an automatically determined choice<br />
; ENSEMBLE <MODLID> TRACE SAMPLING DISTANCE <DIST> <br />
: Set the distance for the sampling of the hexagonal grid explicitly and do not use TARGET to find default sampling distance<br />
; ENSEMBLE <MODLID> TRACE SAMPLING WANG <WANG> <br />
: Scale factor for the size of the Wang mask generated from an ensemble map<br />
; ENSEMBLE <MODLID> TRACE PDB <PDBFILE> <br />
: Use the given set of coordinates for packing rather than using the coordinates for structure factor calculation<br />
* Default: ENSEMBLE <MODLID> DISABLE CHECK OFF<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING MIN 1.0<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING TARGET 1000<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING RANGE 100<br />
addENSE_PDB_ID(str <MODLID>,str <FILE>,float <ID>) <br />
addENSE_PDB_RMS(str <MODLID>,str <FILE>,float <RMS>) <br />
setENSE_TRAC_SAMP_MIN(MODLID,float <MIN>)<br />
setENSE_TRAC_SAMP_TARG(MODLID,int <TARGET>)<br />
setENSE_TRAC_SAMP_RANG(MODLID,int <RANGE>)<br />
setENSE_TRAC_SAMP_USE(MODLID,str)<br />
setENSE_TRAC_SAMP_DIST(MODLID,float <DIST>)<br />
setENSE_TRAC_SAMP_WANG(MODLID,float <WANG>)r <FILE>,float <RMS>)<br />
addENSE_CARD(str <MODLID>,str <FILE>,bool)<br />
addENSE_MAP(str <MODLID>,str <MTZFILE>,str <F>,str <PHI>,dvect3 <EX EY EZ>,<br />
float <RMS>,dvect3 <CX CY CZ>,float <PMW>,float <NMW>,float <CELL>)<br />
setENSE_DISA_CHEC(bool)<br />
<br />
==[[Image:User1.gif|link=]]FIND==<br />
; FIND SCATTERER <ATOMTYPE><br />
: Phassade, type of scatterers to find<br />
; FIND NUMBER <NUMBER><br />
: Phassade, number of scatteres to find<br />
; FIND CLUSTER [ON|OFF]<br />
: Phassade, scatterer name is a cluster<br />
; FIND PEAK SELECT [PERCENT | SIGMA]<br />
: Phassade, peak selection method from Phassade FFT<br />
; FIND PEAK CUTOFF <CUTOFF><br />
: Phassade, peak selection method cutoff from Phassade FFT<br />
; FIND PURGE SELECT [PERCENT | SIGMA]<br />
: Phassade, purge selection method after all Phassade FFT<br />
; FIND PURGE CUTOFF <CUTOFF><br />
: Phassade, purge selection method cutoff after all Phassade FFT<br />
setFIND_SCAT(str <ATOMTYPE>)<br />
setFIND_NUMB(int <NUMBER>)<br />
setFIND_NUMB(int <NUMBER>)<br />
setFIND_CLUS(bool <CLUSTER>)<br />
setFIND_PEAK_SELE(str <SELECT>)<br />
setFIND_PEAK_CUTO(float <CUTOFF>)<br />
setFIND_PURG_SELE(str <SELECT>)<br />
setFIND_PURG_CUTO(float <CUTOFF>)<br />
<br />
==[[Image:User1.gif|link=]]HKLIN==<br />
; HKLIN <FILENAME><br />
: The mtz file containing the data<br />
setHKLI(str <FILENAME>)<br />
<br />
==[[Image:User1.gif|link=]]JOBS== <br />
; JOBS <NUM><br />
: Number of processors to use in parallelized sections of code<br />
* Default: JOBS 2<br />
setJOBS(int <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]LABIN== <br />
; LABIN F = <F> SIGF = <SIGF> <br />
: Columns in mtz file. F must be given. SIGF should be given but is optional<br />
; LABIN I = <nowiki><I></nowiki> SIGI = <SIGI> <br />
: Columns in mtz file. I must be given. SIGI should be given but is optional<br />
; LABIN FMAP = <PH> PHMAP = <PHMAP> <br />
: Columns in mtz file. FMAP/PHMAP are weighted coefficients for use in the Phased Translation Function.<br />
; LABIN FMAP = <PH> PHMAP = <PHMAP> FOM = <FOM><br />
: Columns in mtz file. FMAP/PHMAP are unweighted coefficients for use in the Phased Translation Function and FOM the figure of merit for weighting<br />
setLABI_F_SIGF(str <F>,str <SIGF>)<br />
setLABI_I_SIGI(str <nowiki><I></nowiki>,str <SIGI>)<br />
setLABI_PTF(str <FMAP>,str <PHMAP>,str <FOM>)<br />
<br />
''Data should be input to python run-jobs using one data_refl parameter''<br />
''This is extracted from the ResultMR_DAT object after a call to runMR_DAT''<br />
setREFL_DATA(data_ref)<br />
''Example:''<br />
i = InputMR_DAT()<br />
i.setHKLI("*.mtz")<br />
i.setLABI_F_SIGF("F","SIGF")<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputMR_LLG()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.setREFL_DATA(r.getDATA())<br />
''See also: '' [[Python Example Scripts]]<br />
<br />
''Alternatively, reflection arrays can be set using cctbx::af::shared<double>''<br />
setREFL_F_SIGF(float_array <F>,float_array <SIGF>)<br />
setREFL_I_SIGI(float_array <nowiki><I></nowiki>,float_array <SIGI>)<br />
setREFL_PTF(float_array <FMAP>,float_array <PHMAP>,float_array <FOM>)<br />
<br />
==[[Image:User1.gif|link=]]MODE==<br />
; MODE [ ANO | CCA | SCEDS | NMAXYZ | NCS | MR_ELLG | MR_AUTO | MR_GYRE | MR_ATOM | MR_ROT | MR_TRA | MR_RNP | | MR_OCC | MR_PAK | EP_AUTO | EP_SAD]<br />
: The mode of operation of Phaser. The different modes are described in a separate page on [[Keyword Modes]]<br />
ResultANO r = runANO(InputANO)<br />
ResultCCA r = runCCA(InputCCA)<br />
ResultNMA r = runSCEDS(InputNMA)<br />
ResultNMA r = runNMAXYZ(InputNMA)<br />
ResultNCS r = runNCS(InputNCS)<br />
ResultELLG r = runMR_ELLG(InputMR_ELLG)<br />
ResultMR r = runMR_AUTO(InputMR_AUTO)<br />
ResultEP r = runMR_ATOM(InputMR_ATOM)<br />
ResulrMR_RF r = runMR_FRF(InputMR_FRF)<br />
ResultMR_TF r = runMR_FTF(InputMR_FTF)<br />
ResultMR r = runMR_RNP(InputMR_RNP)<br />
ResultGYRE r = runMR_GYRE(InputMR_RNP)<br />
ResultMR r = runMR_OCC(InputMR_OCC)<br />
ResultMR r = runMR_PAK(InputMR_PAK)<br />
ResultEP r = runEP_AUTO(InputEP_AUTO)<br />
ResultEP_SAD r = runEP_SAD(InputEP_SAD)<br />
<br />
==[[Image:User1.gif|link=]]PARTIAL== <br />
; PARTIAL PDB <PDBFILE> [RMSIDENTITY] <RMS_ID><br />
: The partial structure for MR-SAD substructure completion. Note that this must already be correctly placed, as the experimental phasing module will not carry out molecular replacement.<br />
; PARTIAL HKLIN <MTZFILE> [RMS|IDENTITY] <RMS_ID><br />
: The partial electron density for MR-SAD substructure completion.<br />
; PARTIAL LABIN FC=<FC> PHIC=<PHIC><br />
: Column labels for partial electron density for MR-SAD substructure completion.<br />
setPART_PDB(str <PDBFILE>)<br />
setPART_HKLI(str <MTZFILE>) <br />
setPART_LABI_FC(str <FC>)<br />
setPART_LABI_PHIC(str <PHIC>) <br />
setPART_VARI(str ["ID"|"RMS"])<br />
setPART_DEVI(float <RMS_ID>)<br />
<br />
==[[Image:User1.gif|link=]]SEARCH==<br />
; SEARCH ENSEMBLE <MODLID> ''{OR ENSEMBLE <MODLID>}… NUMBER <NUM><sup>*</sup>''<br />
: The ENSEMBLE to be searched for in a rotation search or an automatic search. When multiple ensembles are given using the OR keyword, the search is performed for each ENSEMBLE in turn. When the keyword is entered multiple times, each SEARCH keyword refers to a new component of the structure. If the component is present multiple times the sub-keyword NUMber can be used (rather than entering the same SEARCH keyword NUMber times).<br />
: <sup>*</sup>For automatic determination of search number use NUMBER 0. If the composition is entered, the maximum number will be that defined by the composition, otherwise the maximum number will fill the asymmetric unit to a minimum solvent content of 20%. Searches for new components will continue until the TFZ score is above 8, and terminate if the TFZ score drops below 8 before the placement of the maximum number of components.<br />
; SEARCH METHOD [FULL|FAST]<br />
: Search using the [[Modes#Modes |full search]] or [[Modes#Modes | fast search]] algorithms.<br />
; SEARCH ORDER AUTO [ON|OFF]<br />
: Search in the "best" order as estimated using estimated rms deviation and completeness of models.<br />
; SEARCH PRUNE [ON|OFF]<br />
: For high TFZ solutions that fail the packing test, carry out a sliding-window occupancy refinement and prune residues that refine to low occupancy, in an effort to resolve packing clashes. If this flag is set to true, the flag for keeping high tfz score solutions (see [[#PACK | PACK]]) that don't pack is also set to true (PACK KEEP HIGH TFZ ON).<br />
; SEARCH AMALGAMATE USE [ON|OFF]<br />
: For multiple high TFZ solutions, enable amalgamation into a single solution<br />
; SEARCH BFACTOR <BFAC><br />
: B-factor applied to search molecule (or atom).<br />
; SEARCH OFACTOR <OFAC><br />
: Occupancy factor applied to search molecule (or atom).<br />
* Default: SEARCH METHOD FAST<br />
* Default: SEARCH ORDER AUTO ON<br />
* Default: SEARCH PRUNE ON<br />
* Default: SEARCH AMALGAMATE USE ON<br />
* Default: SEARCH BFACTOR 0<br />
* Default: SEARCH OFACTOR 1<br />
addSEAR_ENSE_NUM(str <MODLID>,int <NUM>) <br />
addSEAR_ENSE_OR_ENSE_NUM(string_array <MODLIDS>,int <NUM>) <br />
setSEAR_METH(str [ "FULL" | "FAST" ])<br />
setSEAR_ORDE_AUTO(bool)<br />
setSEAR_PRUN(bool <PRUNE>)<br />
setSEAR_AMAL_USE(bool <AMAL>)<br />
setSEAR_BFAC(float <BFAC>)<br />
setSEAR_OFAC(float <OFAC>)<br />
<br />
==[[Image:User1.gif|link=]]SGALTERNATIVE==<br />
; SGALTERNATIVE SELECT [<sup>1</sup>ALL| <sup>2</sup>HAND| <sup>3</sup>LIST| <sup>4</sup>NONE]<br />
: Selection of alternative space groups to test in translation functions i.e. those that are in same laue group as that given in [[#SPACEGROUP | SPACEGROUP]]<br />
: <sup>1</sup> Test all possible space groups, <br />
: <sup>2</sup> Test the given space group and its enantiomorph.<br />
: <sup>3</sup> Test the space groups listed with SGALTERNATIVE TEST <SG>.<br />
: <sup>4</sup> Do not test alternative space groups.<br />
; SGALTERNATIVE TEST <SG><br />
: Alternative space groups to test. Multiple test space groups can be entered.<br />
* Default: SGALTERNATIVE SELECT HAND<br />
setSGAL_SELE(str [ "ALL" | "HAND" | "LIST" | "NONE" ]) <br />
addSGAL_TEST(str <SG>)<br />
<br />
==[[Image:User1.gif|link=]]SOLUTION==<br />
; SOLUTION SET <ANNOTATION><br />
: Start new set of solutions <br />
; SOLUTION TEMPLATE <ANNOTATION><br />
: Specifies a template solution against which other solutions in this run will be compared. Given in place of SOLUTION SET. Template rotation and translations given by subsequent SOLUTION 6DIM cards as per SOLUTION SETS.<br />
; SOLUTION 6DIM ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> [ORTH|FRAC] <X> <Y> <Z> ''FIXR [ON|OFF] FIXT [ON|OFF] FIXB [ON|OFF] BFAC <BFAC> MULT <MULT>''<br />
: This keyword is repeated for each known position and orientation of an ENSEMBLE MODLID. A B G are the Euler angles (z-y-z convention) and X Y Z are the translation elements, expressed either in orthogonal Angstroms (ORTH) or fractions of a cell edge (FRAC). The input ensemble is transformed by a rotation around the origin of the coordinate system, followed by a translation. BFAC default to 0, MULT (for multiplicity) defaults to 1.<br />
; SOLUTION ENSEMBLE <MODLID> VRMS DELTA <DELTA> RMSD <RMSD><br />
: Refined RMS variance terms for pdb files (or map) in ensemble MODLID. RMSD is the input RMSD of the job that produced the sol file, DELTA is the shift with respect to this RMSD. If given as part of a solution, these values overwrite the values used for input in the ENSEMBLE keyword (if refined).<br />
; SOLUTION ENSEMBLE <MODLID> CELL SCALE <SCALE><br />
: Refined cell scale factor. Only applicable to ensembles that are maps<br />
; SOLUTION TRIAL ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> RF <RF> RFZ <RFZ><br />
: Rotation List for translation function<br />
; SOLUTION ORIGIN ENSEMBLE <MODLID><br />
: Create solution for ensemble MODLID at the origin<br />
; SOLUTION SPACEGROUP <SG><br />
: Space Group of the solution (if alternative spacegroups searched)<br />
; SOLUTION RESOLUTION <HIRES><br />
: High resolution limit of data used to find/refine this solution<br />
; SOLUTION PACKS <PACKS><br />
: Flag for whether solution has been retained despite failing packing test, due to having high TFZ<br />
setSOLU(mr_solution <SOL>) <br />
addSOLU_SET(str <ANNOTATION>) <br />
addSOLU_TEMPLATE(str <ANNOTATION>) <br />
addSOLU_6DIM_ENSE(str <MODLID>,dvect3 <A B C>,bool <FRAC>,dvect3 <X Y Z>,<br />
float <BFAC>,bool <FIXR>,bool <FIXT>,bool <FIXB>,int <MULT>, 1.0) <br />
addSOLU_ENSE_DRMS(str <MODLID>, float <DRMS>) <br />
addSOLU_ENSE_CELL(str <MODLID>, float <SCALE>)<br />
addSOLU_TRIAL_ENSE(string <MODLID>,dvect3 <A B C>,float <RF>, float <RFZ>)<br />
addSOLU_ORIG_ENSE(string <MODLID>)<br />
setSOLU_SPAC(str <SG>)<br />
setSOLU_RESO(float <HIRES>)<br />
setSOLU_PACK(bool <PACKS>)<br />
<br />
==[[Image:User1.gif|link=]]SPACEGROUP==<br />
; SPACEGROUP <SG><br />
: Space group may be altered from the one on the MTZ file to a space group in the same point group. The space group can be entered in one of three ways<br />
#The Hermann-Mauguin symbol e.g. P212121 or P 21 21 21 (with or without spaces)<br />
#The international tables number, which gives standard setting e.g. 19 <br />
#The Hall symbols e.g. P 2ac 2ab<br />
: '''The space group can also be a subgroup of the merged space group'''. For example, P1 is always allowed. The reflections will be expanded to the symmetry of the given subgroup. This is only a valid approach when the true symmetry is the symmetry of the subgroup and perfect twinning causes the data to merge "perfectly" in the higher symmetry. <br />
:'''A list of the allowed space groups in the same point group as the given space group (or space group read from MTZ file) and allowed subgroups of these is given in the Cell Content Analysis logfile.'''<br />
* Default: Read from MTZ file<br />
setSPAC_NUM(int <NUM>)<br />
setSPAC_NAME(string <HM>)<br />
setSPAC_HALL(string <HALL>)<br />
<br />
==[[Image:User1.gif|link=]]WAVELENGTH== <br />
; WAVELENGTH <LAMBDA> <br />
: The wavelengh at which the SAD dataset was collected<br />
setWAVE(float <LAMBDA>)<br />
<br><br />
<br><br />
<br />
=Output Control Keywords=<br />
==[[Image:Output.png|link=]]DEBUG== <br />
; DEBUG [ON|OFF]<br />
: Extra verbose output for debugging<br />
* Default: DEBUG OFF<br />
setDEBU(bool) <br />
<br />
==[[Image:Output.png|link=]]EIGEN==<br />
; EIGEN WRITE [ON|OFF]<br />
; EIGEN READ <EIGENFILE><br />
: Read or write a file containing the eigenvectors and eigenvalues. If reading, the eigenvalues and eigenvectors of the Hessian are read from the file generated by a previous run, rather than calculated. This option must be used with the job that generated the eigenfile and the job reading the eigenfile must have identical input for the ENM parameters. Use WRITE to control whether or not the eigenfile is written when not using the READ mode.<br />
* Default: EIGEN WRITE ON<br />
setEIGE_WRIT(bool)<br />
setEIGE_READ(str <EIGENFILE>)<br />
<br />
==[[Image:Output.png|link=]]HKLOUT== <br />
; HKLOUT [ON|OFF]<br />
: Flags for output of an mtz file containing the phasing information<br />
* Default: HKLOUT ON<br />
setHKLO(bool) <br />
<br />
==[[Image:Output.png|link=]]KEYWORDS== <br />
; KEYWORDS [ON|OFF]<br />
: Write output Phaser .sol file (.rlist file for rotation function)<br />
* Default: KEYWORDS ON<br />
setKEYW(bool)<br />
<br />
==[[Image:Output.gif|link=]]LLGMAPS==<br />
; LLGMAPS [ON|OFF]<br />
: Write log-likelihood gradient map coefficients to MTZ file<br />
* Default: LLGMAPS OFF<br />
setLLGM(bool <True|False>)<br />
<br />
==[[Image:Output.png|link=]]MUTE== <br />
; MUTE [ON|OFF]<br />
: Toggle for running in silent/mute mode, where no logfile is written to ''standard output''.<br />
* Default: MUTE OFF<br />
setMUTE(bool) <br />
<br />
==[[Image:Output.png|link=]]KILL== <br />
; KILL TIME [MINS]<br />
: Kill Phaser after MINS minutes of CPU have elapsed, provided parallel section is complete<br />
; KILL FILE [FILENAME]<br />
: Kill Phaser if file FILENAME is present, provided parallel section is complete<br />
* Default: KILL TIME 0 ''Phaser runs to completion''<br />
* Detaulf: KILL FILE "" ''Phaser runs to completion''<br />
setKILL_TIME(float) <br />
setKILL_FILE(string)<br />
<br />
==[[Image:Output.png|link=]]OUTPUT== <br />
; OUTPUT LEVEL [SILENT|CONCISE|SUMMARY|LOGFILE|VERBOSE|DEBUG]<br />
: Output level for logfile<br />
; OUTPUT LEVEL [0|1|2|3|4|5]<br />
: Output level for logfile (equivalent to keyword level setting)<br />
* Default: OUTPUT LEVEL LOGFILE<br />
setOUTP_LEVE(string)<br />
setOUTP(enum)<br />
<br />
==[[Image:Output.png|link=]]TITLE==<br />
; TITLE <TITLE><br />
: Title for job<br />
* Default: TITLE [no title given]<br />
setTITL(str <TITLE>)<br />
<br />
==[[Image:Output.png|link=]]TOPFILES== <br />
; TOPFILES <NUM><br />
: Number of top pdbfiles or mtzfiles to write to output.<br />
* Default: TOPFILES 1<br />
setTOPF(int <NUM>) <br />
<br />
==[[Image:Output.png|link=]]ROOT== <br />
; ROOT <FILEROOT><br />
: Root filename for output files (e.g. FILEROOT.log)<br />
* Default: ROOT PHASER<br />
setROOT(string <FILEROOT>)<br />
<br />
==[[Image:Output.png|link=]]VERBOSE== <br />
; VERBOSE [ON|OFF] <br />
: Toggle to send verbose output to log file.<br />
* Default: VERBOSE OFF<br />
setVERB(bool) <br />
<br />
==[[Image:Output.png|link=]]XYZOUT== <br />
; XYZOUT [ON|OFF] ''ENSEMBLE [ON|OFF]<sup>1</sup> PACKING [ON|OFF]<sup>2</sup>''<br />
: Toggle for output coordinate files. <br />
::<sup>1</sup> If the optional ENSEMBLE keyword is ON, then each placed ensemble is written to its own pdb file. The files are named FILEROOT.#.#.pdb with the first # being the solution number and the second # being the number of the placed ensemble (representing a SOLU 6DIM entry in the .sol file). <br />
::<sup>2</sup> If the optional PACKING keyword is ON, then the hexagonal grid used for the packing analysis is output to its own pdb file FILEROOT.pak.pdb<br />
* Default: XYZOUT OFF (Rotation functions)<br />
* Default: XYZOUT ON ENSEMBLE OFF (all other relevant modes)<br />
* Default: XYZOUT ON PACKING OFF (all other relevant modes)<br />
setXYZO(bool) <br />
setXYZO_ENSE(bool)<br />
setXYZO_PACK(bool)<br />
<br><br />
<br><br />
<br />
=Advanced Keywords=<br />
==[[Image:User2.gif|link=]]ELLG==<br />
([[Molecular_Replacement#Should_Phaser_Solve_It.3F|explained here]])<br />
; ELLG TARGET <TARGET><br />
: Target value for expected LLG for determining resolution limits and search order<br />
<!--; ELLG HIRES <HIRES> Internal control only--><br />
* Default: ELLG TARGET 225<br />
setELLG_TARG(float <TARGET>)<br />
<br />
==[[Image:User2.gif|link=]]FORMFACTORS==<br />
; FORMFACTORS [XRAY | ELECTRON | NEUTRON]<br />
: Use scattering factors from x-ray, electron or neutrons<br />
* Default: FORMFACTORS XRAY<br />
setFORM(string XRAY)<br />
<br />
==[[Image:User2.gif|link=]]HAND==<br />
; HAND [ <sup>1</sup>ON| <sup>2</sup>OFF| <sup>3</sup>BOTH]<br />
: Hand of heavy atoms for experimental phasing<br />
: <sup>1</sup>Phase using the other hand of heavy atoms <br />
: <sup>2</sup>Phase using given hand of heavy atoms <br />
: <sup>3</sup>Phase using both hands of heavy atoms<br />
* Default: HAND BOTH<br />
setHAND(str [ "OFF" | "ON" | "BOTH" ])<br />
<br />
==[[Image:User2.gif|link=]]LLGCOMPLETE==<br />
; LLGCOMPLETE COMPLETE [ON|OFF]<br />
: Toggle for structure completion by log-likelihood gradient maps<br />
; LLGCOMPLETE SCATTERER <TYPE> <br />
: Atom/Cluster type(s) to be used for log-likelihood gradient completion. If more than one element is entered for log-likelihood gradient completion, the atom type that gives the highest Z-score for each peak is selected. Type = "RX" is a purely real scatterer and type="AX" is purely anomalous scatterer<br />
; LLGCOMPLETE REAL ON<br />
: Use a purely real scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER RX)<br />
; LLGCOMPLETE ANOMALOUS ON<br />
: Use a purely anomalous scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER AX)<br />
; LLGCOMPLETE CLASH <CLASH> <br />
: Minimum distance between atoms in log-likelihood gradient maps and also the distance used for determining anisotropy of atoms (default determined by resolution, flagged by CLASH=0)<br />
; LLGCOMPLETE SIGMA <Z><br />
: Z-score (sigma) for accepting peaks as new atoms in log-likelihood gradient maps<br />
; LLGCOMPLETE NCYC <NMAX><br />
: Maximum number of cycles of log-likelihood gradient structure completion. By default, NMAX is 50, but this limit should never be reached, because all features in the log-likelihood gradient maps should be assigned well before 50 cycles are finished. This keyword should be used to reduce the number of cycles to 1 or 2.<br />
; LLGCOMPLETE METHOD [IMAGINARY|ATOMTYPE]<br />
: Pick peaks from the imaginary map only or from all the completion atomtype maps.<br />
* Default: LLGCOMPLETE COMPLETE OFF<br />
* Default: LLGCOMPLETE CLASH 0<br />
* Default: LLGCOMPLETE SIGMA 6<br />
* Default: LLGComplete NCYC 50<br />
* Default: LLGComplete METHOD ATOMTYPE<br />
setLLGC_COMP(bool <True|False>) <br />
setLLGC_CLAS(float <CLASH>) <br />
setLLGC_SIGM(float <Z>) <br />
setLLGC_NCYC(int <NMAX>)<br />
setLLGC_METH(str ["IMAGINARY"|"ATOMTYPE"])<br />
<br />
==[[Image:User2.gif|link=]]NMA== <br />
; NMA MODE <M1> ''{MODE <M2>…}'' <br />
: The MODE keyword gives the mode along which to perturb the structure. If multiple modes are entered, the structure is perturbed along all the modes AND combinations of the modes given. There is no limit on the number of modes that can be entered, but the number of pdb files explodes combinatorially. The first 6 modes are the pure rotation and translation modes and do not lead to perturbation of the structure. If the number M is less than 7 then M is interpreted as the first M modes starting at 7, so for example, MODE 5 would give modes 7 8 9 10 11.<br />
; NMA COMBINATION <NMAX><br />
: Controls how many modes are present in any combination.<br />
* Default: NMA MODE 5<br />
* Default: NMA COMBINATION 2<br />
addNMA_MODE(int <MODE>) <br />
setNMA_COMB(int <NMAX>)<br />
<br />
==[[Image:User2.gif|link=]]PACK==<br />
; PACK SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>ALL ]<br />
: <sup>1</sup>Allow up to the PERCENT of sampling points to clash, considering only pairwise clashes <br />
: <sup>2</sup>Allow all solutions (no packing test)<br />
; PACK CUTOFF <PERCENT> <br />
: Limit on total number (or percent) of clashes <br />
; PACK QUICK [ON|OFF]<br />
: Packing check stops when ALLOWED_CLASHES or MAX_CLASHES is reached. However, all clashes are found when the solution has a high Z-score (see [[#ZSCORE | ZSCORE]]).<br />
; PACK COMPACT [ON|OFF]<br />
: Pack ensembles into a compact association (minimize distances between centres of mass for the addition of each component in a solution).<br />
; PACK KEEP HIGH TFZ [ON|OFF]<br />
: Solutions with high tfz (see [[#ZSCORE | ZSCORE]]) but that fail to pack are retained in the solution list. Set to true if SEARCH PRUNE ON (see [[#SEARCH | SEARCH]])<br />
* Default: PACK SELECT PERCENT<br />
* Default: PACK CUTOFF 5<br />
* Default: PACK COMPACT ON<br />
* Default: PACK QUICK ON<br />
* Default: PACK KEEP HIGH TFZ OFF<br />
* Default: PACK CONSERVATION DISTANCE 1,5<br />
setPACK_SELE(str ["PERCENT"|"ALL"]) <br />
setPACK_CUTO(float <ALLOWED_CLASHES>)<br />
setPACK_QUIC(bool)<br />
setPACK_KEEP_HIGH_TFZ(bool)<br />
setPACK_COMP(bool)<br />
<br />
==[[Image:User2.gif|link=]]PEAKS==<br />
; PEAKS TRA SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL] <br />
; PEAKS ROT SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL]<br />
: Peaks for individual rotation functions (ROT) or individual translation functions (TRA) satisfying selection criteria are saved. To be used for subsequent steps, peaks must also satisfy the overall [[#PURGE | PURGE]] selection criteria, so it will usually be appropriate to set only the PURGE criteria (which over-ride the defaults for the PEAKS criteria if not explicitly set). See [[Molecular_Replacement#How_to_Select_Peaks | How to Select Peaks]]<br />
: <sup>1</sup> Select peaks by taking all peaks over CUTOFF percent of the difference between the top peak and the mean value.<br />
: <sup>2</sup> Select peaks by taking all peaks with a Z-score greater than CUTOFF.<br />
: <sup>3</sup> Select peaks by taking top CUTOFF.<br />
: <sup>4</sup> Select all peaks.<br />
; PEAKS ROT CUTOFF <CUTOFF><br />
; PEAKS TRA CUTOFF <CUTOFF><br />
: Cutoff value for the rotation function (ROT) or translation function (TRA) peak selection criteria.<br />
: If selection is by percent and [[#PURGE | PURGE PERCENT]] is changed from the default, then the PEAKS percent value is set to the lower PURGE percent value.<br />
; PEAKS ROT CLUSTER [ON|OFF] <br />
; PEAKS TRA CLUSTER [ON|OFF]<br />
: Toggle selects clustered or unclustered peaks for rotation function (ROT) or translation function (TRA).<br />
; PEAKS ROT DOWN [PERCENT] <br />
: [[#SEARCH | SEARCH METHOD FAST]] only. Percentage to reduce rotation function cutoff if there is no TFZ over the zscore cutoff that determines a true solution (see [[#ZSCORE | ZSCORE]]) in first search.<br />
* Default: PEAKS ROT SELECT PERCENT<br />
* Default: PEAKS TRA SELECT PERCENT<br />
* Default: PEAKS ROT CUTOFF 75<br />
* Default: PEAKS TRA CUTOFF 75<br />
* Default: PEAKS ROT CLUSTER ON<br />
* Default: PEAKS TRA CLUSTER ON<br />
setPEAK_ROTA_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"]) <br />
setPEAK_TRAN_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"])<br />
setPEAK_ROTA_CUTO(float <CUTOFF>)<br />
setPEAK_TRAN_CUTO(float <CUTOFF>) <br />
setPEAK_ROTA_CLUS(bool <CLUSTER>) <br />
setPEAK_TRAN_CLUS(bool <CLUSTER>)<br />
setPEAK_ROTA_DOWN(float <PERCENT>)<br />
<br />
==[[Image:User2.gif|link=]]PERMUTATIONS== <br />
; PERMUTATIONS [ON|OFF]<br />
: Only relevant to [[#SEARCH | SEARCH METHOD FULL]]. Toggle for whether the order of the search set is to be permuted.<br />
* Default: PERMUTATIONS OFF<br />
setPERM(bool <PERMUTATIONS>)<br />
<br />
==[[Image:User2.gif|link=]]PERTURB== <br />
; PERTURB RMS STEP <RMS><br />
: Increment in rms Ångstroms between pdb files to be written. <br />
; PERTURB RMS MAX <MAXRMS><br />
: The structure will be perturbed along each mode until the MAXRMS deviation has been reached.<br />
; PERTURB RMS DIRECTION [FORWARD|BACKWARD|TOFRO] <br />
: The structure is perturbed either forwards or backwards or to-and-fro (FORWARD|BACKWARD|TOFRO) along the eigenvectors of the modes specified.<br />
; PERTURB INCREMENT [RMS| DQ] <br />
: Perturb the structure by rms devitations along the modes, or by set dq increments<br />
; PERTURB DQ <DQ1> ''{DQ <DQ2>…}''<br />
: Alternatively, the DQ factors (as used by the Elnemo server (K. Suhre & Y-H. Sanejouand, NAR 2004 vol 32) ) by which to perturb the atoms along the eigenvectors can be entered directly.<br />
* Default: PERTURB INCREMENT RMS<br />
* Default: PERTURB RMS STEP 0.2<br />
* Default: PERTURB RMS MAXRMS 0.3<br />
* Default: PERTURB RMS DIRECTION TOFRO<br />
setPERT_INCR(str [ "RMS" | "DQ" ])<br />
setPERT_RMS_MAXI(float <MAX>)<br />
setPERT_RMS_DIRE(str [ "FORWARDS" | "BACKWARDS" | "TOFRO" ]) <br />
addPERT_DQ(float <DQ>)<br />
<br />
==[[Image:User2.gif|link=]]PURGE== <br />
; PURGE ROT ENABLE [ON|OFF]<sup>1</sup><br />
; PURGE ROT PERCENT <PERC><sup>2</sup><br />
; PURGE ROT NUMBER <NUM><sup>3</sup><br />
: Purging criteria for rotation function (RF), where PERCENT and NUMBER are alternative selection criteria (''OR'' criteria)<br />
::<sup>1</sup> Toggle for whether to purge the solution list from the RF according to the top solution found. If there are a number of RF searches with different partial solution backgrounds, the PURGE is applied to the total list of peaks. If there is one clearly significant RF solution from one of the backgrounds it acts to purge all the less significant solutions. If there is only one RF (a single partial solution background) the PURGE gives no additional selection over and above the PEAKS command. <br />
::<sup>2</sup> [[Molecular_Replacement#How_to_Select_Peaks | Selection by percent]]. PERC is percentage of the top peak, where the value of the top peak is defined as 100% and the value of the mean is defined as 0%. Note that this criterion is applied subsequent to any selection criteria applied through the [[#PEAKS | PEAKS]] command. If the [[#PEAKS | PEAKS]] selection is by percent, then the percent cutoff given in the PURGE command over-rides that for [[#PEAKS | PEAKS]], so as to rationalize results in the case of only a single RF (single partial solution background.)<br />
::<sup>3</sup> NUM is the number of solutions to retain in purging. If NUMBER is given (non-zero) it overrides the PERCENT option. NUMBER given as zero is the flag for not applying this criterion.<br />
; PURGE TRA ENABLE [ON|OFF]<br />
; PURGE TRA PERCENT <PERC><br />
; PURGE TRA NUMBER <NUM><br />
: As above, but for translation function<br />
; PURGE RNP ENABLE [ON|OFF]<br />
; PURGE RNP PERCENT <PERC><br />
; PURGE RNP NUMBER <NUM><br />
: As above but for refinement, but with the important distinction that PERCENT and NUMBER are concurrent selection criteria (''AND'' criteria)<br />
* Default: PURGE ROT ENABLE ON <br />
* Default: PURGE ROT PERC 75<br />
* Default: PURGE ROT NUM 0<br />
* Default: PURGE TRA ENABLE ON<br />
* Default: PURGE TRA PERC 75<br />
* Default: PURGE TRA NUM 0<br />
* Default: PURGE RNP ENABLE ON<br />
* Default: PURGE RNP PERC 75<br />
* Default: PURGE RNP NUM 0<br />
setPURG_ROTA_ENAB(bool <ENABLE>)<br />
setPURG_TRAN_ENAB(bool <ENABLE>) <br />
setPURG_RNP_ENAB(bool <ENABLE>)<br />
setPURG_ROTA_PERC(float <PERC>) <br />
setPURG_TRAN_PERC(float <PERC>) <br />
setPURG_RNP_PERC(float <PERC>)<br />
setPURG_ROTA_NUMB(float <NUM>) <br />
setPURG_TRAN_NUMB(float <NUM>)<br />
setPURG_TRAN_NUMB(float <NUM>)<br />
setPURG_RNP_NUMB(float <NUM>)<br />
<br />
==[[Image:User2.gif|link=]]RESOLUTION== <br />
; RESOLUTION HIGH <HIRES> <br />
: High resolution limit in Ångstroms. <br />
; RESOLUTION LOW <LORES><br />
: Low resolution limit in Ångstroms.<br />
; RESOLUTION AUTO HIGH <HIRES> <br />
: High resolution limit in Ångstroms for final high resolution refinement in MR_AUTO mode.<br />
* Default for molecular replacement: Set by [[#ELLG | ELLG TARGET]] for structure solution, final refinement uses all data<br />
* Default for experimental phasing: All data used<br />
setRESO_HIGH(float <HIRES>) <br />
setRESO_LOW(float <LORES>)<br />
setRESO_AUTO_HIGH(float <HIRES>) <br />
setRESO(float <HIRES>,float <LORES>)<br />
<br />
==[[Image:User2.gif|link=]]ROTATE== <br />
; ROTATE VOLUME FULL<br />
: Sample all unique angles <br />
; ROTATE VOLUME AROUND EULER <A> <nowiki><B></nowiki> <C> RANGE <RANGE> <br />
: Restrict the search to the region of +/- RANGE degrees around orientation given by EULER<br />
setROTA_VOLU(string ["FULL"|"AROUND"|) <br />
setROTA_EULE(dvect3 <A B C>) <br />
setROTA_RANG(float <RANGE>)<br />
<br />
==[[Image:User2.gif|link=]]SCATTERING==<br />
; SCATTERING TYPE <TYPE> FP=<FP> FDP=<FDP> FIX [ON|OFF|EDGE]<br />
: Measured scattering factors for a given atom type, from a fluorescence scan. FIX EDGE (default) fixes the fdp value if it is away from an edge, but refines it if it is close to an edge, while FIX ON or FIX OFF does not depend on proximity of edge.<br />
; SCATTERING RESTRAINT [ON|OFF]<br />
: use Fdp restraints<br />
; SCATTERING SIGMA <SIGMA><br />
: Fdp restraint sigma used is SIGMA multiplied by initial fdp value<br />
* Default: SCATTERING SIGMA 0.2<br />
* Default: SCATTERING RESTRAINT ON<br />
addSCAT(str <TYPE>,float <FP>,float <FDP, string <FIXFDP>) <br />
setSCAT_REST(bool) <br />
setSCAT_SIGM(float <SIGMA>)<br />
<br />
==[[Image:User2.gif|link=]]SCEDS== <br />
; SCEDS NDOM <NDOM><br />
:Number of domains into which to split the protein<br />
; SCEDS WEIGHT SPHERICITY <WS><br />
: Weight factor for the the Density Test in the SCED Score. The Sphericity Test scores boundaries that divide the protein into more spherical domains more highly.<br />
; SCEDS WEIGHT CONTINUITY <WC><br />
: Weight factor for the the Continuity Test in the SCED Score. The Continuity Test scores boundaries that divide the protein into domains contigous in sequence more highly. <br />
; SCEDS WEIGHT EQUALITY <WE><br />
: Weight factor for the the Equality Test in the SCED Score. The Equality Test scores boundaries that divide the protein more equally more highly.<br />
; SCEDS WEIGHT DENSITY <WD><br />
: Weight factor for the the Equality Test in the SCED Score. The Density Test scores boundaries that divide the protein into domains more densely packed with atoms more highly. <br />
* Default: SCEDS NDOM 2<br />
* Default: SCEDS WEIGHT EQUALITY 1<br />
* Default: SCEDS WEIGHT SPHERICITY 4 <br />
* Default: SCEDS WEIGHT DENSITY 1<br />
* Default: SCEDS WEIGHT CONTINUITY 0<br />
setSCED_NDOM(int <NDOM>) <br />
setSCED_WEIG_SPHE(float <WS>) <br />
setSCED_WEIG_CONT(float <WC>)<br />
setSCED_WEIG_EQUA(float <WE>) <br />
setSCED_WEIG_DENS(float <WD>)<br />
<br />
==[[Image:User2.gif|link=]]TARGET==<br />
; TARGET ROT [FAST | BRUTE]<br />
: Target function for fast rotation searches (2). BRUTE searches all angles on a grid with the full rotation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these rotations with the full rotation likelihood target.<br />
; TARGET TRA [FAST | BRUTE | PHASED]<br />
: Target function for fast translation searches (3). BRUTE searches all positions on a grid with the full translation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these positions with the full translation likelihood target. PHASED selects the "phased translation function", for which a LABIN command should also be given, specifying FMAP, PHMAP and (optionally) FOM.<br />
* Default: TARGET ROT FAST<br />
* Default: TARGET TRA FAST<br />
setTARG_ROTA(str ["FAST"|"BRUTE"])<br />
setTARG_TRAN(str ["FAST"|"BRUTE"|"PHASED"])<br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS NMOL <NMOL><br />
: Number of molecules/molecular assemblies related by single TNCS vector (usually only 2). If the TNCS is a pseudo-tripling of the cell then NMOL=3, a pseudo-quadrupling then NMOL=4 etc.<br />
* Default: TNCS NMOL 2<br />
setTNCS_NMOL(int <NMOL>)<br />
<br><br />
<br />
==[[Image:User2.gif|link=]]TRANSLATION== <br />
; TRANSLATION VOLUME [ <sup>1</sup>FULL | <sup>2</sup>REGION | <sup>3</sup>LINE | <sup>4</sup>AROUND ])<br />
: Search volume for brute force translation function.<br />
: <sup>1</sup> Cheshire cell or Primitive cell volume. <br />
: <sup>2</sup> Search region.<br />
: <sup>3</sup> Search along line. <br />
: <sup>4</sup> Search around a point.<br />
; <sup>1 2 3</sup>TRANSLATION START <X Y Z> <br />
; <sup>1 2 3</sup>TRANSLATION END <X Y Z><br />
: Search within region or line bounded by START and END.<br />
; <sup>4</sup>TRANSLATION POINT <X Y Z><br />
; <sup>4</sup>TRANSLATION RANGE <RANGE><br />
: Search within +/- RANGE Ångstroms (not fractional coordinates, even if the search point is given as fractional coordinates) of a point <X Y Z>.<br />
; TRANSLATION [ORTH | FRAC]<br />
: Coordinates are given in orthogonal or fractional values.<br />
; TRANSLATION PACKING USE [ON | OFF]<br />
: Top translation function peak will be testes for packing.<br />
; TRANSLATION PACKING CUTOFF <PERC><br />
: Percent pairwise packing used for packing function test of top TF peak. Equivalent to PACK CUTOFF <PERC> for packing function. <br />
; TRANSLATION PACKING NUM <NUM><br />
: Number of translation function peaks to test for packing before bailing out of packing test. Set to 0 to pack all translation function peaks (slow for large packing volumes). <br />
* Default: TRANSLATION VOLUME FULL<br />
* Default: TRANSLATION PACK CUTOFF 50<br />
* Default: TRANSLATION PACK NUM 0 (helices - all packing checked)<br />
* Default: TRANSLATION PACK NUM 500 (non-helices)<br />
setTRAN_VOLU(string ["FULL"|"REGION"|"LINE"|"AROUND"])<br />
setTRAN_START(dvect <START>)<br />
setTRAN_END(dvect <END>)<br />
setTRAN_POINT(dvect <POINT>)<br />
setTRAN_RANGE(float <RANGE>)<br />
setTRAN_FRAC(bool <True=FRAC False=ORTH>)<br />
setTRAN_PACK_USE(bool)<br />
setTRAN_PACK_CUTO(float)<br />
<br />
==[[Image:User2.gif|link=]]ZSCORE== <br />
; ZSCORE USE [ON|OFF]<br />
: Use the TFZ tests. Only applicable with [[#SEARCH | SEARCH METHOD FAST]]. (Note Phaser-2.4.0 and below use "ZSCORE SOLVED 0" to turn off the TFZ tests)<br />
; ZSCORE SOLVED <ZSCORE_SOLVED><br />
: Set the minimum TFZ that indicates a definite solution for amalgamating solutions in FAST search method. <br />
;ZSCORE STOP [ON|OFF]<br />
: Stop adding components beyond point where TFZ is below cutoff when adding multiple components in FAST mode. However, FAST mode will always add one component even if TFZ is below cutoff, or two components if starting search with no components input (no input solution).<br />
; ZSCORE HALF [ON|OFF]<br />
: Set the TFZ for amalgamating solutions in the FAST search method to the maximum of ZSCORE_SOLVED and half the maximum TFZ, to accommodate cases of partially correct solutions in very high TFZ cases (e.g. TFZ > 16)<br />
* Default: ZSCORE USE ON<br />
* Default: ZSCORE SOLVED 8<br />
* Default: ZSCORE HALF ON<br />
* Default: ZSCORE STOP ON<br />
setZSCO_USE(bool <True=ON False=OFF>)<br />
setZSCO_SOLV(floatType ZSCORE_SOLVED)<br />
setZSCO_HALF(bool <True=ON False=OFF>)<br />
setZSCO_STOP(bool <True=ON False=OFF>)<br />
<br><br />
<br><br />
<br />
=Expert Keywords=<br />
<br />
==[[Image:Expert.gif|link=]]MACANO== <br />
; MACANO PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for the refinement of SigmaN in the anisotropy correction<br />
; MACANO ANISO [ON|OFF] BINS [ON|OFF] SOLK [ON|OFF] SOLB [ON|OFF] ''{NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}''<br />
: Macrocycle for the custom refinement of SigmaN in the anisotropy correction. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACANO PROTOCOL DEFAULT<br />
setMACA_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACA(bool <ANISO>,bool <BINS>,bool <SOLK>,bool <SOLB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACMR== <br />
; MACMR PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACMR ROT [ON|OFF] TRA [ON|OFF] BFAC [ON|OFF] VRMS [ON|OFF] ''CELL [ON|OFF] LAST [ON|OFF] NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of molecular replacement solutions. Macrocycles are performed in the order in which they are entered. For description of VRMS see the [[FAQ]]. CELL is the scale factor for the unit cell for maps (EM maps). LAST is a flag that refines the parameters for the last component of a solution only, fixing all the others.<br />
; MACMR CHAINS [ON|OFF]<br />
: Split the ensembles into chains for refinement<br />
: Not possible as part of an automated mode<br />
* Default: MACMR PROTOCOL DEFAULT<br />
* Default: MACMR CHAINS OFF<br />
setMACM_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACM(bool <ROT>,bool <TRA>,bool <BFAC>,bool <VRMS>,bool <CELL>,bool <LAST>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
setMACM_CHAI(bool])<br />
<br />
==[[Image:Expert.gif|link=]]MACOCC== <br />
; MACOCC PROTOCOL [ DEFAULT | CUSTOM | OFF | ALL ]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACOCC NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of occupancy for solutions. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACOCC PROTOCOL DEFAULT<br />
setMACO_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACO(int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACGYRE== <br />
; MACGYRE PROTOCOL [ DEFAULT | CUSTOM | OFF | ALL ]<br />
: Protocol for refinement of gyre rotations<br />
; MACGYRE ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] ''ANCHOR [ON|OFF] SIGROT <SIGR> SIGTRA <SIGT> NCYCLE <NCYC> MINIMIZER [ BFGS | NEWTON | DESCENT ]''<br />
: Macrocycle for custom refinement of occupancy for solutions. Macrocycles are performed in the order in which they are entered.<br />
; MACGYRE SIGROT <SIGROT> <br />
; MACGYRE SIGTRA <SIGTRA> <br />
; MACGYRE ANCHOR [ON|OFF]<br />
: Override default values for harmonic restraints for rotation and translation refinement, and whether or not to anchor one fragment (no translation) for all macrocycles<br />
* Default: MACGYRE PROTOCOL DEFAULT<br />
setMACG_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACG(bool <REF>,bool <REF>, bool <REF>)<br />
addMACG_FULL(bool <REF>,bool <REF>,bool<REF>,bool <ANCHOR>,float <SIGROT>,float <SIGTRA>,int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
setMACG_SIGR(bool <SIGROT>)<br />
setMACG_SIGT(bool <SIGTRA>)<br />
setMACG_ANCH(bool <ANCHOR>)<br />
<br />
==[[Image:Expert.gif|link=]]MACSAD== <br />
; MACSAD PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for SAD refinement.<br />
:''n.b. PROTOCOL ALL will crash phaser and is only useful for debugging - see code for details''<br />
; MACSAD XYZ [ON|OFF] OCC [ON|OFF] BFAC [ON|OFF] FDP [ON|OFF] SA [ON|OFF] SB [ON|OFF] SP [ON|OFF] SD [ON|OFF] ''{PK [ON|OFF]} {PB [ON|OFF]} {NCYCLE <NCYC>} MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for SAD refinement. Macrocycles are performed in the order in which they are entered.<br />
*Default: MACSAD PROTOCOL DEFAULT<br />
setMACS_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACS(<br />
bool <XYZ>,bool <OCC>,bool <BFAC>,bool <FDP><br />
bool <SA>,bool <SB>,bool <SP>,bool <SD>,<br />
bool <PK>, bool <PB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACTNCS== <br />
; MACTNCS PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for pseudo-translational NCS refinement.<br />
; MACTNCS ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] ''NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for pseudo-translational NCS refinement. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACTNCS PROTOCOL DEFAULT<br />
setMACT_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACT(bool <ROT>,bool <TRA>,bool <VRMS>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]OCCUPANCY== <br />
; OCCUPANCY WINDOW ELLG <ELLG><br />
: Target eLLG for determining number of residues in window for occupancy refinement. The number of residues in a window will be an odd number. Occupancy refinement will be done for each offset of the refinement window.<br />
; OCCUPANCY WINDOW NRES <NRES><br />
: As an alternative to using the eLLG to define the number of residues in window for occupancy refinement, the number may be input directly. NRES must be an odd number.<br />
; OCCUPANCY WINDOW MAX <NRES><br />
: Maximum number of residues in an occupancy window (determined either by ellg or given as NRES) for which occupancy is refined. Prevents the refinement windows from spanning non-local regions of space.<br />
; OCCUPANCY MIN <MINOCC> MAX <MAXOCC><br />
: Minimum and maximum values of occupancy during refinement.<br />
; OCCUPANCY MERGE [ON/OFF]<br />
: Merge refined occupancies from different window offsets to give final occupancies per residue. If OFF, occupancies from a single window offset will be used, selected using OCCUPANCY OFFSET <N><br />
; OCCUPANCY FRAC <FRAC><br />
: Minimum fraction of the protein for which the occupancy may be set to zero.<br />
; OCCUPANCY OFFSET <N><br />
: If OCCUPANCY MERGE OFF, then <N> defines the single window offset from which final occupancies will be taken<br />
* Default: OCCUPANCY WINDOW ELLG 5<br />
* Default: OCCUPANCY WINDOW MAX 111<br />
* Default: OCCUPANCY MIN 0.01 MAX 1<br />
* Default: OCCUPANCY NCYCLES 1<br />
* Default: OCCUPANCY MERGE ON<br />
* Default: OCCUPANCY FRAC 0.5<br />
* Default: OCCUPANCY OFFSET 0<br />
setOCCU_WIND_ELLG(float <ELLG>)<br />
setOCCU_WIND_NRES(int <NRES>)<br />
setOCCU_WIND_MAX(int <NRES>)<br />
setOCCU_MIN(float <MIN>)<br />
setOCCU_MAX(float <MAX>)<br />
setOCCU_MERG(float <FRAC>)<br />
setOCCU_FRAC(bool)<br />
setOCCU_OFFS(int <N>)<br />
<br />
==[[Image:Expert.gif|link=]]RESCORE== <br />
; RESCORE ROT [ON|OFF]<br />
; RESCORE TRA [ON|OFF]<br />
: Toggle for rescoring of fast rotation function (ROT) or fast translation function (TRA) search peaks. <br />
* Default: RESCORE ROT ON<br />
* Default: RESCORE TRA ON|OFF will depend on whether phaser is running in the mode [[#MODE | MODE MR_AUTO]] with [[#SEARCH | SEARCH METHOD FAST]] or with [[#SEARCH | SEARCH METHOD FULL]], or running the translation function separately [[#MODE | MODE MR_FTF]]. For [[#SEARCH | SEARCH METHOD FAST]] the default also depends on whether or not the expected LLG target [[#ELLG | ELLG TARGET <TARGET>]] value is reached.<br />
setRESC_ROTA(bool)<br />
setRESC_TRAN(bool)<br />
<br />
==[[Image:Expert.gif|link=]]RFACTOR== <br />
; RFACTOR USE [ON|OFF]<br />
: For cases of searching for one ensemble when there is one ensemble in the asymmetric unit, the R-factor for the ensemble at the orientation and position in the input is calculated. If this value is low then MR is not performed in the MR_AUTO job in FAST search mode. Instead, rigid body refinement is performed before exiting. Note that the same R-factor test and cutoff is used for judging success in single-atom molecular replacement (MR_ATOM mode).<br />
; RFACTOR CUTOFF <VALUE><br />
: Rfactor in percent used as cutoff for deciding whether or not the R-factor indicates that MR is not necessary.<br />
* Default: RFACTOR USE ON CUTOFF 35<br />
setRFAC_USE(bool)<br />
setRFAC_CUTO(float <PERCENT>)<br />
<br />
==[[Image:Expert.gif|link=]]SAMPLING==<br />
; SAMPLING ROT <SAMP><br />
; SAMPLING TRA <SAMP><br />
: Sampling of search given in degrees for a rotation search and Ångstroms for a translation search. Sampling for rotation search depends on the mean radius of the Ensemble and the high resolution limit (dmin) of the search.<br />
* Default: SAMP = 2*atan(dmin/(4*meanRadius)) (ROTATION FUNCTION)<br />
* Default: SAMP = dmin/5; (BRUTE TRANSLATION FUNCTION)<br />
* Default: SAMP = dmin/4; (FAST TRANSLATION FUNCTION)<br />
setSAMP_ROTA(float <SAMP>)<br />
setSAMP_TRAN(float <SAMP>)<br />
<br><br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS USE [ON|OFF]<br />
: Use TNCS if present: apply TNCS corrections. (Note: was TNCS IGNORE [ON|OFF] in Phaser-2.4.0)<br />
; TNCS RLIST ADD [ON | OFF]<br />
: Supplement the rotation list used in the translation function with rotations already present in the list of known solutions. New molecules in the same orientation as those in the known search (as occurs with translational ncs) may not have peaks associated with them from the rotation function because the known molecules mask the presence of the ones not yet found. <br />
; TNCS PATT HIRES <hires><br />
: High resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT LORES <lores><br />
: Low resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT PERCENT <percent><br />
: Percent of origin Patterson peak that qualifies as a TNCS vector<br />
; TNCS PATT DISTANCE <distance><br />
: Minimum distance of Patterson peak from origin that qualifies as a TNCS vector<br />
; TNCS TRANSLATION PERTURB [ON | OFF]<br />
: If the TNCS translation vector is on a special position, perturb the vector from the special position before refinement<br />
; TNCS ROTATION RANGE <angle><br />
: Maximum deviation from initial rotation from which to look for rotational deviation. Default uses internally determined value based on resolution of data and size of G-function effective molecular radius. Value of 0 turns rotational refinement off.<br />
; TNCS ROTATION SAMPLING <sampling><br />
: Sampling for rotation search. Default uses internally determined value based on resolution of data and size of G-function effective molecular radius. Value of 0 turns rotational refinement off.<br />
* Default: TNCS USE ON<br />
* Default: TNCS RLIST ADD ON<br />
* Default: TNCS PATT HIRES 5<br />
* Default: TNCS PATT LORES 10<br />
* Default: TNCS PATT PERCENT 20<br />
* Default: TNCS PATT DISTANCE 15 <br />
* Default: TNCS TRANSLATION PERTURB ON<br />
setTNCS_USE(bool)<br />
setTNCS_RLIS_ADD(bool)<br />
setTNCS_PATT_HIRE(float <HIRES>)<br />
setTNCS_PATT_LORE(float <LORES>) <br />
setTNCS_PATT_PERC(float <PERCENT>) <br />
setTNCS_PATT_DIST(float <DISTANCE>)<br />
setTNCS_TRAN_PERT(bool)<br />
setTNCS_ROTA_RANG(float <RANGE>) <br />
setTNCS_ROTA_SAMP(float <SAMPLING>) <br />
<br><br />
<br><br />
<br />
=Developer Keywords=<br />
==[[Image:Developer.gif|link=]]BINS== <br />
; BINS DATA [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the data.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections<br />
; BINS ENSE [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the calaculated structure factos for the ensembles.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections<br />
* Default: BINS DATA MIN 6 MAX 50 WIDTH 500 <br />
* Default: BINS ENSE MIN 6 MAX 1000 WIDTH 1000 <br />
setBINS_DATA_MINI(float <L>)<br />
setBINS_DATA_MAXI(float <H>)<br />
setBINS_DATA_WIDT(float <W>)<br />
setBINS_ENSE_MINI(float <L>)<br />
setBINS_ENSE_MAXI(float <H>)<br />
setBINS_ENSE_WIDT(float <W>)<br />
<br />
==[[Image:Developer.gif|link=]]BFACTOR==<br />
; BFACTOR WILSON RESTRAINT [ON|OFF]<br />
: Toggle to use the Wilson restraint on the isotropic component of the atomic B-factors in SAD phasing.<br />
; BFACTOR SPHERICITY RESTRAINT [ON|OFF] <br />
: Toggle to use the sphericity restraint on the anisotropic B-factors in SAD phasing<br />
; BFACTOR REFINE RESTRAINT [ON|OFF] <br />
: Toggle to use the restraint to zero for the molecular B-factor in molecular replacement.<br />
; BFACTOR WILSON SIGMA <SIGMA><br />
: The sigma of the Wilson restraint.<br />
; BFACTOR SPHERICITY SIGMA <SIGMA><br />
: The sigma of the sphericity restraint.<br />
; BFACTOR REFINE SIGMA <SIGMA><br />
: The sigma of the restraint to zero for the molecular B-factor in molecular replacement.<br />
* Default: BFACTOR WILSON RESTRAINT ON <br />
* Default: BFACTOR SPHERICITY RESTRAINT ON <br />
* Default: BFACTOR REFINE RESTRAINT ON <br />
* Default: BFACTOR WILSON SIGMA 5<br />
* Default: BFACTOR SPHERICITY SIGMA 5<br />
* Default: BFACTOR REFINE SIGMA 6<br />
setBFAC_WILS_REST(bool <True|False>)<br />
setBFAC_SPHE_REST(bool <True|False>)<br />
setBFAC_REFI_REST(bool <True|False>) <br />
setBFAC_WILS_SIGM(float <SIGMA>) <br />
setBFAC_SPHE_SIGM(float <SIGMA>) <br />
setBFAC_REFI_SIGM(float <SIGMA>)<br />
<br />
==[[Image:Developer.gif|link=]]BOXSCALE==<br />
; BOXSCALE <BOXSCALE><br />
: Scale for box for calculating structure factors. The ensembles are put in a box equal to (extent of molecule)*BOXSCALE<br />
* Default: BOXSCALE 4<br />
setBOXS<float <BOXSCALE>)<br />
<br />
==[[Image:Developer.gif|link=]]CELL==<br />
; <span style="color:darkorange">Python Only</span> <br />
: Unit cell dimensions<br />
* Default: Cell read from MTZ file<br />
setCELL(float <A>,float <nowiki><B></nowiki>,float <C>,float <ALPHA>,float <BETA>,float <GAMMA>)<br />
setCELL6(float_array <A B C ALPHA BETA GAMMA>)<br />
<br />
==[[Image:Developer.gif|link=]]COMPOSITION== <br />
; COMPOSITION MIN SOLVENT <PERC><br />
: Minimum solvent to give maximum asu packing volume for automated search copy determination (NUM 0)<br />
* Default: COMPOSITION MIN SOLVENT 0.2<br />
setCOMP_MIN_SOLV(float)<br />
<br />
==[[Image:Developer.gif|link=]]DDM== <br />
; DDM SLIDER <VAL> <br />
: The SLIDER window width is used to smooth the Difference Distance Matrix. <br />
; DDM DISTANCE MIN <VAL> MAX <VAL> STEP <VAL><br />
: The range and step interval, as the fraction of the difference between the lowest and highest DDM values used to step.<br />
; DDM SEPARATION MIN <VAL> MAX <VAL><br />
: Through space separation in Angstroms used.<br />
; DDM SEQUENCE MIN <VAL> MAX <VAL><br />
: The range of sequence separations between matrix pairs.<br />
; DDM JOIN MIN <VAL> MAX <VAL><br />
: The range of lengths of the sequences to join if domain segments are discontinuous in percentages of the polypeptide chain.<br />
* Default: DDM SLIDER 0<br />
* Default: DDM DISTANCE MIN 1 MAX 5 STEP 50<br />
* Default: DDM SEPARATION MIN 7 MAX 14<br />
* Default: DDM SEQUENCE MIN 0 MAX 1<br />
* Default: DDM JOIN MIN 2 MAX 12<br />
setDDM_SLID(int <VAL>) <br />
setDDM_DIST_STEP(int <VAL>) <br />
setDDM_DIST_MINI(int <VAL>) <br />
setDDM_DIST_MAXI(int <VAL>) <br />
setDDM_SEPA_MINI(float <VAL>) <br />
setDDM_SEPA_MAXI(float <VAL>)<br />
setDDM_JOIN_MINI(int <VAL>) <br />
setDDM_JOIN_MAXI(int <VAL>) <br />
setDDM_SEQU_MINI(int <VAL>) <br />
setDDM_SEQU_MAXI(int <VAL>)<br />
<br />
==[[Image:Developer.gif|link=]]ENM== <br />
; ENM OSCILLATORS [ <sup>1</sup>RTB | <sup>2</sup>ALL ] <br />
: Define the way the atoms are used for the elastic network model.<br />
: <sup>1</sup>Use the rotation-translation block method.<br />
: <sup>2</sup>Use all atoms to determine the modes (only for use on very small molecules, less than 250 atoms). <br />
; ENM MAXBLOCKS <MAXBLOCKS><br />
: MAXBLOCKS is the number of rotation-translation blocks for the RTB analysis.<br />
; ENM NRES <NRES><br />
: For the RTB analysis, by default NRES=0 and then it is calculated so that it is as small as it can be without reaching MAXBlocks. <br />
; ENM RADIUS <RADIUS><br />
: Elastic Network Model interaction radius (Angstroms)<br />
; ENM FORCE <FORCE><br />
: Elastic Network Model force constant<br />
* Default: ENM OSCILLATORS RTB MAXBLOCKS 250 NRES 0 RADIUS 5 FORCE 1<br />
setENM_OSCI(str ["RTB"|"CA"|"ALL"])<br />
setENM_RTB_MAXB(float <MAXB>)<br />
setENM_RTB_NRES(float <NRES>) <br />
setENM_RADI(float <RADIUS>) <br />
setENM_FORC(float <FORCE>)<br />
<br />
==[[Image:Developer.gif|link=]]NORMALIZATION==<br />
; <span style="color:darkorange">Scripting Only</span><br />
; NORM EPSFAC WRITE <FILENAME><br />
: The normalization factors that correct for anisotropy in the data are written to BINARY file FILENAME<br />
; NORM EPSFAC READ <FILENAME><br />
: The normalization factors that correct for anisotropy in the data are read from BINARY file FILENAME. Further refinement is automatically turned off.<br />
; <span style="color:darkorange">Python Only</span><br />
The normalization factors that correct for anisotropy in the data, extracted from ResultANO object with getSigmaN(). Anisotropy should subsequently be turned off with setMACA_PROT("OFF").<br />
setNORM_DATA(data_norm <SIGMAN>)<br />
<br />
==[[Image:Developer.gif|link=]]OUTLIER==<br />
; OUTLIER REJECT [ON|OFF]<br />
: Reject low probability data outliers<br />
; OUTLIER PROB <PROB><br />
: Cutoff for rejection of low probablity outliers<br />
* Default: OUTLIER REJECT ON PROB 0.000001<br />
setOUTL_REJE(bool) <br />
setOUTL_PROB(float <PROB>)<br />
<br />
==[[Image:Developer.gif|link=]]PTGROUP== <br />
; PTGROUP COVERAGE <COVERAGE><br />
: Percentage coverage for two sequences to be considered in same pointgroup<br />
; PTGROUP IDENTITY <IDENTITY><br />
: Percentage identity for two sequences to be considered in same pointgroup<br />
; PTGROUP RMSD <RMSD><br />
: Percentage rmsd for two models to be considered in same pointgroup<br />
; PTGROUP TOLERANCE ANGULAR <ANG><br />
: Angular tolerance for pointgroup<br />
; PTGROUP TOLERANCE SPATIAL <DIST><br />
: Spatial tolerance for pointgroup<br />
setPTGR_COVE(float <COVERAGE>) <br />
setPTGR_IDEN(float <IDENTITY>) <br />
setPTGR_RMSD(float <RMSD>) <br />
setPTGR_TOLE_ANGU(float <ANG>) <br />
setPTGR_TOLE_SPAT(float <DIST>)<br />
<br />
==[[Image:Developer.gif|link=]]RESHARPEN== <br />
; RESHARPEN PERCENTAGE <PERC><br />
: Perecentage of the B-factor in the direction of lowest fall-off (in anisotropic data) to add back into the structure factors F_ISO and FWT and FDELWT so as to sharpen the electron density maps<br />
* Default: RESHARPEN PERCENT 100<br />
setRESH_PERC(float <PERCENT>)<br />
<br />
==[[Image:Developer.gif|link=]]SOLPARAMETERS==<br />
; SOLPARAMETERS SIGA FSOL <FSOL> BSOL <BSOL> MIN <MINSIGA><br />
: Babinet solvent parameters for Sigma(A) curves. MINSIGA is the minimum SIGA for Babinet solvent term (low resolution only). The solvent term in the Sigma(A) curve is given by <BR>max(1 - FSOL*exp(-BSOL/(4d^2)),MINSIGA).<br />
; SOLPARAMETERS BULK USE [ON|OFF]<br />
: Toggle for use of solvent mask scaling parameters for ensemble structure factors, applied to Fmask.<br />
; SOLPARAMETERS BULK FSOL <FSOL> BSOL <BSOL> <br />
: Solvent mask scaling parameters for ensemble structure factors, applied to Fmask.<br />
* Default: SOLPARAMETERS SIGA FSOL 1.05 BSOL 501 MIN 0.1<br />
* Default: SOLPARAMETERS SIGA RESTRAINT ON<br />
* Default: SOLPARAMETERS BULK USE OFF<br />
* Default: SOLPARAMETERS BULK FSOL 0.35 BSOL 45<br />
setSOLP_SIGA_FSOL(float <FSOL>) <br />
setSOLP_SIGA_BSOL(float <BSOL>)<br />
setSOLP_SIGA_MIN(float <MINSIGA>)<br />
setSOLP_BULK_USE(bool)<br />
setSOLP_BULK_FSOL(float <FSOL>) <br />
setSOLP_BULK_BSOL(float <BSOL>)<br />
<br />
==[[Image:Developer.gif|link=]]TARGET== <br />
; TARGET ROT FAST TYPE [LERF1 | CROWTHER]<br />
: Target function type for fast rotation searches<br />
; TARGET TRA FAST TYPE [LETF1 | LETF2 | CORRELATION]<br />
: Target function type for fast translation searches<br />
setTARG_ROTA_TYPE(string TYPE)<br />
setTARG_TRAN_TYPE(string TYPE)<br />
<br />
==[[Image:Developer.gif|link=]]TNCS==<br />
; TNCS ROTATION ANGLE <A> <nowiki><B></nowiki> <C><br />
: Input rotational difference between molecules related by the pseudo-translational symmetry vector, specified as rotations in degrees about x, y and z axes. Central value for grid search (RANGE > 0).<br />
; TNCS ROTATION RANGE <A><br />
: Range of angular difference in rotation angles to explore around central angle.<br />
; TNCS ROTATION SAMPLING <A><br />
: Sampling step for rotational grid search.<br />
; TNCS TRA VECTOR <x y z> <br />
: Input pseudo-translational symmetry vector (fractional coordinates). By default the translation is determined from the Patterson.<br />
; TNCS VARIANCE RMSD <num><br />
: Input estimated rms deviation between pseudo-translational symmetry vector related molecules.<br />
; TNCS VARIANCE FRAC <num><br />
: Input estimated fraction of cell content that obeys pseudo-translational symmetry.<br />
; TNCS LINK RESTRAINT [ON | OFF]<br />
: Link the occupancy of atoms related by TNCS in SAD phasing<br />
; TNCS LINK SIGMA <sigma><br />
: Sigma of link restraint of the occupancy of atoms related by TNCS in SAD phasing<br />
* Default: TNCS ROTATION ANGLE 0 0 0<br />
* Default: TNCS ROTATION RANGE -999 (determine from structure size and resolution)<br />
* Default: TNCS ROTATION SAMPLING -999 (determine from structure size and resolution)<br />
* Default: TNCS TRANSLATION VECTOR determined from position of Patterson peak<br />
* Default: TNCS VARIANCE RMSD 0.4 <br />
* Default: TNCS VARIANCE FRAC 1 <br />
* Default: TNCS LINK RESTRAINT ON<br />
* Default: TNCS LINK SIGMA 0.1<br />
setTNCS_ROTA_ANGL(dvect3 <A B C>) <br />
setTNCS_TRAN_VECT(dvect3 <X Y Z>) <br />
setTNCS_VARI_RMSD(float <RMSD>) <br />
setTNCS_VARI_FRAC(float <FRAC>)<br />
setTNCS_LINK_REST(bool)<br />
setTNCS_LINK_SIGM(float <SIGMA>)<br />
; <span style="color:darkorange">Scripting Only</span><br />
; TNCS EPSFAC WRITE <FILENAME><br />
: The normalization factors that correct for tNCS in the data are written to BINARY file FILENAME<br />
; TNCS EPSFAC READ <FILENAME><br />
: The normalization factors that correct for tNCS in the data are read from BINARY file FILENAME. Further refinement is automatically turned off.<br />
; <span style="color:darkorange">Python Only</span><br />
The normalization factors that correct for tNCS in the data, extracted from ResultNCS object with getPtNcs(). tNCS refinement should subsequently be turned off with setMACT_PROT("OFF").<br />
setTNCS(data_tncs <PTNCS>)<br />
<br />
==[[Image:Developer.gif|link=]]TRANSLATION== <br />
; TRANSLATION MAPS [ON | OFF]<br />
: Output maps of fast translation function FSS scoring functions<br />
: Maps take the names <ROOT>.<ensemble>.k.e.map where k is the Known backgound number and e is the Euler angle number for that known background<br />
* Default: TRANSLATION MAPS OFF<br />
setTRAN_MAPS(bool)</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Keywords&diff=2405Keywords2017-01-24T11:40:00Z<p>Airlie: /* link=RESOLUTION */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
===Phaser Executable===<br />
<br />
The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the [[#MODE | MODE]] keyword. The different modes and the keywords relevant to each mode are described in [[Modes]].<br />
<br />
Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. However, some keywords are meaningful when entered multiple times. The order may or may not be important. <br />
<br />
*[[Image:User1.gif|link=]] [[#Basic Keywords | Basic Keywords]]<br />
<br />
*[[Image:Output.png|link=]] [[#Output Control Keywords | Output Control Keywords]]<br />
<br />
*[[Image:User2.gif|link=]] [[#Advanced Keywords |Advanced Keywords ]]<br />
<br />
*[[Image:Expert.gif|link=]] [[#Expert Keywords | Expert Keywords]]<br />
<br />
*[[Image:Developer.gif|link=]] [[#Developer Keywords | Developer Keywords]]<br />
<br />
<br />
===Python Interface===<br />
<br />
Phaser can be compiled as a python library. The mode is selected by calling the appropriate run-job. Input to the run-job is via input-objects, which are passed to the run-job. Setter function on the input objects are equivalent to the keywords for input to the phaser executable. The different modes and the keywords relevant to each mode are described in [[Modes]]. See [[Python Interface]] for details. <br />
<br />
The python interface uses standard python and cctbx/scitbx variable types.<br />
<br />
str string<br />
float double precision floating point<br />
Miller cctbx::miller::index<int> <br />
dvect3 scitbx::vec3<float> <br />
dmat33 scitbx::mat3<float> <br />
'''type'''_array scitbx::af::shared<'''type'''> arrays<br />
<br />
=Basic Keywords=<br />
==[[Image:User1.gif|link=]]ATOM== <br />
; ATOM CRYSTAL <XTALID> PDB <FILENAME><br />
: Definition of atom positions using a pdb file.<br />
; ATOM CRYSTAL <XTALID> HA <FILENAME><br />
: Definition of atom positions using a ha file (from RANTAN, MLPHARE etc.).<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> <br />
: Minimal definition of atom position. B-factor defaults to isotropic and Wilson B-factor. Use <TYPE>=TX for Ta6Br12 cluster and <TYPE>=XX for all other clusters. Scattering for cluster is spherically averaged. Coordinates of cluster compounds other than Ta6Br12 must be entered with CLUSTER keyword. Ta6Br12 coordinates are in phaser code and do not need to be given with CLUSTER keyword.<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> [ ISOB <ISOB> | ANOU <HH KK LL HK HL KL> | USTAR <HH KK LL HK HL KL>] FIXX [ON|OFF] FIXO [ON|OFF] FIXB [ON|OFF] BSWAP [ON|OFF] LABEL <SITE_NAME><br />
: Full definition of atom position including B-factor.<br />
;ATOM CHANGE BFACTOR WILSON [ON|OFF]<br />
: Reset all atomic B-factors to the Wilson B-factor.<br />
; ATOM CHANGE SCATTERER <SCATTERER><br />
:Reset all atomic scatterers to element (or cluster) type.<br />
setATOM_PDB(str <XTALID>,str <PDB FILENAME>)<br />
setATOM_IOTBX(str <XTALID>,iotbx::pdb::hierarchy::root <iotbx object>)<br />
setATOM_STR(str <XTALID>,str <pdb format string>)<br />
setATOM_HA(str <XTALID>,str <FILENAME>)<br />
addATOM(str <XTALID>,str <TYPE>,<br />
float <X>,float <Y>,float <Z>,float <OCC>)<br />
addATOM_FULL(str <XTALID>,str <TYPE>,bool <ORTH>,<br />
dvect3 <X Y Z>,float <OCC>,bool <ISO>,float <ISOB>,<br />
bool <ANOU>,dmat6 <HH KK LL HK HL KL>,<br />
bool <FIXX>,bool <FIXO>,bool <FIXB>,bool <SWAPB>,<br />
str <SITE_NAME>)<br />
setATOM_CHAN_BFAC_WILS(bool)<br />
setATOM_CHAN_SCAT(bool)<br />
setATOM_CHAN_SCAT_TYPE(str <TYPE>)<br />
<br />
==[[Image:User1.gif|link=]]CLUSTER== <br />
; CLUSTER PDB <PDBFILE><br />
: Sample coordinates for a cluster compound for experimental phasing. Clusters are specified with type XX. Ta6Br12 clusters do not need to have coordinates specified as the coordinates are in the phaser code. To use Ta6Br12 clusters, specify atomtypes/clusters as TX.<br />
setCLUS_PDB(str <PDBFILE>)<br />
addCLUS_PDB(str <ID>, str <PDBFILE>)<br />
<br />
==[[Image:User1.gif|link=]]COMPOSITION== <br />
; COMPOSITION BY [ <sup>1</sup>AVERAGE| <sup>2</sup>SOLVENT| <sup>3</sup>ASU ]<br />
: Alternative ways of defining composition<br />
: <sup>1</sup> AVERAGE solvent fraction for crystals (50%)<br />
: <sup>2</sup> Composition entered by solvent content.<br />
: <sup>3</sup> Explicit description of composition of ASU by sequence or molecular weight<br />
; <sup>2</sup>COMPOSITION PERCENTAGE <SOLVENT><br />
: Specified SOLVENT content<br />
; <sup>3</sup>COMPOSITION PROTEIN [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of protein in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION NUCLEIC [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of nucleic acid in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION ATOM <TYPE> NUMBER <NUM><br />
: Add NUM copies of an atom (usually a heavy atom) to the composition<br />
* Default: COMPOSITION BY ASU<br />
setCOMP_BY(str ["AVERAGE" | "SOLVENT" | "ASU" ])<br />
setCOMP_PERC(float <SOLVENT>)<br />
addCOMP_PROT_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_PROT_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_PROT_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_PROT_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_NUCL_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_NUCL_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_NUCL_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_NUCL_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_ATOM(str <TYPE>,float <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]CRYSTAL== <br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN Fpos =<F+> SIGFpos=<SIG+> Fneg=<F-> SIGFneg=<SIG-><br />
: Columns of MTZ file to read for this (anomalous) dataset<br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN F =<F> SIGF=<SIGF><br />
: Columns of MTZ file to read for this (non-anomalous) dataset. Used for LLG completion in SAD phasing when there is no anomalous signal (single atom MR protocol). Use LABIN for MR.<br />
setCRYS_ANOM_LABI(str <F+>,str <SIGF+>,str <F->,str <SIGF->) <br />
setCRYS_MEAN_LABI(str <F>,str <SIGF>)<br />
<br />
==[[Image:User1.gif|link=]]ENSEMBLE== <br />
; ENSEMBLE <MODLID> [PDB|CIF] <PDBFILE> [RMS <RMS><sup>1</sup> | ID <ID><sup>2</sup> | CARD ON<sup>3</sup>] ''CHAIN "<CHAIN>"<sup>4</sup> MODEL <NUM><sup>5</sup>''<br />
: The names of the PDB/CIF files used to build the ENSEMBLE, and either<br />
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
:: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file (e.g. "REMARK PHASER ENSEMBLE MODEL 1 ID 31.2") containing the superimposed models concatenated in the one file. This syntax enables simple automation of the use of ensembles. The pdb file can be non-standard because the atom list for the different models need not be the same.<br />
:: <sup>4</sup> CHAIN is selected from the pdb file. <br />
:: <sup>5</sup> MODEL number is selected from the pdb file.<br />
; ENSEMBLE <MODLID> HKLIN <MTZFILE> F=<F> PHI=<PHI> EXTENT <EX> <EY> <EZ> RMS <RMS> CENTRE <CX> <CY> <CZ> PROTEIN MW <PMW> NUCLEIC MW <NMW> ''CELL SCALE <SCALE>''<br />
: An ENSEMBLE defined from a map (via an mtz file). The molecular weight of the object the map represents is required for scaling. The effective RMS coordinate error is needed to judge how the map accuracy falls off with resolution. For density obtained from an EM image reconstruction, a good first guess would be to take the resolution where the FSC curve drops below 0.5 and divide by 3. The extent (difference between maximum and minimum x,y,z coordinates of region containing model density) is needed to determine reasonable rotation steps, and the centre is needed to carry out a proper interpolation of the molecular transform. The extent and the centre are both given in Ångstroms. The cell scale factor defaults to 1 and can be refined (for example, if the map is from electron microscopy when the cell scale may be unknown to within a few percent).<br />
; ENSEMBLE <MODLID> ATOM <TYPE> RMS <RMS><br />
: Define an ensemble as a single atom for single atom MR<br />
; ENSEMBLE <MODLID> HELIX <NUM> <br />
: Define an ensemble as a helix with NUM residues<br />
; ENSEMBLE <MODLID> HETATM [ON|OFF]<br />
: Use scattering from HETATM records in pdb file. See [[Molecular_Replacement#Coordinate_Editing | Coordinate Editing ]]<br />
; ENSEMBLE <MODLID> DISABLE CHECK [ON|OFF]<br />
: Toggle to disable checking of deviation between models in an ensemble. '''Use with extreme caution'''. Results of computations are not guaranteed to be sensible.<br />
; ENSEMBLE <MODLID> ESTIMATOR [OEFFNER | OEFFNERHI | OEFFNERLO | CHOTHIALESK ]<br />
: Define the estimator function for converting ID to RMS<br />
; ENSEMBLE <MODLID> PTGRP [COVERAGE | IDENTITY | RMSD | TOLANG | TOLSPC | EULER | SYMM ]<br />
: Define the pointgroup parameters <br />
; ENSEMBLE <MODLID> BINS [MIN <N>| MAX <M>| WIDTH <W> ]<br />
: Define the Fcalc reflection binning parameters <br />
; ENSEMBLE <MODLID> TRACE [PDB|CIF] <PDBFILE><br />
: Define the coordinates used for packing independent of the coordinates used for structure factor calculation<br />
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
:: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file <br />
; ENSEMBLE <MODLID> TRACE SAMPLING MIN <DIST> <br />
: Set the minimum distance for the sampling of packing grid<br />
; ENSEMBLE <MODLID> TRACE SAMPLING TARGET <NUM> <br />
: Set the target for the number of points to sample the smallest molecule to be packed<br />
; ENSEMBLE <MODLID> TRACE SAMPLING RANGE <NUM> <br />
: Target range (TARGET+/-RANGE) for search for hexgrid points in protein volume<br />
; ENSEMBLE <MODLID> TRACE SAMPLING USE [AUTO | ALL | CALPHA | HEXGRID ]<br />
: Sample trace coordinates using all atoms, C-alpha atoms, a hexagonal grid in the atomic volume or use an automatically determined choice<br />
; ENSEMBLE <MODLID> TRACE SAMPLING DISTANCE <DIST> <br />
: Set the distance for the sampling of the hexagonal grid explicitly and do not use TARGET to find default sampling distance<br />
; ENSEMBLE <MODLID> TRACE SAMPLING WANG <WANG> <br />
: Scale factor for the size of the Wang mask generated from an ensemble map<br />
; ENSEMBLE <MODLID> TRACE PDB <PDBFILE> <br />
: Use the given set of coordinates for packing rather than using the coordinates for structure factor calculation<br />
* Default: ENSEMBLE <MODLID> DISABLE CHECK OFF<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING MIN 1.0<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING TARGET 1000<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING RANGE 100<br />
addENSE_PDB_ID(str <MODLID>,str <FILE>,float <ID>) <br />
addENSE_PDB_RMS(str <MODLID>,str <FILE>,float <RMS>) <br />
setENSE_TRAC_SAMP_MIN(MODLID,float <MIN>)<br />
setENSE_TRAC_SAMP_TARG(MODLID,int <TARGET>)<br />
setENSE_TRAC_SAMP_RANG(MODLID,int <RANGE>)<br />
setENSE_TRAC_SAMP_USE(MODLID,str)<br />
setENSE_TRAC_SAMP_DIST(MODLID,float <DIST>)<br />
setENSE_TRAC_SAMP_WANG(MODLID,float <WANG>)r <FILE>,float <RMS>)<br />
addENSE_CARD(str <MODLID>,str <FILE>,bool)<br />
addENSE_MAP(str <MODLID>,str <MTZFILE>,str <F>,str <PHI>,dvect3 <EX EY EZ>,<br />
float <RMS>,dvect3 <CX CY CZ>,float <PMW>,float <NMW>,float <CELL>)<br />
setENSE_DISA_CHEC(bool)<br />
<br />
==[[Image:User1.gif|link=]]HKLIN==<br />
; HKLIN <FILENAME><br />
: The mtz file containing the data<br />
setHKLI(str <FILENAME>)<br />
<br />
==[[Image:User1.gif|link=]]JOBS== <br />
; JOBS <NUM><br />
: Number of processors to use in parallelized sections of code<br />
* Default: JOBS 2<br />
setJOBS(int <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]LABIN== <br />
; LABIN F = <F> SIGF = <SIGF> <br />
: Columns in mtz file. F must be given. SIGF should be given but is optional<br />
; LABIN I = <nowiki><I></nowiki> SIGI = <SIGI> <br />
: Columns in mtz file. I must be given. SIGI should be given but is optional<br />
; LABIN FMAP = <PH> PHMAP = <PHMAP> <br />
: Columns in mtz file. FMAP/PHMAP are weighted coefficients for use in the Phased Translation Function.<br />
; LABIN FMAP = <PH> PHMAP = <PHMAP> FOM = <FOM><br />
: Columns in mtz file. FMAP/PHMAP are unweighted coefficients for use in the Phased Translation Function and FOM the figure of merit for weighting<br />
setLABI_F_SIGF(str <F>,str <SIGF>)<br />
setLABI_I_SIGI(str <nowiki><I></nowiki>,str <SIGI>)<br />
setLABI_PTF(str <FMAP>,str <PHMAP>,str <FOM>)<br />
<br />
''Data should be input to python run-jobs using one data_refl parameter''<br />
''This is extracted from the ResultMR_DAT object after a call to runMR_DAT''<br />
setREFL_DATA(data_ref)<br />
''Example:''<br />
i = InputMR_DAT()<br />
i.setHKLI("*.mtz")<br />
i.setLABI_F_SIGF("F","SIGF")<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputMR_LLG()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.setREFL_DATA(r.getDATA())<br />
''See also: '' [[Python Example Scripts]]<br />
<br />
''Alternatively, reflection arrays can be set using cctbx::af::shared<double>''<br />
setREFL_F_SIGF(float_array <F>,float_array <SIGF>)<br />
setREFL_I_SIGI(float_array <nowiki><I></nowiki>,float_array <SIGI>)<br />
setREFL_PTF(float_array <FMAP>,float_array <PHMAP>,float_array <FOM>)<br />
<br />
==[[Image:User1.gif|link=]]MODE==<br />
; MODE [ ANO | CCA | SCEDS | NMAXYZ | NCS | MR_ELLG | MR_AUTO | MR_GYRE | MR_ATOM | MR_ROT | MR_TRA | MR_RNP | | MR_OCC | MR_PAK | EP_AUTO | EP_SAD]<br />
: The mode of operation of Phaser. The different modes are described in a separate page on [[Keyword Modes]]<br />
ResultANO r = runANO(InputANO)<br />
ResultCCA r = runCCA(InputCCA)<br />
ResultNMA r = runSCEDS(InputNMA)<br />
ResultNMA r = runNMAXYZ(InputNMA)<br />
ResultNCS r = runNCS(InputNCS)<br />
ResultELLG r = runMR_ELLG(InputMR_ELLG)<br />
ResultMR r = runMR_AUTO(InputMR_AUTO)<br />
ResultEP r = runMR_ATOM(InputMR_ATOM)<br />
ResulrMR_RF r = runMR_FRF(InputMR_FRF)<br />
ResultMR_TF r = runMR_FTF(InputMR_FTF)<br />
ResultMR r = runMR_RNP(InputMR_RNP)<br />
ResultGYRE r = runMR_GYRE(InputMR_RNP)<br />
ResultMR r = runMR_OCC(InputMR_OCC)<br />
ResultMR r = runMR_PAK(InputMR_PAK)<br />
ResultEP r = runEP_AUTO(InputEP_AUTO)<br />
ResultEP_SAD r = runEP_SAD(InputEP_SAD)<br />
<br />
==[[Image:User1.gif|link=]]PARTIAL== <br />
; PARTIAL PDB <PDBFILE> [RMSIDENTITY] <RMS_ID><br />
: The partial structure for MR-SAD substructure completion. Note that this must already be correctly placed, as the experimental phasing module will not carry out molecular replacement.<br />
; PARTIAL HKLIN <MTZFILE> [RMS|IDENTITY] <RMS_ID><br />
: The partial electron density for MR-SAD substructure completion.<br />
; PARTIAL LABIN FC=<FC> PHIC=<PHIC><br />
: Column labels for partial electron density for MR-SAD substructure completion.<br />
setPART_PDB(str <PDBFILE>)<br />
setPART_HKLI(str <MTZFILE>) <br />
setPART_LABI_FC(str <FC>)<br />
setPART_LABI_PHIC(str <PHIC>) <br />
setPART_VARI(str ["ID"|"RMS"])<br />
setPART_DEVI(float <RMS_ID>)<br />
<br />
==[[Image:User1.gif|link=]]SEARCH==<br />
; SEARCH ENSEMBLE <MODLID> ''{OR ENSEMBLE <MODLID>}… NUMBER <NUM><sup>*</sup>''<br />
: The ENSEMBLE to be searched for in a rotation search or an automatic search. When multiple ensembles are given using the OR keyword, the search is performed for each ENSEMBLE in turn. When the keyword is entered multiple times, each SEARCH keyword refers to a new component of the structure. If the component is present multiple times the sub-keyword NUMber can be used (rather than entering the same SEARCH keyword NUMber times).<br />
: <sup>*</sup>For automatic determination of search number use NUMBER 0. If the composition is entered, the maximum number will be that defined by the composition, otherwise the maximum number will fill the asymmetric unit to a minimum solvent content of 20%. Searches for new components will continue until the TFZ score is above 8, and terminate if the TFZ score drops below 8 before the placement of the maximum number of components.<br />
; SEARCH METHOD [FULL|FAST]<br />
: Search using the [[Modes#Modes |full search]] or [[Modes#Modes | fast search]] algorithms.<br />
; SEARCH ORDER AUTO [ON|OFF]<br />
: Search in the "best" order as estimated using estimated rms deviation and completeness of models.<br />
; SEARCH PRUNE [ON|OFF]<br />
: For high TFZ solutions that fail the packing test, carry out a sliding-window occupancy refinement and prune residues that refine to low occupancy, in an effort to resolve packing clashes. If this flag is set to true, the flag for keeping high tfz score solutions (see [[#PACK | PACK]]) that don't pack is also set to true (PACK KEEP HIGH TFZ ON).<br />
; SEARCH AMALGAMATE USE [ON|OFF]<br />
: For multiple high TFZ solutions, enable amalgamation into a single solution<br />
; SEARCH BFACTOR <BFAC><br />
: B-factor applied to search molecule (or atom).<br />
; SEARCH OFACTOR <OFAC><br />
: Occupancy factor applied to search molecule (or atom).<br />
* Default: SEARCH METHOD FAST<br />
* Default: SEARCH ORDER AUTO ON<br />
* Default: SEARCH PRUNE ON<br />
* Default: SEARCH AMALGAMATE USE ON<br />
* Default: SEARCH BFACTOR 0<br />
* Default: SEARCH OFACTOR 1<br />
addSEAR_ENSE_NUM(str <MODLID>,int <NUM>) <br />
addSEAR_ENSE_OR_ENSE_NUM(string_array <MODLIDS>,int <NUM>) <br />
setSEAR_METH(str [ "FULL" | "FAST" ])<br />
setSEAR_ORDE_AUTO(bool)<br />
setSEAR_PRUN(bool <PRUNE>)<br />
setSEAR_AMAL_USE(bool <AMAL>)<br />
setSEAR_BFAC(float <BFAC>)<br />
setSEAR_OFAC(float <OFAC>)<br />
<br />
==[[Image:User1.gif|link=]]SGALTERNATIVE==<br />
; SGALTERNATIVE SELECT [<sup>1</sup>ALL| <sup>2</sup>HAND| <sup>3</sup>LIST| <sup>4</sup>NONE]<br />
: Selection of alternative space groups to test in translation functions i.e. those that are in same laue group as that given in [[#SPACEGROUP | SPACEGROUP]]<br />
: <sup>1</sup> Test all possible space groups, <br />
: <sup>2</sup> Test the given space group and its enantiomorph.<br />
: <sup>3</sup> Test the space groups listed with SGALTERNATIVE TEST <SG>.<br />
: <sup>4</sup> Do not test alternative space groups.<br />
; SGALTERNATIVE TEST <SG><br />
: Alternative space groups to test. Multiple test space groups can be entered.<br />
* Default: SGALTERNATIVE SELECT HAND<br />
setSGAL_SELE(str [ "ALL" | "HAND" | "LIST" | "NONE" ]) <br />
addSGAL_TEST(str <SG>)<br />
<br />
==[[Image:User1.gif|link=]]SOLUTION==<br />
; SOLUTION SET <ANNOTATION><br />
: Start new set of solutions <br />
; SOLUTION TEMPLATE <ANNOTATION><br />
: Specifies a template solution against which other solutions in this run will be compared. Given in place of SOLUTION SET. Template rotation and translations given by subsequent SOLUTION 6DIM cards as per SOLUTION SETS.<br />
; SOLUTION 6DIM ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> [ORTH|FRAC] <X> <Y> <Z> ''FIXR [ON|OFF] FIXT [ON|OFF] FIXB [ON|OFF] BFAC <BFAC> MULT <MULT>''<br />
: This keyword is repeated for each known position and orientation of an ENSEMBLE MODLID. A B G are the Euler angles (z-y-z convention) and X Y Z are the translation elements, expressed either in orthogonal Angstroms (ORTH) or fractions of a cell edge (FRAC). The input ensemble is transformed by a rotation around the origin of the coordinate system, followed by a translation. BFAC default to 0, MULT (for multiplicity) defaults to 1.<br />
; SOLUTION ENSEMBLE <MODLID> VRMS DELTA <DELTA> RMSD <RMSD><br />
: Refined RMS variance terms for pdb files (or map) in ensemble MODLID. RMSD is the input RMSD of the job that produced the sol file, DELTA is the shift with respect to this RMSD. If given as part of a solution, these values overwrite the values used for input in the ENSEMBLE keyword (if refined).<br />
; SOLUTION ENSEMBLE <MODLID> CELL SCALE <SCALE><br />
: Refined cell scale factor. Only applicable to ensembles that are maps<br />
; SOLUTION TRIAL ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> RF <RF> RFZ <RFZ><br />
: Rotation List for translation function<br />
; SOLUTION ORIGIN ENSEMBLE <MODLID><br />
: Create solution for ensemble MODLID at the origin<br />
; SOLUTION SPACEGROUP <SG><br />
: Space Group of the solution (if alternative spacegroups searched)<br />
; SOLUTION RESOLUTION <HIRES><br />
: High resolution limit of data used to find/refine this solution<br />
; SOLUTION PACKS <PACKS><br />
: Flag for whether solution has been retained despite failing packing test, due to having high TFZ<br />
setSOLU(mr_solution <SOL>) <br />
addSOLU_SET(str <ANNOTATION>) <br />
addSOLU_TEMPLATE(str <ANNOTATION>) <br />
addSOLU_6DIM_ENSE(str <MODLID>,dvect3 <A B C>,bool <FRAC>,dvect3 <X Y Z>,<br />
float <BFAC>,bool <FIXR>,bool <FIXT>,bool <FIXB>,int <MULT>, 1.0) <br />
addSOLU_ENSE_DRMS(str <MODLID>, float <DRMS>) <br />
addSOLU_ENSE_CELL(str <MODLID>, float <SCALE>)<br />
addSOLU_TRIAL_ENSE(string <MODLID>,dvect3 <A B C>,float <RF>, float <RFZ>)<br />
addSOLU_ORIG_ENSE(string <MODLID>)<br />
setSOLU_SPAC(str <SG>)<br />
setSOLU_RESO(float <HIRES>)<br />
setSOLU_PACK(bool <PACKS>)<br />
<br />
==[[Image:User1.gif|link=]]SPACEGROUP==<br />
; SPACEGROUP <SG><br />
: Space group may be altered from the one on the MTZ file to a space group in the same point group. The space group can be entered in one of three ways<br />
#The Hermann-Mauguin symbol e.g. P212121 or P 21 21 21 (with or without spaces)<br />
#The international tables number, which gives standard setting e.g. 19 <br />
#The Hall symbols e.g. P 2ac 2ab<br />
: '''The space group can also be a subgroup of the merged space group'''. For example, P1 is always allowed. The reflections will be expanded to the symmetry of the given subgroup. This is only a valid approach when the true symmetry is the symmetry of the subgroup and perfect twinning causes the data to merge "perfectly" in the higher symmetry. <br />
:'''A list of the allowed space groups in the same point group as the given space group (or space group read from MTZ file) and allowed subgroups of these is given in the Cell Content Analysis logfile.'''<br />
* Default: Read from MTZ file<br />
setSPAC_NUM(int <NUM>)<br />
setSPAC_NAME(string <HM>)<br />
setSPAC_HALL(string <HALL>)<br />
<br />
==[[Image:User1.gif|link=]]WAVELENGTH== <br />
; WAVELENGTH <LAMBDA> <br />
: The wavelengh at which the SAD dataset was collected<br />
setWAVE(float <LAMBDA>)<br />
<br><br />
<br><br />
<br />
=Output Control Keywords=<br />
==[[Image:Output.png|link=]]DEBUG== <br />
; DEBUG [ON|OFF]<br />
: Extra verbose output for debugging<br />
* Default: DEBUG OFF<br />
setDEBU(bool) <br />
<br />
==[[Image:Output.png|link=]]EIGEN==<br />
; EIGEN WRITE [ON|OFF]<br />
; EIGEN READ <EIGENFILE><br />
: Read or write a file containing the eigenvectors and eigenvalues. If reading, the eigenvalues and eigenvectors of the Hessian are read from the file generated by a previous run, rather than calculated. This option must be used with the job that generated the eigenfile and the job reading the eigenfile must have identical input for the ENM parameters. Use WRITE to control whether or not the eigenfile is written when not using the READ mode.<br />
* Default: EIGEN WRITE ON<br />
setEIGE_WRIT(bool)<br />
setEIGE_READ(str <EIGENFILE>)<br />
<br />
==[[Image:Output.png|link=]]HKLOUT== <br />
; HKLOUT [ON|OFF]<br />
: Flags for output of an mtz file containing the phasing information<br />
* Default: HKLOUT ON<br />
setHKLO(bool) <br />
<br />
==[[Image:Output.png|link=]]KEYWORDS== <br />
; KEYWORDS [ON|OFF]<br />
: Write output Phaser .sol file (.rlist file for rotation function)<br />
* Default: KEYWORDS ON<br />
setKEYW(bool)<br />
<br />
==[[Image:Output.gif|link=]]LLGMAPS==<br />
; LLGMAPS [ON|OFF]<br />
: Write log-likelihood gradient map coefficients to MTZ file<br />
* Default: LLGMAPS OFF<br />
setLLGM(bool <True|False>)<br />
<br />
==[[Image:Output.png|link=]]MUTE== <br />
; MUTE [ON|OFF]<br />
: Toggle for running in silent/mute mode, where no logfile is written to ''standard output''.<br />
* Default: MUTE OFF<br />
setMUTE(bool) <br />
<br />
==[[Image:Output.png|link=]]KILL== <br />
; KILL TIME [MINS]<br />
: Kill Phaser after MINS minutes of CPU have elapsed, provided parallel section is complete<br />
; KILL FILE [FILENAME]<br />
: Kill Phaser if file FILENAME is present, provided parallel section is complete<br />
* Default: KILL TIME 0 ''Phaser runs to completion''<br />
* Detaulf: KILL FILE "" ''Phaser runs to completion''<br />
setKILL_TIME(float) <br />
setKILL_FILE(string)<br />
<br />
==[[Image:Output.png|link=]]OUTPUT== <br />
; OUTPUT LEVEL [SILENT|CONCISE|SUMMARY|LOGFILE|VERBOSE|DEBUG]<br />
: Output level for logfile<br />
; OUTPUT LEVEL [0|1|2|3|4|5]<br />
: Output level for logfile (equivalent to keyword level setting)<br />
* Default: OUTPUT LEVEL LOGFILE<br />
setOUTP_LEVE(string)<br />
setOUTP(enum)<br />
<br />
==[[Image:Output.png|link=]]TITLE==<br />
; TITLE <TITLE><br />
: Title for job<br />
* Default: TITLE [no title given]<br />
setTITL(str <TITLE>)<br />
<br />
==[[Image:Output.png|link=]]TOPFILES== <br />
; TOPFILES <NUM><br />
: Number of top pdbfiles or mtzfiles to write to output.<br />
* Default: TOPFILES 1<br />
setTOPF(int <NUM>) <br />
<br />
==[[Image:Output.png|link=]]ROOT== <br />
; ROOT <FILEROOT><br />
: Root filename for output files (e.g. FILEROOT.log)<br />
* Default: ROOT PHASER<br />
setROOT(string <FILEROOT>)<br />
<br />
==[[Image:Output.png|link=]]VERBOSE== <br />
; VERBOSE [ON|OFF] <br />
: Toggle to send verbose output to log file.<br />
* Default: VERBOSE OFF<br />
setVERB(bool) <br />
<br />
==[[Image:Output.png|link=]]XYZOUT== <br />
; XYZOUT [ON|OFF] ''ENSEMBLE [ON|OFF]<sup>1</sup> PACKING [ON|OFF]<sup>2</sup>''<br />
: Toggle for output coordinate files. <br />
::<sup>1</sup> If the optional ENSEMBLE keyword is ON, then each placed ensemble is written to its own pdb file. The files are named FILEROOT.#.#.pdb with the first # being the solution number and the second # being the number of the placed ensemble (representing a SOLU 6DIM entry in the .sol file). <br />
::<sup>2</sup> If the optional PACKING keyword is ON, then the hexagonal grid used for the packing analysis is output to its own pdb file FILEROOT.pak.pdb<br />
* Default: XYZOUT OFF (Rotation functions)<br />
* Default: XYZOUT ON ENSEMBLE OFF (all other relevant modes)<br />
* Default: XYZOUT ON PACKING OFF (all other relevant modes)<br />
setXYZO(bool) <br />
setXYZO_ENSE(bool)<br />
setXYZO_PACK(bool)<br />
<br><br />
<br><br />
<br />
=Advanced Keywords=<br />
==[[Image:User2.gif|link=]]ELLG==<br />
([[Molecular_Replacement#Should_Phaser_Solve_It.3F|explained here]])<br />
; ELLG TARGET <TARGET><br />
: Target value for expected LLG for determining resolution limits and search order<br />
<!--; ELLG HIRES <HIRES> Internal control only--><br />
* Default: ELLG TARGET 225<br />
setELLG_TARG(float <TARGET>)<br />
<br />
==[[Image:User2.gif|link=]]FORMFACTORS==<br />
; FORMFACTORS [XRAY | ELECTRON | NEUTRON]<br />
: Use scattering factors from x-ray, electron or neutrons<br />
* Default: FORMFACTORS XRAY<br />
setFORM(string XRAY)<br />
<br />
==[[Image:User2.gif|link=]]HAND==<br />
; HAND [ <sup>1</sup>ON| <sup>2</sup>OFF| <sup>3</sup>BOTH]<br />
: Hand of heavy atoms for experimental phasing<br />
: <sup>1</sup>Phase using the other hand of heavy atoms <br />
: <sup>2</sup>Phase using given hand of heavy atoms <br />
: <sup>3</sup>Phase using both hands of heavy atoms<br />
* Default: HAND BOTH<br />
setHAND(str [ "OFF" | "ON" | "BOTH" ])<br />
<br />
==[[Image:User2.gif|link=]]LLGCOMPLETE==<br />
; LLGCOMPLETE COMPLETE [ON|OFF]<br />
: Toggle for structure completion by log-likelihood gradient maps<br />
; LLGCOMPLETE SCATTERER <TYPE> <br />
: Atom/Cluster type(s) to be used for log-likelihood gradient completion. If more than one element is entered for log-likelihood gradient completion, the atom type that gives the highest Z-score for each peak is selected. Type = "RX" is a purely real scatterer and type="AX" is purely anomalous scatterer<br />
; LLGCOMPLETE REAL ON<br />
: Use a purely real scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER RX)<br />
; LLGCOMPLETE ANOMALOUS ON<br />
: Use a purely anomalous scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER AX)<br />
; LLGCOMPLETE CLASH <CLASH> <br />
: Minimum distance between atoms in log-likelihood gradient maps and also the distance used for determining anisotropy of atoms (default determined by resolution, flagged by CLASH=0)<br />
; LLGCOMPLETE SIGMA <Z><br />
: Z-score (sigma) for accepting peaks as new atoms in log-likelihood gradient maps<br />
; LLGCOMPLETE NCYC <NMAX><br />
: Maximum number of cycles of log-likelihood gradient structure completion. By default, NMAX is 50, but this limit should never be reached, because all features in the log-likelihood gradient maps should be assigned well before 50 cycles are finished. This keyword should be used to reduce the number of cycles to 1 or 2.<br />
; LLGCOMPLETE METHOD [IMAGINARY|ATOMTYPE]<br />
: Pick peaks from the imaginary map only or from all the completion atomtype maps.<br />
* Default: LLGCOMPLETE COMPLETE OFF<br />
* Default: LLGCOMPLETE CLASH 0<br />
* Default: LLGCOMPLETE SIGMA 6<br />
* Default: LLGComplete NCYC 50<br />
* Default: LLGComplete METHOD ATOMTYPE<br />
setLLGC_COMP(bool <True|False>) <br />
setLLGC_CLAS(float <CLASH>) <br />
setLLGC_SIGM(float <Z>) <br />
setLLGC_NCYC(int <NMAX>)<br />
setLLGC_METH(str ["IMAGINARY"|"ATOMTYPE"])<br />
<br />
==[[Image:User2.gif|link=]]NMA== <br />
; NMA MODE <M1> ''{MODE <M2>…}'' <br />
: The MODE keyword gives the mode along which to perturb the structure. If multiple modes are entered, the structure is perturbed along all the modes AND combinations of the modes given. There is no limit on the number of modes that can be entered, but the number of pdb files explodes combinatorially. The first 6 modes are the pure rotation and translation modes and do not lead to perturbation of the structure. If the number M is less than 7 then M is interpreted as the first M modes starting at 7, so for example, MODE 5 would give modes 7 8 9 10 11.<br />
; NMA COMBINATION <NMAX><br />
: Controls how many modes are present in any combination.<br />
* Default: NMA MODE 5<br />
* Default: NMA COMBINATION 2<br />
addNMA_MODE(int <MODE>) <br />
setNMA_COMB(int <NMAX>)<br />
<br />
==[[Image:User2.gif|link=]]PACK==<br />
; PACK SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>ALL ]<br />
: <sup>1</sup>Allow up to the PERCENT of sampling points to clash, considering only pairwise clashes <br />
: <sup>2</sup>Allow all solutions (no packing test)<br />
; PACK CUTOFF <PERCENT> <br />
: Limit on total number (or percent) of clashes <br />
; PACK QUICK [ON|OFF]<br />
: Packing check stops when ALLOWED_CLASHES or MAX_CLASHES is reached. However, all clashes are found when the solution has a high Z-score (see [[#ZSCORE | ZSCORE]]).<br />
; PACK COMPACT [ON|OFF]<br />
: Pack ensembles into a compact association (minimize distances between centres of mass for the addition of each component in a solution).<br />
; PACK KEEP HIGH TFZ [ON|OFF]<br />
: Solutions with high tfz (see [[#ZSCORE | ZSCORE]]) but that fail to pack are retained in the solution list. Set to true if SEARCH PRUNE ON (see [[#SEARCH | SEARCH]])<br />
* Default: PACK SELECT PERCENT<br />
* Default: PACK CUTOFF 5<br />
* Default: PACK COMPACT ON<br />
* Default: PACK QUICK ON<br />
* Default: PACK KEEP HIGH TFZ OFF<br />
* Default: PACK CONSERVATION DISTANCE 1,5<br />
setPACK_SELE(str ["PERCENT"|"ALL"]) <br />
setPACK_CUTO(float <ALLOWED_CLASHES>)<br />
setPACK_QUIC(bool)<br />
setPACK_KEEP_HIGH_TFZ(bool)<br />
setPACK_COMP(bool)<br />
<br />
==[[Image:User2.gif|link=]]PEAKS==<br />
; PEAKS TRA SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL] <br />
; PEAKS ROT SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL]<br />
: Peaks for individual rotation functions (ROT) or individual translation functions (TRA) satisfying selection criteria are saved. To be used for subsequent steps, peaks must also satisfy the overall [[#PURGE | PURGE]] selection criteria, so it will usually be appropriate to set only the PURGE criteria (which over-ride the defaults for the PEAKS criteria if not explicitly set). See [[Molecular_Replacement#How_to_Select_Peaks | How to Select Peaks]]<br />
: <sup>1</sup> Select peaks by taking all peaks over CUTOFF percent of the difference between the top peak and the mean value.<br />
: <sup>2</sup> Select peaks by taking all peaks with a Z-score greater than CUTOFF.<br />
: <sup>3</sup> Select peaks by taking top CUTOFF.<br />
: <sup>4</sup> Select all peaks.<br />
; PEAKS ROT CUTOFF <CUTOFF><br />
; PEAKS TRA CUTOFF <CUTOFF><br />
: Cutoff value for the rotation function (ROT) or translation function (TRA) peak selection criteria.<br />
: If selection is by percent and [[#PURGE | PURGE PERCENT]] is changed from the default, then the PEAKS percent value is set to the lower PURGE percent value.<br />
; PEAKS ROT CLUSTER [ON|OFF] <br />
; PEAKS TRA CLUSTER [ON|OFF]<br />
: Toggle selects clustered or unclustered peaks for rotation function (ROT) or translation function (TRA).<br />
; PEAKS ROT DOWN [PERCENT] <br />
: [[#SEARCH | SEARCH METHOD FAST]] only. Percentage to reduce rotation function cutoff if there is no TFZ over the zscore cutoff that determines a true solution (see [[#ZSCORE | ZSCORE]]) in first search.<br />
* Default: PEAKS ROT SELECT PERCENT<br />
* Default: PEAKS TRA SELECT PERCENT<br />
* Default: PEAKS ROT CUTOFF 75<br />
* Default: PEAKS TRA CUTOFF 75<br />
* Default: PEAKS ROT CLUSTER ON<br />
* Default: PEAKS TRA CLUSTER ON<br />
setPEAK_ROTA_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"]) <br />
setPEAK_TRAN_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"])<br />
setPEAK_ROTA_CUTO(float <CUTOFF>)<br />
setPEAK_TRAN_CUTO(float <CUTOFF>) <br />
setPEAK_ROTA_CLUS(bool <CLUSTER>) <br />
setPEAK_TRAN_CLUS(bool <CLUSTER>)<br />
setPEAK_ROTA_DOWN(float <PERCENT>)<br />
<br />
==[[Image:User2.gif|link=]]PERMUTATIONS== <br />
; PERMUTATIONS [ON|OFF]<br />
: Only relevant to [[#SEARCH | SEARCH METHOD FULL]]. Toggle for whether the order of the search set is to be permuted.<br />
* Default: PERMUTATIONS OFF<br />
setPERM(bool <PERMUTATIONS>)<br />
<br />
==[[Image:User2.gif|link=]]PERTURB== <br />
; PERTURB RMS STEP <RMS><br />
: Increment in rms Ångstroms between pdb files to be written. <br />
; PERTURB RMS MAX <MAXRMS><br />
: The structure will be perturbed along each mode until the MAXRMS deviation has been reached.<br />
; PERTURB RMS DIRECTION [FORWARD|BACKWARD|TOFRO] <br />
: The structure is perturbed either forwards or backwards or to-and-fro (FORWARD|BACKWARD|TOFRO) along the eigenvectors of the modes specified.<br />
; PERTURB INCREMENT [RMS| DQ] <br />
: Perturb the structure by rms devitations along the modes, or by set dq increments<br />
; PERTURB DQ <DQ1> ''{DQ <DQ2>…}''<br />
: Alternatively, the DQ factors (as used by the Elnemo server (K. Suhre & Y-H. Sanejouand, NAR 2004 vol 32) ) by which to perturb the atoms along the eigenvectors can be entered directly.<br />
* Default: PERTURB INCREMENT RMS<br />
* Default: PERTURB RMS STEP 0.2<br />
* Default: PERTURB RMS MAXRMS 0.3<br />
* Default: PERTURB RMS DIRECTION TOFRO<br />
setPERT_INCR(str [ "RMS" | "DQ" ])<br />
setPERT_RMS_MAXI(float <MAX>)<br />
setPERT_RMS_DIRE(str [ "FORWARDS" | "BACKWARDS" | "TOFRO" ]) <br />
addPERT_DQ(float <DQ>)<br />
<br />
==[[Image:User2.gif|link=]]PURGE== <br />
; PURGE ROT ENABLE [ON|OFF]<sup>1</sup><br />
; PURGE ROT PERCENT <PERC><sup>2</sup><br />
; PURGE ROT NUMBER <NUM><sup>3</sup><br />
: Purging criteria for rotation function (RF), where PERCENT and NUMBER are alternative selection criteria (''OR'' criteria)<br />
::<sup>1</sup> Toggle for whether to purge the solution list from the RF according to the top solution found. If there are a number of RF searches with different partial solution backgrounds, the PURGE is applied to the total list of peaks. If there is one clearly significant RF solution from one of the backgrounds it acts to purge all the less significant solutions. If there is only one RF (a single partial solution background) the PURGE gives no additional selection over and above the PEAKS command. <br />
::<sup>2</sup> [[Molecular_Replacement#How_to_Select_Peaks | Selection by percent]]. PERC is percentage of the top peak, where the value of the top peak is defined as 100% and the value of the mean is defined as 0%. Note that this criterion is applied subsequent to any selection criteria applied through the [[#PEAKS | PEAKS]] command. If the [[#PEAKS | PEAKS]] selection is by percent, then the percent cutoff given in the PURGE command over-rides that for [[#PEAKS | PEAKS]], so as to rationalize results in the case of only a single RF (single partial solution background.)<br />
::<sup>3</sup> NUM is the number of solutions to retain in purging. If NUMBER is given (non-zero) it overrides the PERCENT option. NUMBER given as zero is the flag for not applying this criterion.<br />
; PURGE TRA ENABLE [ON|OFF]<br />
; PURGE TRA PERCENT <PERC><br />
; PURGE TRA NUMBER <NUM><br />
: As above, but for translation function<br />
; PURGE RNP ENABLE [ON|OFF]<br />
; PURGE RNP PERCENT <PERC><br />
; PURGE RNP NUMBER <NUM><br />
: As above but for refinement, but with the important distinction that PERCENT and NUMBER are concurrent selection criteria (''AND'' criteria)<br />
* Default: PURGE ROT ENABLE ON <br />
* Default: PURGE ROT PERC 75<br />
* Default: PURGE ROT NUM 0<br />
* Default: PURGE TRA ENABLE ON<br />
* Default: PURGE TRA PERC 75<br />
* Default: PURGE TRA NUM 0<br />
* Default: PURGE RNP ENABLE ON<br />
* Default: PURGE RNP PERC 75<br />
* Default: PURGE RNP NUM 0<br />
setPURG_ROTA_ENAB(bool <ENABLE>)<br />
setPURG_TRAN_ENAB(bool <ENABLE>) <br />
setPURG_RNP_ENAB(bool <ENABLE>)<br />
setPURG_ROTA_PERC(float <PERC>) <br />
setPURG_TRAN_PERC(float <PERC>) <br />
setPURG_RNP_PERC(float <PERC>)<br />
setPURG_ROTA_NUMB(float <NUM>) <br />
setPURG_TRAN_NUMB(float <NUM>)<br />
setPURG_TRAN_NUMB(float <NUM>)<br />
setPURG_RNP_NUMB(float <NUM>)<br />
<br />
==[[Image:User2.gif|link=]]RESOLUTION== <br />
; RESOLUTION HIGH <HIRES> <br />
: High resolution limit in Ångstroms. <br />
; RESOLUTION LOW <LORES><br />
: Low resolution limit in Ångstroms.<br />
; RESOLUTION AUTO HIGH <HIRES> <br />
: High resolution limit in Ångstroms for final high resolution refinement in MR_AUTO mode.<br />
* Default for molecular replacement: Set by [[#ELLG | ELLG TARGET]] for structure solution, final refinement uses all data<br />
* Default for experimental phasing: All data used<br />
setRESO_HIGH(float <HIRES>) <br />
setRESO_LOW(float <LORES>)<br />
setRESO_AUTO_HIGH(float <HIRES>) <br />
setRESO(float <HIRES>,float <LORES>)<br />
<br />
==[[Image:User2.gif|link=]]ROTATE== <br />
; ROTATE VOLUME FULL<br />
: Sample all unique angles <br />
; ROTATE VOLUME AROUND EULER <A> <nowiki><B></nowiki> <C> RANGE <RANGE> <br />
: Restrict the search to the region of +/- RANGE degrees around orientation given by EULER<br />
setROTA_VOLU(string ["FULL"|"AROUND"|) <br />
setROTA_EULE(dvect3 <A B C>) <br />
setROTA_RANG(float <RANGE>)<br />
<br />
==[[Image:User2.gif|link=]]SCATTERING==<br />
; SCATTERING TYPE <TYPE> FP=<FP> FDP=<FDP> FIX [ON|OFF|EDGE]<br />
: Measured scattering factors for a given atom type, from a fluorescence scan. FIX EDGE (default) fixes the fdp value if it is away from an edge, but refines it if it is close to an edge, while FIX ON or FIX OFF does not depend on proximity of edge.<br />
; SCATTERING RESTRAINT [ON|OFF]<br />
: use Fdp restraints<br />
; SCATTERING SIGMA <SIGMA><br />
: Fdp restraint sigma used is SIGMA multiplied by initial fdp value<br />
* Default: SCATTERING SIGMA 0.2<br />
* Default: SCATTERING RESTRAINT ON<br />
addSCAT(str <TYPE>,float <FP>,float <FDP, string <FIXFDP>) <br />
setSCAT_REST(bool) <br />
setSCAT_SIGM(float <SIGMA>)<br />
<br />
==[[Image:User2.gif|link=]]SCEDS== <br />
; SCEDS NDOM <NDOM><br />
:Number of domains into which to split the protein<br />
; SCEDS WEIGHT SPHERICITY <WS><br />
: Weight factor for the the Density Test in the SCED Score. The Sphericity Test scores boundaries that divide the protein into more spherical domains more highly.<br />
; SCEDS WEIGHT CONTINUITY <WC><br />
: Weight factor for the the Continuity Test in the SCED Score. The Continuity Test scores boundaries that divide the protein into domains contigous in sequence more highly. <br />
; SCEDS WEIGHT EQUALITY <WE><br />
: Weight factor for the the Equality Test in the SCED Score. The Equality Test scores boundaries that divide the protein more equally more highly.<br />
; SCEDS WEIGHT DENSITY <WD><br />
: Weight factor for the the Equality Test in the SCED Score. The Density Test scores boundaries that divide the protein into domains more densely packed with atoms more highly. <br />
* Default: SCEDS NDOM 2<br />
* Default: SCEDS WEIGHT EQUALITY 1<br />
* Default: SCEDS WEIGHT SPHERICITY 4 <br />
* Default: SCEDS WEIGHT DENSITY 1<br />
* Default: SCEDS WEIGHT CONTINUITY 0<br />
setSCED_NDOM(int <NDOM>) <br />
setSCED_WEIG_SPHE(float <WS>) <br />
setSCED_WEIG_CONT(float <WC>)<br />
setSCED_WEIG_EQUA(float <WE>) <br />
setSCED_WEIG_DENS(float <WD>)<br />
<br />
==[[Image:User2.gif|link=]]TARGET==<br />
; TARGET ROT [FAST | BRUTE]<br />
: Target function for fast rotation searches (2). BRUTE searches all angles on a grid with the full rotation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these rotations with the full rotation likelihood target.<br />
; TARGET TRA [FAST | BRUTE | PHASED]<br />
: Target function for fast translation searches (3). BRUTE searches all positions on a grid with the full translation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these positions with the full translation likelihood target. PHASED selects the "phased translation function", for which a LABIN command should also be given, specifying FMAP, PHMAP and (optionally) FOM.<br />
* Default: TARGET ROT FAST<br />
* Default: TARGET TRA FAST<br />
setTARG_ROTA(str ["FAST"|"BRUTE"])<br />
setTARG_TRAN(str ["FAST"|"BRUTE"|"PHASED"])<br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS NMOL <NMOL><br />
: Number of molecules/molecular assemblies related by single TNCS vector (usually only 2). If the TNCS is a pseudo-tripling of the cell then NMOL=3, a pseudo-quadrupling then NMOL=4 etc.<br />
* Default: TNCS NMOL 2<br />
setTNCS_NMOL(int <NMOL>)<br />
<br><br />
<br />
==[[Image:User2.gif|link=]]TRANSLATION== <br />
; TRANSLATION VOLUME [ <sup>1</sup>FULL | <sup>2</sup>REGION | <sup>3</sup>LINE | <sup>4</sup>AROUND ])<br />
: Search volume for brute force translation function.<br />
: <sup>1</sup> Cheshire cell or Primitive cell volume. <br />
: <sup>2</sup> Search region.<br />
: <sup>3</sup> Search along line. <br />
: <sup>4</sup> Search around a point.<br />
; <sup>1 2 3</sup>TRANSLATION START <X Y Z> <br />
; <sup>1 2 3</sup>TRANSLATION END <X Y Z><br />
: Search within region or line bounded by START and END.<br />
; <sup>4</sup>TRANSLATION POINT <X Y Z><br />
; <sup>4</sup>TRANSLATION RANGE <RANGE><br />
: Search within +/- RANGE Ångstroms (not fractional coordinates, even if the search point is given as fractional coordinates) of a point <X Y Z>.<br />
; TRANSLATION [ORTH | FRAC]<br />
: Coordinates are given in orthogonal or fractional values.<br />
; TRANSLATION PACKING USE [ON | OFF]<br />
: Top translation function peak will be testes for packing.<br />
; TRANSLATION PACKING CUTOFF <PERC><br />
: Percent pairwise packing used for packing function test of top TF peak. Equivalent to PACK CUTOFF <PERC> for packing function. <br />
; TRANSLATION PACKING NUM <NUM><br />
: Number of translation function peaks to test for packing before bailing out of packing test. Set to 0 to pack all translation function peaks (slow for large packing volumes). <br />
* Default: TRANSLATION VOLUME FULL<br />
* Default: TRANSLATION PACK CUTOFF 50<br />
* Default: TRANSLATION PACK NUM 0 (helices - all packing checked)<br />
* Default: TRANSLATION PACK NUM 500 (non-helices)<br />
setTRAN_VOLU(string ["FULL"|"REGION"|"LINE"|"AROUND"])<br />
setTRAN_START(dvect <START>)<br />
setTRAN_END(dvect <END>)<br />
setTRAN_POINT(dvect <POINT>)<br />
setTRAN_RANGE(float <RANGE>)<br />
setTRAN_FRAC(bool <True=FRAC False=ORTH>)<br />
setTRAN_PACK_USE(bool)<br />
setTRAN_PACK_CUTO(float)<br />
<br />
==[[Image:User2.gif|link=]]ZSCORE== <br />
; ZSCORE USE [ON|OFF]<br />
: Use the TFZ tests. Only applicable with [[#SEARCH | SEARCH METHOD FAST]]. (Note Phaser-2.4.0 and below use "ZSCORE SOLVED 0" to turn off the TFZ tests)<br />
; ZSCORE SOLVED <ZSCORE_SOLVED><br />
: Set the minimum TFZ that indicates a definite solution for amalgamating solutions in FAST search method. <br />
;ZSCORE STOP [ON|OFF]<br />
: Stop adding components beyond point where TFZ is below cutoff when adding multiple components in FAST mode. However, FAST mode will always add one component even if TFZ is below cutoff, or two components if starting search with no components input (no input solution).<br />
; ZSCORE HALF [ON|OFF]<br />
: Set the TFZ for amalgamating solutions in the FAST search method to the maximum of ZSCORE_SOLVED and half the maximum TFZ, to accommodate cases of partially correct solutions in very high TFZ cases (e.g. TFZ > 16)<br />
* Default: ZSCORE USE ON<br />
* Default: ZSCORE SOLVED 8<br />
* Default: ZSCORE HALF ON<br />
* Default: ZSCORE STOP ON<br />
setZSCO_USE(bool <True=ON False=OFF>)<br />
setZSCO_SOLV(floatType ZSCORE_SOLVED)<br />
setZSCO_HALF(bool <True=ON False=OFF>)<br />
setZSCO_STOP(bool <True=ON False=OFF>)<br />
<br><br />
<br><br />
<br />
=Expert Keywords=<br />
<br />
==[[Image:Expert.gif|link=]]MACANO== <br />
; MACANO PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for the refinement of SigmaN in the anisotropy correction<br />
; MACANO ANISO [ON|OFF] BINS [ON|OFF] SOLK [ON|OFF] SOLB [ON|OFF] ''{NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}''<br />
: Macrocycle for the custom refinement of SigmaN in the anisotropy correction. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACANO PROTOCOL DEFAULT<br />
setMACA_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACA(bool <ANISO>,bool <BINS>,bool <SOLK>,bool <SOLB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACMR== <br />
; MACMR PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACMR ROT [ON|OFF] TRA [ON|OFF] BFAC [ON|OFF] VRMS [ON|OFF] ''CELL [ON|OFF] LAST [ON|OFF] NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of molecular replacement solutions. Macrocycles are performed in the order in which they are entered. For description of VRMS see the [[FAQ]]. CELL is the scale factor for the unit cell for maps (EM maps). LAST is a flag that refines the parameters for the last component of a solution only, fixing all the others.<br />
; MACMR CHAINS [ON|OFF]<br />
: Split the ensembles into chains for refinement<br />
: Not possible as part of an automated mode<br />
* Default: MACMR PROTOCOL DEFAULT<br />
* Default: MACMR CHAINS OFF<br />
setMACM_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACM(bool <ROT>,bool <TRA>,bool <BFAC>,bool <VRMS>,bool <CELL>,bool <LAST>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
setMACM_CHAI(bool])<br />
<br />
==[[Image:Expert.gif|link=]]MACOCC== <br />
; MACOCC PROTOCOL [ DEFAULT | CUSTOM | OFF | ALL ]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACOCC NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of occupancy for solutions. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACOCC PROTOCOL DEFAULT<br />
setMACO_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACO(int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACGYRE== <br />
; MACGYRE PROTOCOL [ DEFAULT | CUSTOM | OFF | ALL ]<br />
: Protocol for refinement of gyre rotations<br />
; MACGYRE ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] ''ANCHOR [ON|OFF] SIGROT <SIGR> SIGTRA <SIGT> NCYCLE <NCYC> MINIMIZER [ BFGS | NEWTON | DESCENT ]''<br />
: Macrocycle for custom refinement of occupancy for solutions. Macrocycles are performed in the order in which they are entered.<br />
; MACGYRE SIGROT <SIGROT> <br />
; MACGYRE SIGTRA <SIGTRA> <br />
; MACGYRE ANCHOR [ON|OFF]<br />
: Override default values for harmonic restraints for rotation and translation refinement, and whether or not to anchor one fragment (no translation) for all macrocycles<br />
* Default: MACGYRE PROTOCOL DEFAULT<br />
setMACG_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACG(bool <REF>,bool <REF>, bool <REF>)<br />
addMACG_FULL(bool <REF>,bool <REF>,bool<REF>,bool <ANCHOR>,float <SIGROT>,float <SIGTRA>,int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
setMACG_SIGR(bool <SIGROT>)<br />
setMACG_SIGT(bool <SIGTRA>)<br />
setMACG_ANCH(bool <ANCHOR>)<br />
<br />
==[[Image:Expert.gif|link=]]MACSAD== <br />
; MACSAD PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for SAD refinement.<br />
:''n.b. PROTOCOL ALL will crash phaser and is only useful for debugging - see code for details''<br />
; MACSAD XYZ [ON|OFF] OCC [ON|OFF] BFAC [ON|OFF] FDP [ON|OFF] SA [ON|OFF] SB [ON|OFF] SP [ON|OFF] SD [ON|OFF] ''{PK [ON|OFF]} {PB [ON|OFF]} {NCYCLE <NCYC>} MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for SAD refinement. Macrocycles are performed in the order in which they are entered.<br />
*Default: MACSAD PROTOCOL DEFAULT<br />
setMACS_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACS(<br />
bool <XYZ>,bool <OCC>,bool <BFAC>,bool <FDP><br />
bool <SA>,bool <SB>,bool <SP>,bool <SD>,<br />
bool <PK>, bool <PB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACTNCS== <br />
; MACTNCS PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for pseudo-translational NCS refinement.<br />
; MACTNCS ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] ''NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for pseudo-translational NCS refinement. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACTNCS PROTOCOL DEFAULT<br />
setMACT_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACT(bool <ROT>,bool <TRA>,bool <VRMS>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]OCCUPANCY== <br />
; OCCUPANCY WINDOW ELLG <ELLG><br />
: Target eLLG for determining number of residues in window for occupancy refinement. The number of residues in a window will be an odd number. Occupancy refinement will be done for each offset of the refinement window.<br />
; OCCUPANCY WINDOW NRES <NRES><br />
: As an alternative to using the eLLG to define the number of residues in window for occupancy refinement, the number may be input directly. NRES must be an odd number.<br />
; OCCUPANCY WINDOW MAX <NRES><br />
: Maximum number of residues in an occupancy window (determined either by ellg or given as NRES) for which occupancy is refined. Prevents the refinement windows from spanning non-local regions of space.<br />
; OCCUPANCY MIN <MINOCC> MAX <MAXOCC><br />
: Minimum and maximum values of occupancy during refinement.<br />
; OCCUPANCY MERGE [ON/OFF]<br />
: Merge refined occupancies from different window offsets to give final occupancies per residue. If OFF, occupancies from a single window offset will be used, selected using OCCUPANCY OFFSET <N><br />
; OCCUPANCY FRAC <FRAC><br />
: Minimum fraction of the protein for which the occupancy may be set to zero.<br />
; OCCUPANCY OFFSET <N><br />
: If OCCUPANCY MERGE OFF, then <N> defines the single window offset from which final occupancies will be taken<br />
* Default: OCCUPANCY WINDOW ELLG 5<br />
* Default: OCCUPANCY WINDOW MAX 111<br />
* Default: OCCUPANCY MIN 0.01 MAX 1<br />
* Default: OCCUPANCY NCYCLES 1<br />
* Default: OCCUPANCY MERGE ON<br />
* Default: OCCUPANCY FRAC 0.5<br />
* Default: OCCUPANCY OFFSET 0<br />
setOCCU_WIND_ELLG(float <ELLG>)<br />
setOCCU_WIND_NRES(int <NRES>)<br />
setOCCU_WIND_MAX(int <NRES>)<br />
setOCCU_MIN(float <MIN>)<br />
setOCCU_MAX(float <MAX>)<br />
setOCCU_MERG(float <FRAC>)<br />
setOCCU_FRAC(bool)<br />
setOCCU_OFFS(int <N>)<br />
<br />
==[[Image:Expert.gif|link=]]RESCORE== <br />
; RESCORE ROT [ON|OFF]<br />
; RESCORE TRA [ON|OFF]<br />
: Toggle for rescoring of fast rotation function (ROT) or fast translation function (TRA) search peaks. <br />
* Default: RESCORE ROT ON<br />
* Default: RESCORE TRA ON|OFF will depend on whether phaser is running in the mode [[#MODE | MODE MR_AUTO]] with [[#SEARCH | SEARCH METHOD FAST]] or with [[#SEARCH | SEARCH METHOD FULL]], or running the translation function separately [[#MODE | MODE MR_FTF]]. For [[#SEARCH | SEARCH METHOD FAST]] the default also depends on whether or not the expected LLG target [[#ELLG | ELLG TARGET <TARGET>]] value is reached.<br />
setRESC_ROTA(bool)<br />
setRESC_TRAN(bool)<br />
<br />
==[[Image:Expert.gif|link=]]RFACTOR== <br />
; RFACTOR USE [ON|OFF]<br />
: For cases of searching for one ensemble when there is one ensemble in the asymmetric unit, the R-factor for the ensemble at the orientation and position in the input is calculated. If this value is low then MR is not performed in the MR_AUTO job in FAST search mode. Instead, rigid body refinement is performed before exiting. Note that the same R-factor test and cutoff is used for judging success in single-atom molecular replacement (MR_ATOM mode).<br />
; RFACTOR CUTOFF <VALUE><br />
: Rfactor in percent used as cutoff for deciding whether or not the R-factor indicates that MR is not necessary.<br />
* Default: RFACTOR USE ON CUTOFF 35<br />
setRFAC_USE(bool)<br />
setRFAC_CUTO(float <PERCENT>)<br />
<br />
==[[Image:Expert.gif|link=]]SAMPLING==<br />
; SAMPLING ROT <SAMP><br />
; SAMPLING TRA <SAMP><br />
: Sampling of search given in degrees for a rotation search and Ångstroms for a translation search. Sampling for rotation search depends on the mean radius of the Ensemble and the high resolution limit (dmin) of the search.<br />
* Default: SAMP = 2*atan(dmin/(4*meanRadius)) (ROTATION FUNCTION)<br />
* Default: SAMP = dmin/5; (BRUTE TRANSLATION FUNCTION)<br />
* Default: SAMP = dmin/4; (FAST TRANSLATION FUNCTION)<br />
setSAMP_ROTA(float <SAMP>)<br />
setSAMP_TRAN(float <SAMP>)<br />
<br><br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS USE [ON|OFF]<br />
: Use TNCS if present: apply TNCS corrections. (Note: was TNCS IGNORE [ON|OFF] in Phaser-2.4.0)<br />
; TNCS RLIST ADD [ON | OFF]<br />
: Supplement the rotation list used in the translation function with rotations already present in the list of known solutions. New molecules in the same orientation as those in the known search (as occurs with translational ncs) may not have peaks associated with them from the rotation function because the known molecules mask the presence of the ones not yet found. <br />
; TNCS PATT HIRES <hires><br />
: High resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT LORES <lores><br />
: Low resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT PERCENT <percent><br />
: Percent of origin Patterson peak that qualifies as a TNCS vector<br />
; TNCS PATT DISTANCE <distance><br />
: Minimum distance of Patterson peak from origin that qualifies as a TNCS vector<br />
; TNCS TRANSLATION PERTURB [ON | OFF]<br />
: If the TNCS translation vector is on a special position, perturb the vector from the special position before refinement<br />
; TNCS ROTATION RANGE <angle><br />
: Maximum deviation from initial rotation from which to look for rotational deviation. Default uses internally determined value based on resolution of data and size of G-function effective molecular radius. Value of 0 turns rotational refinement off.<br />
; TNCS ROTATION SAMPLING <sampling><br />
: Sampling for rotation search. Default uses internally determined value based on resolution of data and size of G-function effective molecular radius. Value of 0 turns rotational refinement off.<br />
* Default: TNCS USE ON<br />
* Default: TNCS RLIST ADD ON<br />
* Default: TNCS PATT HIRES 5<br />
* Default: TNCS PATT LORES 10<br />
* Default: TNCS PATT PERCENT 20<br />
* Default: TNCS PATT DISTANCE 15 <br />
* Default: TNCS TRANSLATION PERTURB ON<br />
setTNCS_USE(bool)<br />
setTNCS_RLIS_ADD(bool)<br />
setTNCS_PATT_HIRE(float <HIRES>)<br />
setTNCS_PATT_LORE(float <LORES>) <br />
setTNCS_PATT_PERC(float <PERCENT>) <br />
setTNCS_PATT_DIST(float <DISTANCE>)<br />
setTNCS_TRAN_PERT(bool)<br />
setTNCS_ROTA_RANG(float <RANGE>) <br />
setTNCS_ROTA_SAMP(float <SAMPLING>) <br />
<br><br />
<br><br />
<br />
=Developer Keywords=<br />
==[[Image:Developer.gif|link=]]BINS== <br />
; BINS DATA [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the data.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections<br />
; BINS ENSE [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the calaculated structure factos for the ensembles.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections<br />
* Default: BINS DATA MIN 6 MAX 50 WIDTH 500 <br />
* Default: BINS ENSE MIN 6 MAX 1000 WIDTH 1000 <br />
setBINS_DATA_MINI(float <L>)<br />
setBINS_DATA_MAXI(float <H>)<br />
setBINS_DATA_WIDT(float <W>)<br />
setBINS_ENSE_MINI(float <L>)<br />
setBINS_ENSE_MAXI(float <H>)<br />
setBINS_ENSE_WIDT(float <W>)<br />
<br />
==[[Image:Developer.gif|link=]]BFACTOR==<br />
; BFACTOR WILSON RESTRAINT [ON|OFF]<br />
: Toggle to use the Wilson restraint on the isotropic component of the atomic B-factors in SAD phasing.<br />
; BFACTOR SPHERICITY RESTRAINT [ON|OFF] <br />
: Toggle to use the sphericity restraint on the anisotropic B-factors in SAD phasing<br />
; BFACTOR REFINE RESTRAINT [ON|OFF] <br />
: Toggle to use the restraint to zero for the molecular B-factor in molecular replacement.<br />
; BFACTOR WILSON SIGMA <SIGMA><br />
: The sigma of the Wilson restraint.<br />
; BFACTOR SPHERICITY SIGMA <SIGMA><br />
: The sigma of the sphericity restraint.<br />
; BFACTOR REFINE SIGMA <SIGMA><br />
: The sigma of the restraint to zero for the molecular B-factor in molecular replacement.<br />
* Default: BFACTOR WILSON RESTRAINT ON <br />
* Default: BFACTOR SPHERICITY RESTRAINT ON <br />
* Default: BFACTOR REFINE RESTRAINT ON <br />
* Default: BFACTOR WILSON SIGMA 5<br />
* Default: BFACTOR SPHERICITY SIGMA 5<br />
* Default: BFACTOR REFINE SIGMA 6<br />
setBFAC_WILS_REST(bool <True|False>)<br />
setBFAC_SPHE_REST(bool <True|False>)<br />
setBFAC_REFI_REST(bool <True|False>) <br />
setBFAC_WILS_SIGM(float <SIGMA>) <br />
setBFAC_SPHE_SIGM(float <SIGMA>) <br />
setBFAC_REFI_SIGM(float <SIGMA>)<br />
<br />
==[[Image:Developer.gif|link=]]BOXSCALE==<br />
; BOXSCALE <BOXSCALE><br />
: Scale for box for calculating structure factors. The ensembles are put in a box equal to (extent of molecule)*BOXSCALE<br />
* Default: BOXSCALE 4<br />
setBOXS<float <BOXSCALE>)<br />
<br />
==[[Image:Developer.gif|link=]]CELL==<br />
; <span style="color:darkorange">Python Only</span> <br />
: Unit cell dimensions<br />
* Default: Cell read from MTZ file<br />
setCELL(float <A>,float <nowiki><B></nowiki>,float <C>,float <ALPHA>,float <BETA>,float <GAMMA>)<br />
setCELL6(float_array <A B C ALPHA BETA GAMMA>)<br />
<br />
==[[Image:Developer.gif|link=]]COMPOSITION== <br />
; COMPOSITION MIN SOLVENT <PERC><br />
: Minimum solvent to give maximum asu packing volume for automated search copy determination (NUM 0)<br />
* Default: COMPOSITION MIN SOLVENT 0.2<br />
setCOMP_MIN_SOLV(float)<br />
<br />
==[[Image:Developer.gif|link=]]DDM== <br />
; DDM SLIDER <VAL> <br />
: The SLIDER window width is used to smooth the Difference Distance Matrix. <br />
; DDM DISTANCE MIN <VAL> MAX <VAL> STEP <VAL><br />
: The range and step interval, as the fraction of the difference between the lowest and highest DDM values used to step.<br />
; DDM SEPARATION MIN <VAL> MAX <VAL><br />
: Through space separation in Angstroms used.<br />
; DDM SEQUENCE MIN <VAL> MAX <VAL><br />
: The range of sequence separations between matrix pairs.<br />
; DDM JOIN MIN <VAL> MAX <VAL><br />
: The range of lengths of the sequences to join if domain segments are discontinuous in percentages of the polypeptide chain.<br />
* Default: DDM SLIDER 0<br />
* Default: DDM DISTANCE MIN 1 MAX 5 STEP 50<br />
* Default: DDM SEPARATION MIN 7 MAX 14<br />
* Default: DDM SEQUENCE MIN 0 MAX 1<br />
* Default: DDM JOIN MIN 2 MAX 12<br />
setDDM_SLID(int <VAL>) <br />
setDDM_DIST_STEP(int <VAL>) <br />
setDDM_DIST_MINI(int <VAL>) <br />
setDDM_DIST_MAXI(int <VAL>) <br />
setDDM_SEPA_MINI(float <VAL>) <br />
setDDM_SEPA_MAXI(float <VAL>)<br />
setDDM_JOIN_MINI(int <VAL>) <br />
setDDM_JOIN_MAXI(int <VAL>) <br />
setDDM_SEQU_MINI(int <VAL>) <br />
setDDM_SEQU_MAXI(int <VAL>)<br />
<br />
==[[Image:Developer.gif|link=]]ENM== <br />
; ENM OSCILLATORS [ <sup>1</sup>RTB | <sup>2</sup>ALL ] <br />
: Define the way the atoms are used for the elastic network model.<br />
: <sup>1</sup>Use the rotation-translation block method.<br />
: <sup>2</sup>Use all atoms to determine the modes (only for use on very small molecules, less than 250 atoms). <br />
; ENM MAXBLOCKS <MAXBLOCKS><br />
: MAXBLOCKS is the number of rotation-translation blocks for the RTB analysis.<br />
; ENM NRES <NRES><br />
: For the RTB analysis, by default NRES=0 and then it is calculated so that it is as small as it can be without reaching MAXBlocks. <br />
; ENM RADIUS <RADIUS><br />
: Elastic Network Model interaction radius (Angstroms)<br />
; ENM FORCE <FORCE><br />
: Elastic Network Model force constant<br />
* Default: ENM OSCILLATORS RTB MAXBLOCKS 250 NRES 0 RADIUS 5 FORCE 1<br />
setENM_OSCI(str ["RTB"|"CA"|"ALL"])<br />
setENM_RTB_MAXB(float <MAXB>)<br />
setENM_RTB_NRES(float <NRES>) <br />
setENM_RADI(float <RADIUS>) <br />
setENM_FORC(float <FORCE>)<br />
<br />
==[[Image:Developer.gif|link=]]NORMALIZATION==<br />
; <span style="color:darkorange">Scripting Only</span><br />
; NORM EPSFAC WRITE <FILENAME><br />
: The normalization factors that correct for anisotropy in the data are written to BINARY file FILENAME<br />
; NORM EPSFAC READ <FILENAME><br />
: The normalization factors that correct for anisotropy in the data are read from BINARY file FILENAME. Further refinement is automatically turned off.<br />
; <span style="color:darkorange">Python Only</span><br />
The normalization factors that correct for anisotropy in the data, extracted from ResultANO object with getSigmaN(). Anisotropy should subsequently be turned off with setMACA_PROT("OFF").<br />
setNORM_DATA(data_norm <SIGMAN>)<br />
<br />
==[[Image:Developer.gif|link=]]OUTLIER==<br />
; OUTLIER REJECT [ON|OFF]<br />
: Reject low probability data outliers<br />
; OUTLIER PROB <PROB><br />
: Cutoff for rejection of low probablity outliers<br />
* Default: OUTLIER REJECT ON PROB 0.000001<br />
setOUTL_REJE(bool) <br />
setOUTL_PROB(float <PROB>)<br />
<br />
==[[Image:Developer.gif|link=]]PTGROUP== <br />
; PTGROUP COVERAGE <COVERAGE><br />
: Percentage coverage for two sequences to be considered in same pointgroup<br />
; PTGROUP IDENTITY <IDENTITY><br />
: Percentage identity for two sequences to be considered in same pointgroup<br />
; PTGROUP RMSD <RMSD><br />
: Percentage rmsd for two models to be considered in same pointgroup<br />
; PTGROUP TOLERANCE ANGULAR <ANG><br />
: Angular tolerance for pointgroup<br />
; PTGROUP TOLERANCE SPATIAL <DIST><br />
: Spatial tolerance for pointgroup<br />
setPTGR_COVE(float <COVERAGE>) <br />
setPTGR_IDEN(float <IDENTITY>) <br />
setPTGR_RMSD(float <RMSD>) <br />
setPTGR_TOLE_ANGU(float <ANG>) <br />
setPTGR_TOLE_SPAT(float <DIST>)<br />
<br />
==[[Image:Developer.gif|link=]]RESHARPEN== <br />
; RESHARPEN PERCENTAGE <PERC><br />
: Perecentage of the B-factor in the direction of lowest fall-off (in anisotropic data) to add back into the structure factors F_ISO and FWT and FDELWT so as to sharpen the electron density maps<br />
* Default: RESHARPEN PERCENT 100<br />
setRESH_PERC(float <PERCENT>)<br />
<br />
==[[Image:Developer.gif|link=]]SOLPARAMETERS==<br />
; SOLPARAMETERS SIGA FSOL <FSOL> BSOL <BSOL> MIN <MINSIGA><br />
: Babinet solvent parameters for Sigma(A) curves. MINSIGA is the minimum SIGA for Babinet solvent term (low resolution only). The solvent term in the Sigma(A) curve is given by <BR>max(1 - FSOL*exp(-BSOL/(4d^2)),MINSIGA).<br />
; SOLPARAMETERS BULK USE [ON|OFF]<br />
: Toggle for use of solvent mask scaling parameters for ensemble structure factors, applied to Fmask.<br />
; SOLPARAMETERS BULK FSOL <FSOL> BSOL <BSOL> <br />
: Solvent mask scaling parameters for ensemble structure factors, applied to Fmask.<br />
* Default: SOLPARAMETERS SIGA FSOL 1.05 BSOL 501 MIN 0.1<br />
* Default: SOLPARAMETERS SIGA RESTRAINT ON<br />
* Default: SOLPARAMETERS BULK USE OFF<br />
* Default: SOLPARAMETERS BULK FSOL 0.35 BSOL 45<br />
setSOLP_SIGA_FSOL(float <FSOL>) <br />
setSOLP_SIGA_BSOL(float <BSOL>)<br />
setSOLP_SIGA_MIN(float <MINSIGA>)<br />
setSOLP_BULK_USE(bool)<br />
setSOLP_BULK_FSOL(float <FSOL>) <br />
setSOLP_BULK_BSOL(float <BSOL>)<br />
<br />
==[[Image:Developer.gif|link=]]TARGET== <br />
; TARGET ROT FAST TYPE [LERF1 | CROWTHER]<br />
: Target function type for fast rotation searches<br />
; TARGET TRA FAST TYPE [LETF1 | LETF2 | CORRELATION]<br />
: Target function type for fast translation searches<br />
setTARG_ROTA_TYPE(string TYPE)<br />
setTARG_TRAN_TYPE(string TYPE)<br />
<br />
==[[Image:Developer.gif|link=]]TNCS==<br />
; TNCS ROTATION ANGLE <A> <nowiki><B></nowiki> <C><br />
: Input rotational difference between molecules related by the pseudo-translational symmetry vector, specified as rotations in degrees about x, y and z axes. Central value for grid search (RANGE > 0).<br />
; TNCS ROTATION RANGE <A><br />
: Range of angular difference in rotation angles to explore around central angle.<br />
; TNCS ROTATION SAMPLING <A><br />
: Sampling step for rotational grid search.<br />
; TNCS TRA VECTOR <x y z> <br />
: Input pseudo-translational symmetry vector (fractional coordinates). By default the translation is determined from the Patterson.<br />
; TNCS VARIANCE RMSD <num><br />
: Input estimated rms deviation between pseudo-translational symmetry vector related molecules.<br />
; TNCS VARIANCE FRAC <num><br />
: Input estimated fraction of cell content that obeys pseudo-translational symmetry.<br />
; TNCS LINK RESTRAINT [ON | OFF]<br />
: Link the occupancy of atoms related by TNCS in SAD phasing<br />
; TNCS LINK SIGMA <sigma><br />
: Sigma of link restraint of the occupancy of atoms related by TNCS in SAD phasing<br />
* Default: TNCS ROTATION ANGLE 0 0 0<br />
* Default: TNCS ROTATION RANGE -999 (determine from structure size and resolution)<br />
* Default: TNCS ROTATION SAMPLING -999 (determine from structure size and resolution)<br />
* Default: TNCS TRANSLATION VECTOR determined from position of Patterson peak<br />
* Default: TNCS VARIANCE RMSD 0.4 <br />
* Default: TNCS VARIANCE FRAC 1 <br />
* Default: TNCS LINK RESTRAINT ON<br />
* Default: TNCS LINK SIGMA 0.1<br />
setTNCS_ROTA_ANGL(dvect3 <A B C>) <br />
setTNCS_TRAN_VECT(dvect3 <X Y Z>) <br />
setTNCS_VARI_RMSD(float <RMSD>) <br />
setTNCS_VARI_FRAC(float <FRAC>)<br />
setTNCS_LINK_REST(bool)<br />
setTNCS_LINK_SIGM(float <SIGMA>)<br />
; <span style="color:darkorange">Scripting Only</span><br />
; TNCS EPSFAC WRITE <FILENAME><br />
: The normalization factors that correct for tNCS in the data are written to BINARY file FILENAME<br />
; TNCS EPSFAC READ <FILENAME><br />
: The normalization factors that correct for tNCS in the data are read from BINARY file FILENAME. Further refinement is automatically turned off.<br />
; <span style="color:darkorange">Python Only</span><br />
The normalization factors that correct for tNCS in the data, extracted from ResultNCS object with getPtNcs(). tNCS refinement should subsequently be turned off with setMACT_PROT("OFF").<br />
setTNCS(data_tncs <PTNCS>)<br />
<br />
==[[Image:Developer.gif|link=]]TRANSLATION== <br />
; TRANSLATION MAPS [ON | OFF]<br />
: Output maps of fast translation function FSS scoring functions<br />
: Maps take the names <ROOT>.<ensemble>.k.e.map where k is the Known backgound number and e is the Euler angle number for that known background<br />
* Default: TRANSLATION MAPS OFF<br />
setTRAN_MAPS(bool)</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Keywords&diff=2404Keywords2017-01-24T11:39:40Z<p>Airlie: Undo revision 2403 by Airlie (talk)</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
===Phaser Executable===<br />
<br />
The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the [[#MODE | MODE]] keyword. The different modes and the keywords relevant to each mode are described in [[Modes]].<br />
<br />
Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. However, some keywords are meaningful when entered multiple times. The order may or may not be important. <br />
<br />
*[[Image:User1.gif|link=]] [[#Basic Keywords | Basic Keywords]]<br />
<br />
*[[Image:Output.png|link=]] [[#Output Control Keywords | Output Control Keywords]]<br />
<br />
*[[Image:User2.gif|link=]] [[#Advanced Keywords |Advanced Keywords ]]<br />
<br />
*[[Image:Expert.gif|link=]] [[#Expert Keywords | Expert Keywords]]<br />
<br />
*[[Image:Developer.gif|link=]] [[#Developer Keywords | Developer Keywords]]<br />
<br />
<br />
===Python Interface===<br />
<br />
Phaser can be compiled as a python library. The mode is selected by calling the appropriate run-job. Input to the run-job is via input-objects, which are passed to the run-job. Setter function on the input objects are equivalent to the keywords for input to the phaser executable. The different modes and the keywords relevant to each mode are described in [[Modes]]. See [[Python Interface]] for details. <br />
<br />
The python interface uses standard python and cctbx/scitbx variable types.<br />
<br />
str string<br />
float double precision floating point<br />
Miller cctbx::miller::index<int> <br />
dvect3 scitbx::vec3<float> <br />
dmat33 scitbx::mat3<float> <br />
'''type'''_array scitbx::af::shared<'''type'''> arrays<br />
<br />
=Basic Keywords=<br />
==[[Image:User1.gif|link=]]ATOM== <br />
; ATOM CRYSTAL <XTALID> PDB <FILENAME><br />
: Definition of atom positions using a pdb file.<br />
; ATOM CRYSTAL <XTALID> HA <FILENAME><br />
: Definition of atom positions using a ha file (from RANTAN, MLPHARE etc.).<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> <br />
: Minimal definition of atom position. B-factor defaults to isotropic and Wilson B-factor. Use <TYPE>=TX for Ta6Br12 cluster and <TYPE>=XX for all other clusters. Scattering for cluster is spherically averaged. Coordinates of cluster compounds other than Ta6Br12 must be entered with CLUSTER keyword. Ta6Br12 coordinates are in phaser code and do not need to be given with CLUSTER keyword.<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> [ ISOB <ISOB> | ANOU <HH KK LL HK HL KL> | USTAR <HH KK LL HK HL KL>] FIXX [ON|OFF] FIXO [ON|OFF] FIXB [ON|OFF] BSWAP [ON|OFF] LABEL <SITE_NAME><br />
: Full definition of atom position including B-factor.<br />
;ATOM CHANGE BFACTOR WILSON [ON|OFF]<br />
: Reset all atomic B-factors to the Wilson B-factor.<br />
; ATOM CHANGE SCATTERER <SCATTERER><br />
:Reset all atomic scatterers to element (or cluster) type.<br />
setATOM_PDB(str <XTALID>,str <PDB FILENAME>)<br />
setATOM_IOTBX(str <XTALID>,iotbx::pdb::hierarchy::root <iotbx object>)<br />
setATOM_STR(str <XTALID>,str <pdb format string>)<br />
setATOM_HA(str <XTALID>,str <FILENAME>)<br />
addATOM(str <XTALID>,str <TYPE>,<br />
float <X>,float <Y>,float <Z>,float <OCC>)<br />
addATOM_FULL(str <XTALID>,str <TYPE>,bool <ORTH>,<br />
dvect3 <X Y Z>,float <OCC>,bool <ISO>,float <ISOB>,<br />
bool <ANOU>,dmat6 <HH KK LL HK HL KL>,<br />
bool <FIXX>,bool <FIXO>,bool <FIXB>,bool <SWAPB>,<br />
str <SITE_NAME>)<br />
setATOM_CHAN_BFAC_WILS(bool)<br />
setATOM_CHAN_SCAT(bool)<br />
setATOM_CHAN_SCAT_TYPE(str <TYPE>)<br />
<br />
==[[Image:User1.gif|link=]]CLUSTER== <br />
; CLUSTER PDB <PDBFILE><br />
: Sample coordinates for a cluster compound for experimental phasing. Clusters are specified with type XX. Ta6Br12 clusters do not need to have coordinates specified as the coordinates are in the phaser code. To use Ta6Br12 clusters, specify atomtypes/clusters as TX.<br />
setCLUS_PDB(str <PDBFILE>)<br />
addCLUS_PDB(str <ID>, str <PDBFILE>)<br />
<br />
==[[Image:User1.gif|link=]]COMPOSITION== <br />
; COMPOSITION BY [ <sup>1</sup>AVERAGE| <sup>2</sup>SOLVENT| <sup>3</sup>ASU ]<br />
: Alternative ways of defining composition<br />
: <sup>1</sup> AVERAGE solvent fraction for crystals (50%)<br />
: <sup>2</sup> Composition entered by solvent content.<br />
: <sup>3</sup> Explicit description of composition of ASU by sequence or molecular weight<br />
; <sup>2</sup>COMPOSITION PERCENTAGE <SOLVENT><br />
: Specified SOLVENT content<br />
; <sup>3</sup>COMPOSITION PROTEIN [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of protein in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION NUCLEIC [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of nucleic acid in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION ATOM <TYPE> NUMBER <NUM><br />
: Add NUM copies of an atom (usually a heavy atom) to the composition<br />
* Default: COMPOSITION BY ASU<br />
setCOMP_BY(str ["AVERAGE" | "SOLVENT" | "ASU" ])<br />
setCOMP_PERC(float <SOLVENT>)<br />
addCOMP_PROT_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_PROT_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_PROT_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_PROT_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_NUCL_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_NUCL_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_NUCL_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_NUCL_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_ATOM(str <TYPE>,float <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]CRYSTAL== <br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN Fpos =<F+> SIGFpos=<SIG+> Fneg=<F-> SIGFneg=<SIG-><br />
: Columns of MTZ file to read for this (anomalous) dataset<br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN F =<F> SIGF=<SIGF><br />
: Columns of MTZ file to read for this (non-anomalous) dataset. Used for LLG completion in SAD phasing when there is no anomalous signal (single atom MR protocol). Use LABIN for MR.<br />
setCRYS_ANOM_LABI(str <F+>,str <SIGF+>,str <F->,str <SIGF->) <br />
setCRYS_MEAN_LABI(str <F>,str <SIGF>)<br />
<br />
==[[Image:User1.gif|link=]]ENSEMBLE== <br />
; ENSEMBLE <MODLID> [PDB|CIF] <PDBFILE> [RMS <RMS><sup>1</sup> | ID <ID><sup>2</sup> | CARD ON<sup>3</sup>] ''CHAIN "<CHAIN>"<sup>4</sup> MODEL <NUM><sup>5</sup>''<br />
: The names of the PDB/CIF files used to build the ENSEMBLE, and either<br />
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
:: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file (e.g. "REMARK PHASER ENSEMBLE MODEL 1 ID 31.2") containing the superimposed models concatenated in the one file. This syntax enables simple automation of the use of ensembles. The pdb file can be non-standard because the atom list for the different models need not be the same.<br />
:: <sup>4</sup> CHAIN is selected from the pdb file. <br />
:: <sup>5</sup> MODEL number is selected from the pdb file.<br />
; ENSEMBLE <MODLID> HKLIN <MTZFILE> F=<F> PHI=<PHI> EXTENT <EX> <EY> <EZ> RMS <RMS> CENTRE <CX> <CY> <CZ> PROTEIN MW <PMW> NUCLEIC MW <NMW> ''CELL SCALE <SCALE>''<br />
: An ENSEMBLE defined from a map (via an mtz file). The molecular weight of the object the map represents is required for scaling. The effective RMS coordinate error is needed to judge how the map accuracy falls off with resolution. For density obtained from an EM image reconstruction, a good first guess would be to take the resolution where the FSC curve drops below 0.5 and divide by 3. The extent (difference between maximum and minimum x,y,z coordinates of region containing model density) is needed to determine reasonable rotation steps, and the centre is needed to carry out a proper interpolation of the molecular transform. The extent and the centre are both given in Ångstroms. The cell scale factor defaults to 1 and can be refined (for example, if the map is from electron microscopy when the cell scale may be unknown to within a few percent).<br />
; ENSEMBLE <MODLID> ATOM <TYPE> RMS <RMS><br />
: Define an ensemble as a single atom for single atom MR<br />
; ENSEMBLE <MODLID> HELIX <NUM> <br />
: Define an ensemble as a helix with NUM residues<br />
; ENSEMBLE <MODLID> HETATM [ON|OFF]<br />
: Use scattering from HETATM records in pdb file. See [[Molecular_Replacement#Coordinate_Editing | Coordinate Editing ]]<br />
; ENSEMBLE <MODLID> DISABLE CHECK [ON|OFF]<br />
: Toggle to disable checking of deviation between models in an ensemble. '''Use with extreme caution'''. Results of computations are not guaranteed to be sensible.<br />
; ENSEMBLE <MODLID> ESTIMATOR [OEFFNER | OEFFNERHI | OEFFNERLO | CHOTHIALESK ]<br />
: Define the estimator function for converting ID to RMS<br />
; ENSEMBLE <MODLID> PTGRP [COVERAGE | IDENTITY | RMSD | TOLANG | TOLSPC | EULER | SYMM ]<br />
: Define the pointgroup parameters <br />
; ENSEMBLE <MODLID> BINS [MIN <N>| MAX <M>| WIDTH <W> ]<br />
: Define the Fcalc reflection binning parameters <br />
; ENSEMBLE <MODLID> TRACE [PDB|CIF] <PDBFILE><br />
: Define the coordinates used for packing independent of the coordinates used for structure factor calculation<br />
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
:: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file <br />
; ENSEMBLE <MODLID> TRACE SAMPLING MIN <DIST> <br />
: Set the minimum distance for the sampling of packing grid<br />
; ENSEMBLE <MODLID> TRACE SAMPLING TARGET <NUM> <br />
: Set the target for the number of points to sample the smallest molecule to be packed<br />
; ENSEMBLE <MODLID> TRACE SAMPLING RANGE <NUM> <br />
: Target range (TARGET+/-RANGE) for search for hexgrid points in protein volume<br />
; ENSEMBLE <MODLID> TRACE SAMPLING USE [AUTO | ALL | CALPHA | HEXGRID ]<br />
: Sample trace coordinates using all atoms, C-alpha atoms, a hexagonal grid in the atomic volume or use an automatically determined choice<br />
; ENSEMBLE <MODLID> TRACE SAMPLING DISTANCE <DIST> <br />
: Set the distance for the sampling of the hexagonal grid explicitly and do not use TARGET to find default sampling distance<br />
; ENSEMBLE <MODLID> TRACE SAMPLING WANG <WANG> <br />
: Scale factor for the size of the Wang mask generated from an ensemble map<br />
; ENSEMBLE <MODLID> TRACE PDB <PDBFILE> <br />
: Use the given set of coordinates for packing rather than using the coordinates for structure factor calculation<br />
* Default: ENSEMBLE <MODLID> DISABLE CHECK OFF<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING MIN 1.0<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING TARGET 1000<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING RANGE 100<br />
addENSE_PDB_ID(str <MODLID>,str <FILE>,float <ID>) <br />
addENSE_PDB_RMS(str <MODLID>,str <FILE>,float <RMS>) <br />
setENSE_TRAC_SAMP_MIN(MODLID,float <MIN>)<br />
setENSE_TRAC_SAMP_TARG(MODLID,int <TARGET>)<br />
setENSE_TRAC_SAMP_RANG(MODLID,int <RANGE>)<br />
setENSE_TRAC_SAMP_USE(MODLID,str)<br />
setENSE_TRAC_SAMP_DIST(MODLID,float <DIST>)<br />
setENSE_TRAC_SAMP_WANG(MODLID,float <WANG>)r <FILE>,float <RMS>)<br />
addENSE_CARD(str <MODLID>,str <FILE>,bool)<br />
addENSE_MAP(str <MODLID>,str <MTZFILE>,str <F>,str <PHI>,dvect3 <EX EY EZ>,<br />
float <RMS>,dvect3 <CX CY CZ>,float <PMW>,float <NMW>,float <CELL>)<br />
setENSE_DISA_CHEC(bool)<br />
<br />
==[[Image:User1.gif|link=]]HKLIN==<br />
; HKLIN <FILENAME><br />
: The mtz file containing the data<br />
setHKLI(str <FILENAME>)<br />
<br />
==[[Image:User1.gif|link=]]JOBS== <br />
; JOBS <NUM><br />
: Number of processors to use in parallelized sections of code<br />
* Default: JOBS 2<br />
setJOBS(int <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]LABIN== <br />
; LABIN F = <F> SIGF = <SIGF> <br />
: Columns in mtz file. F must be given. SIGF should be given but is optional<br />
; LABIN I = <nowiki><I></nowiki> SIGI = <SIGI> <br />
: Columns in mtz file. I must be given. SIGI should be given but is optional<br />
; LABIN FMAP = <PH> PHMAP = <PHMAP> <br />
: Columns in mtz file. FMAP/PHMAP are weighted coefficients for use in the Phased Translation Function.<br />
; LABIN FMAP = <PH> PHMAP = <PHMAP> FOM = <FOM><br />
: Columns in mtz file. FMAP/PHMAP are unweighted coefficients for use in the Phased Translation Function and FOM the figure of merit for weighting<br />
setLABI_F_SIGF(str <F>,str <SIGF>)<br />
setLABI_I_SIGI(str <nowiki><I></nowiki>,str <SIGI>)<br />
setLABI_PTF(str <FMAP>,str <PHMAP>,str <FOM>)<br />
<br />
''Data should be input to python run-jobs using one data_refl parameter''<br />
''This is extracted from the ResultMR_DAT object after a call to runMR_DAT''<br />
setREFL_DATA(data_ref)<br />
''Example:''<br />
i = InputMR_DAT()<br />
i.setHKLI("*.mtz")<br />
i.setLABI_F_SIGF("F","SIGF")<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputMR_LLG()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.setREFL_DATA(r.getDATA())<br />
''See also: '' [[Python Example Scripts]]<br />
<br />
''Alternatively, reflection arrays can be set using cctbx::af::shared<double>''<br />
setREFL_F_SIGF(float_array <F>,float_array <SIGF>)<br />
setREFL_I_SIGI(float_array <nowiki><I></nowiki>,float_array <SIGI>)<br />
setREFL_PTF(float_array <FMAP>,float_array <PHMAP>,float_array <FOM>)<br />
<br />
==[[Image:User1.gif|link=]]MODE==<br />
; MODE [ ANO | CCA | SCEDS | NMAXYZ | NCS | MR_ELLG | MR_AUTO | MR_GYRE | MR_ATOM | MR_ROT | MR_TRA | MR_RNP | | MR_OCC | MR_PAK | EP_AUTO | EP_SAD]<br />
: The mode of operation of Phaser. The different modes are described in a separate page on [[Keyword Modes]]<br />
ResultANO r = runANO(InputANO)<br />
ResultCCA r = runCCA(InputCCA)<br />
ResultNMA r = runSCEDS(InputNMA)<br />
ResultNMA r = runNMAXYZ(InputNMA)<br />
ResultNCS r = runNCS(InputNCS)<br />
ResultELLG r = runMR_ELLG(InputMR_ELLG)<br />
ResultMR r = runMR_AUTO(InputMR_AUTO)<br />
ResultEP r = runMR_ATOM(InputMR_ATOM)<br />
ResulrMR_RF r = runMR_FRF(InputMR_FRF)<br />
ResultMR_TF r = runMR_FTF(InputMR_FTF)<br />
ResultMR r = runMR_RNP(InputMR_RNP)<br />
ResultGYRE r = runMR_GYRE(InputMR_RNP)<br />
ResultMR r = runMR_OCC(InputMR_OCC)<br />
ResultMR r = runMR_PAK(InputMR_PAK)<br />
ResultEP r = runEP_AUTO(InputEP_AUTO)<br />
ResultEP_SAD r = runEP_SAD(InputEP_SAD)<br />
<br />
==[[Image:User1.gif|link=]]PARTIAL== <br />
; PARTIAL PDB <PDBFILE> [RMSIDENTITY] <RMS_ID><br />
: The partial structure for MR-SAD substructure completion. Note that this must already be correctly placed, as the experimental phasing module will not carry out molecular replacement.<br />
; PARTIAL HKLIN <MTZFILE> [RMS|IDENTITY] <RMS_ID><br />
: The partial electron density for MR-SAD substructure completion.<br />
; PARTIAL LABIN FC=<FC> PHIC=<PHIC><br />
: Column labels for partial electron density for MR-SAD substructure completion.<br />
setPART_PDB(str <PDBFILE>)<br />
setPART_HKLI(str <MTZFILE>) <br />
setPART_LABI_FC(str <FC>)<br />
setPART_LABI_PHIC(str <PHIC>) <br />
setPART_VARI(str ["ID"|"RMS"])<br />
setPART_DEVI(float <RMS_ID>)<br />
<br />
==[[Image:User1.gif|link=]]SEARCH==<br />
; SEARCH ENSEMBLE <MODLID> ''{OR ENSEMBLE <MODLID>}… NUMBER <NUM><sup>*</sup>''<br />
: The ENSEMBLE to be searched for in a rotation search or an automatic search. When multiple ensembles are given using the OR keyword, the search is performed for each ENSEMBLE in turn. When the keyword is entered multiple times, each SEARCH keyword refers to a new component of the structure. If the component is present multiple times the sub-keyword NUMber can be used (rather than entering the same SEARCH keyword NUMber times).<br />
: <sup>*</sup>For automatic determination of search number use NUMBER 0. If the composition is entered, the maximum number will be that defined by the composition, otherwise the maximum number will fill the asymmetric unit to a minimum solvent content of 20%. Searches for new components will continue until the TFZ score is above 8, and terminate if the TFZ score drops below 8 before the placement of the maximum number of components.<br />
; SEARCH METHOD [FULL|FAST]<br />
: Search using the [[Modes#Modes |full search]] or [[Modes#Modes | fast search]] algorithms.<br />
; SEARCH ORDER AUTO [ON|OFF]<br />
: Search in the "best" order as estimated using estimated rms deviation and completeness of models.<br />
; SEARCH PRUNE [ON|OFF]<br />
: For high TFZ solutions that fail the packing test, carry out a sliding-window occupancy refinement and prune residues that refine to low occupancy, in an effort to resolve packing clashes. If this flag is set to true, the flag for keeping high tfz score solutions (see [[#PACK | PACK]]) that don't pack is also set to true (PACK KEEP HIGH TFZ ON).<br />
; SEARCH AMALGAMATE USE [ON|OFF]<br />
: For multiple high TFZ solutions, enable amalgamation into a single solution<br />
; SEARCH BFACTOR <BFAC><br />
: B-factor applied to search molecule (or atom).<br />
; SEARCH OFACTOR <OFAC><br />
: Occupancy factor applied to search molecule (or atom).<br />
* Default: SEARCH METHOD FAST<br />
* Default: SEARCH ORDER AUTO ON<br />
* Default: SEARCH PRUNE ON<br />
* Default: SEARCH AMALGAMATE USE ON<br />
* Default: SEARCH BFACTOR 0<br />
* Default: SEARCH OFACTOR 1<br />
addSEAR_ENSE_NUM(str <MODLID>,int <NUM>) <br />
addSEAR_ENSE_OR_ENSE_NUM(string_array <MODLIDS>,int <NUM>) <br />
setSEAR_METH(str [ "FULL" | "FAST" ])<br />
setSEAR_ORDE_AUTO(bool)<br />
setSEAR_PRUN(bool <PRUNE>)<br />
setSEAR_AMAL_USE(bool <AMAL>)<br />
setSEAR_BFAC(float <BFAC>)<br />
setSEAR_OFAC(float <OFAC>)<br />
<br />
==[[Image:User1.gif|link=]]SGALTERNATIVE==<br />
; SGALTERNATIVE SELECT [<sup>1</sup>ALL| <sup>2</sup>HAND| <sup>3</sup>LIST| <sup>4</sup>NONE]<br />
: Selection of alternative space groups to test in translation functions i.e. those that are in same laue group as that given in [[#SPACEGROUP | SPACEGROUP]]<br />
: <sup>1</sup> Test all possible space groups, <br />
: <sup>2</sup> Test the given space group and its enantiomorph.<br />
: <sup>3</sup> Test the space groups listed with SGALTERNATIVE TEST <SG>.<br />
: <sup>4</sup> Do not test alternative space groups.<br />
; SGALTERNATIVE TEST <SG><br />
: Alternative space groups to test. Multiple test space groups can be entered.<br />
* Default: SGALTERNATIVE SELECT HAND<br />
setSGAL_SELE(str [ "ALL" | "HAND" | "LIST" | "NONE" ]) <br />
addSGAL_TEST(str <SG>)<br />
<br />
==[[Image:User1.gif|link=]]SOLUTION==<br />
; SOLUTION SET <ANNOTATION><br />
: Start new set of solutions <br />
; SOLUTION TEMPLATE <ANNOTATION><br />
: Specifies a template solution against which other solutions in this run will be compared. Given in place of SOLUTION SET. Template rotation and translations given by subsequent SOLUTION 6DIM cards as per SOLUTION SETS.<br />
; SOLUTION 6DIM ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> [ORTH|FRAC] <X> <Y> <Z> ''FIXR [ON|OFF] FIXT [ON|OFF] FIXB [ON|OFF] BFAC <BFAC> MULT <MULT>''<br />
: This keyword is repeated for each known position and orientation of an ENSEMBLE MODLID. A B G are the Euler angles (z-y-z convention) and X Y Z are the translation elements, expressed either in orthogonal Angstroms (ORTH) or fractions of a cell edge (FRAC). The input ensemble is transformed by a rotation around the origin of the coordinate system, followed by a translation. BFAC default to 0, MULT (for multiplicity) defaults to 1.<br />
; SOLUTION ENSEMBLE <MODLID> VRMS DELTA <DELTA> RMSD <RMSD><br />
: Refined RMS variance terms for pdb files (or map) in ensemble MODLID. RMSD is the input RMSD of the job that produced the sol file, DELTA is the shift with respect to this RMSD. If given as part of a solution, these values overwrite the values used for input in the ENSEMBLE keyword (if refined).<br />
; SOLUTION ENSEMBLE <MODLID> CELL SCALE <SCALE><br />
: Refined cell scale factor. Only applicable to ensembles that are maps<br />
; SOLUTION TRIAL ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> RF <RF> RFZ <RFZ><br />
: Rotation List for translation function<br />
; SOLUTION ORIGIN ENSEMBLE <MODLID><br />
: Create solution for ensemble MODLID at the origin<br />
; SOLUTION SPACEGROUP <SG><br />
: Space Group of the solution (if alternative spacegroups searched)<br />
; SOLUTION RESOLUTION <HIRES><br />
: High resolution limit of data used to find/refine this solution<br />
; SOLUTION PACKS <PACKS><br />
: Flag for whether solution has been retained despite failing packing test, due to having high TFZ<br />
setSOLU(mr_solution <SOL>) <br />
addSOLU_SET(str <ANNOTATION>) <br />
addSOLU_TEMPLATE(str <ANNOTATION>) <br />
addSOLU_6DIM_ENSE(str <MODLID>,dvect3 <A B C>,bool <FRAC>,dvect3 <X Y Z>,<br />
float <BFAC>,bool <FIXR>,bool <FIXT>,bool <FIXB>,int <MULT>, 1.0) <br />
addSOLU_ENSE_DRMS(str <MODLID>, float <DRMS>) <br />
addSOLU_ENSE_CELL(str <MODLID>, float <SCALE>)<br />
addSOLU_TRIAL_ENSE(string <MODLID>,dvect3 <A B C>,float <RF>, float <RFZ>)<br />
addSOLU_ORIG_ENSE(string <MODLID>)<br />
setSOLU_SPAC(str <SG>)<br />
setSOLU_RESO(float <HIRES>)<br />
setSOLU_PACK(bool <PACKS>)<br />
<br />
==[[Image:User1.gif|link=]]SPACEGROUP==<br />
; SPACEGROUP <SG><br />
: Space group may be altered from the one on the MTZ file to a space group in the same point group. The space group can be entered in one of three ways<br />
#The Hermann-Mauguin symbol e.g. P212121 or P 21 21 21 (with or without spaces)<br />
#The international tables number, which gives standard setting e.g. 19 <br />
#The Hall symbols e.g. P 2ac 2ab<br />
: '''The space group can also be a subgroup of the merged space group'''. For example, P1 is always allowed. The reflections will be expanded to the symmetry of the given subgroup. This is only a valid approach when the true symmetry is the symmetry of the subgroup and perfect twinning causes the data to merge "perfectly" in the higher symmetry. <br />
:'''A list of the allowed space groups in the same point group as the given space group (or space group read from MTZ file) and allowed subgroups of these is given in the Cell Content Analysis logfile.'''<br />
* Default: Read from MTZ file<br />
setSPAC_NUM(int <NUM>)<br />
setSPAC_NAME(string <HM>)<br />
setSPAC_HALL(string <HALL>)<br />
<br />
==[[Image:User1.gif|link=]]WAVELENGTH== <br />
; WAVELENGTH <LAMBDA> <br />
: The wavelengh at which the SAD dataset was collected<br />
setWAVE(float <LAMBDA>)<br />
<br><br />
<br><br />
<br />
=Output Control Keywords=<br />
==[[Image:Output.png|link=]]DEBUG== <br />
; DEBUG [ON|OFF]<br />
: Extra verbose output for debugging<br />
* Default: DEBUG OFF<br />
setDEBU(bool) <br />
<br />
==[[Image:Output.png|link=]]EIGEN==<br />
; EIGEN WRITE [ON|OFF]<br />
; EIGEN READ <EIGENFILE><br />
: Read or write a file containing the eigenvectors and eigenvalues. If reading, the eigenvalues and eigenvectors of the Hessian are read from the file generated by a previous run, rather than calculated. This option must be used with the job that generated the eigenfile and the job reading the eigenfile must have identical input for the ENM parameters. Use WRITE to control whether or not the eigenfile is written when not using the READ mode.<br />
* Default: EIGEN WRITE ON<br />
setEIGE_WRIT(bool)<br />
setEIGE_READ(str <EIGENFILE>)<br />
<br />
==[[Image:Output.png|link=]]HKLOUT== <br />
; HKLOUT [ON|OFF]<br />
: Flags for output of an mtz file containing the phasing information<br />
* Default: HKLOUT ON<br />
setHKLO(bool) <br />
<br />
==[[Image:Output.png|link=]]KEYWORDS== <br />
; KEYWORDS [ON|OFF]<br />
: Write output Phaser .sol file (.rlist file for rotation function)<br />
* Default: KEYWORDS ON<br />
setKEYW(bool)<br />
<br />
==[[Image:Output.gif|link=]]LLGMAPS==<br />
; LLGMAPS [ON|OFF]<br />
: Write log-likelihood gradient map coefficients to MTZ file<br />
* Default: LLGMAPS OFF<br />
setLLGM(bool <True|False>)<br />
<br />
==[[Image:Output.png|link=]]MUTE== <br />
; MUTE [ON|OFF]<br />
: Toggle for running in silent/mute mode, where no logfile is written to ''standard output''.<br />
* Default: MUTE OFF<br />
setMUTE(bool) <br />
<br />
==[[Image:Output.png|link=]]KILL== <br />
; KILL TIME [MINS]<br />
: Kill Phaser after MINS minutes of CPU have elapsed, provided parallel section is complete<br />
; KILL FILE [FILENAME]<br />
: Kill Phaser if file FILENAME is present, provided parallel section is complete<br />
* Default: KILL TIME 0 ''Phaser runs to completion''<br />
* Detaulf: KILL FILE "" ''Phaser runs to completion''<br />
setKILL_TIME(float) <br />
setKILL_FILE(string)<br />
<br />
==[[Image:Output.png|link=]]OUTPUT== <br />
; OUTPUT LEVEL [SILENT|CONCISE|SUMMARY|LOGFILE|VERBOSE|DEBUG]<br />
: Output level for logfile<br />
; OUTPUT LEVEL [0|1|2|3|4|5]<br />
: Output level for logfile (equivalent to keyword level setting)<br />
* Default: OUTPUT LEVEL LOGFILE<br />
setOUTP_LEVE(string)<br />
setOUTP(enum)<br />
<br />
==[[Image:Output.png|link=]]TITLE==<br />
; TITLE <TITLE><br />
: Title for job<br />
* Default: TITLE [no title given]<br />
setTITL(str <TITLE>)<br />
<br />
==[[Image:Output.png|link=]]TOPFILES== <br />
; TOPFILES <NUM><br />
: Number of top pdbfiles or mtzfiles to write to output.<br />
* Default: TOPFILES 1<br />
setTOPF(int <NUM>) <br />
<br />
==[[Image:Output.png|link=]]ROOT== <br />
; ROOT <FILEROOT><br />
: Root filename for output files (e.g. FILEROOT.log)<br />
* Default: ROOT PHASER<br />
setROOT(string <FILEROOT>)<br />
<br />
==[[Image:Output.png|link=]]VERBOSE== <br />
; VERBOSE [ON|OFF] <br />
: Toggle to send verbose output to log file.<br />
* Default: VERBOSE OFF<br />
setVERB(bool) <br />
<br />
==[[Image:Output.png|link=]]XYZOUT== <br />
; XYZOUT [ON|OFF] ''ENSEMBLE [ON|OFF]<sup>1</sup> PACKING [ON|OFF]<sup>2</sup>''<br />
: Toggle for output coordinate files. <br />
::<sup>1</sup> If the optional ENSEMBLE keyword is ON, then each placed ensemble is written to its own pdb file. The files are named FILEROOT.#.#.pdb with the first # being the solution number and the second # being the number of the placed ensemble (representing a SOLU 6DIM entry in the .sol file). <br />
::<sup>2</sup> If the optional PACKING keyword is ON, then the hexagonal grid used for the packing analysis is output to its own pdb file FILEROOT.pak.pdb<br />
* Default: XYZOUT OFF (Rotation functions)<br />
* Default: XYZOUT ON ENSEMBLE OFF (all other relevant modes)<br />
* Default: XYZOUT ON PACKING OFF (all other relevant modes)<br />
setXYZO(bool) <br />
setXYZO_ENSE(bool)<br />
setXYZO_PACK(bool)<br />
<br><br />
<br><br />
<br />
=Advanced Keywords=<br />
==[[Image:User2.gif|link=]]ELLG==<br />
([[Molecular_Replacement#Should_Phaser_Solve_It.3F|explained here]])<br />
; ELLG TARGET <TARGET><br />
: Target value for expected LLG for determining resolution limits and search order<br />
<!--; ELLG HIRES <HIRES> Internal control only--><br />
* Default: ELLG TARGET 225<br />
setELLG_TARG(float <TARGET>)<br />
<br />
==[[Image:User2.gif|link=]]FORMFACTORS==<br />
; FORMFACTORS [XRAY | ELECTRON | NEUTRON]<br />
: Use scattering factors from x-ray, electron or neutrons<br />
* Default: FORMFACTORS XRAY<br />
setFORM(string XRAY)<br />
<br />
==[[Image:User2.gif|link=]]HAND==<br />
; HAND [ <sup>1</sup>ON| <sup>2</sup>OFF| <sup>3</sup>BOTH]<br />
: Hand of heavy atoms for experimental phasing<br />
: <sup>1</sup>Phase using the other hand of heavy atoms <br />
: <sup>2</sup>Phase using given hand of heavy atoms <br />
: <sup>3</sup>Phase using both hands of heavy atoms<br />
* Default: HAND BOTH<br />
setHAND(str [ "OFF" | "ON" | "BOTH" ])<br />
<br />
==[[Image:User2.gif|link=]]LLGCOMPLETE==<br />
; LLGCOMPLETE COMPLETE [ON|OFF]<br />
: Toggle for structure completion by log-likelihood gradient maps<br />
; LLGCOMPLETE SCATTERER <TYPE> <br />
: Atom/Cluster type(s) to be used for log-likelihood gradient completion. If more than one element is entered for log-likelihood gradient completion, the atom type that gives the highest Z-score for each peak is selected. Type = "RX" is a purely real scatterer and type="AX" is purely anomalous scatterer<br />
; LLGCOMPLETE REAL ON<br />
: Use a purely real scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER RX)<br />
; LLGCOMPLETE ANOMALOUS ON<br />
: Use a purely anomalous scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER AX)<br />
; LLGCOMPLETE CLASH <CLASH> <br />
: Minimum distance between atoms in log-likelihood gradient maps and also the distance used for determining anisotropy of atoms (default determined by resolution, flagged by CLASH=0)<br />
; LLGCOMPLETE SIGMA <Z><br />
: Z-score (sigma) for accepting peaks as new atoms in log-likelihood gradient maps<br />
; LLGCOMPLETE NCYC <NMAX><br />
: Maximum number of cycles of log-likelihood gradient structure completion. By default, NMAX is 50, but this limit should never be reached, because all features in the log-likelihood gradient maps should be assigned well before 50 cycles are finished. This keyword should be used to reduce the number of cycles to 1 or 2.<br />
; LLGCOMPLETE METHOD [IMAGINARY|ATOMTYPE]<br />
: Pick peaks from the imaginary map only or from all the completion atomtype maps.<br />
* Default: LLGCOMPLETE COMPLETE OFF<br />
* Default: LLGCOMPLETE CLASH 0<br />
* Default: LLGCOMPLETE SIGMA 6<br />
* Default: LLGComplete NCYC 50<br />
* Default: LLGComplete METHOD ATOMTYPE<br />
setLLGC_COMP(bool <True|False>) <br />
setLLGC_CLAS(float <CLASH>) <br />
setLLGC_SIGM(float <Z>) <br />
setLLGC_NCYC(int <NMAX>)<br />
setLLGC_METH(str ["IMAGINARY"|"ATOMTYPE"])<br />
<br />
==[[Image:User2.gif|link=]]NMA== <br />
; NMA MODE <M1> ''{MODE <M2>…}'' <br />
: The MODE keyword gives the mode along which to perturb the structure. If multiple modes are entered, the structure is perturbed along all the modes AND combinations of the modes given. There is no limit on the number of modes that can be entered, but the number of pdb files explodes combinatorially. The first 6 modes are the pure rotation and translation modes and do not lead to perturbation of the structure. If the number M is less than 7 then M is interpreted as the first M modes starting at 7, so for example, MODE 5 would give modes 7 8 9 10 11.<br />
; NMA COMBINATION <NMAX><br />
: Controls how many modes are present in any combination.<br />
* Default: NMA MODE 5<br />
* Default: NMA COMBINATION 2<br />
addNMA_MODE(int <MODE>) <br />
setNMA_COMB(int <NMAX>)<br />
<br />
==[[Image:User2.gif|link=]]PACK==<br />
; PACK SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>ALL ]<br />
: <sup>1</sup>Allow up to the PERCENT of sampling points to clash, considering only pairwise clashes <br />
: <sup>2</sup>Allow all solutions (no packing test)<br />
; PACK CUTOFF <PERCENT> <br />
: Limit on total number (or percent) of clashes <br />
; PACK QUICK [ON|OFF]<br />
: Packing check stops when ALLOWED_CLASHES or MAX_CLASHES is reached. However, all clashes are found when the solution has a high Z-score (see [[#ZSCORE | ZSCORE]]).<br />
; PACK COMPACT [ON|OFF]<br />
: Pack ensembles into a compact association (minimize distances between centres of mass for the addition of each component in a solution).<br />
; PACK KEEP HIGH TFZ [ON|OFF]<br />
: Solutions with high tfz (see [[#ZSCORE | ZSCORE]]) but that fail to pack are retained in the solution list. Set to true if SEARCH PRUNE ON (see [[#SEARCH | SEARCH]])<br />
* Default: PACK SELECT PERCENT<br />
* Default: PACK CUTOFF 5<br />
* Default: PACK COMPACT ON<br />
* Default: PACK QUICK ON<br />
* Default: PACK KEEP HIGH TFZ OFF<br />
* Default: PACK CONSERVATION DISTANCE 1,5<br />
setPACK_SELE(str ["PERCENT"|"ALL"]) <br />
setPACK_CUTO(float <ALLOWED_CLASHES>)<br />
setPACK_QUIC(bool)<br />
setPACK_KEEP_HIGH_TFZ(bool)<br />
setPACK_COMP(bool)<br />
<br />
==[[Image:User2.gif|link=]]PEAKS==<br />
; PEAKS TRA SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL] <br />
; PEAKS ROT SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL]<br />
: Peaks for individual rotation functions (ROT) or individual translation functions (TRA) satisfying selection criteria are saved. To be used for subsequent steps, peaks must also satisfy the overall [[#PURGE | PURGE]] selection criteria, so it will usually be appropriate to set only the PURGE criteria (which over-ride the defaults for the PEAKS criteria if not explicitly set). See [[Molecular_Replacement#How_to_Select_Peaks | How to Select Peaks]]<br />
: <sup>1</sup> Select peaks by taking all peaks over CUTOFF percent of the difference between the top peak and the mean value.<br />
: <sup>2</sup> Select peaks by taking all peaks with a Z-score greater than CUTOFF.<br />
: <sup>3</sup> Select peaks by taking top CUTOFF.<br />
: <sup>4</sup> Select all peaks.<br />
; PEAKS ROT CUTOFF <CUTOFF><br />
; PEAKS TRA CUTOFF <CUTOFF><br />
: Cutoff value for the rotation function (ROT) or translation function (TRA) peak selection criteria.<br />
: If selection is by percent and [[#PURGE | PURGE PERCENT]] is changed from the default, then the PEAKS percent value is set to the lower PURGE percent value.<br />
; PEAKS ROT CLUSTER [ON|OFF] <br />
; PEAKS TRA CLUSTER [ON|OFF]<br />
: Toggle selects clustered or unclustered peaks for rotation function (ROT) or translation function (TRA).<br />
; PEAKS ROT DOWN [PERCENT] <br />
: [[#SEARCH | SEARCH METHOD FAST]] only. Percentage to reduce rotation function cutoff if there is no TFZ over the zscore cutoff that determines a true solution (see [[#ZSCORE | ZSCORE]]) in first search.<br />
* Default: PEAKS ROT SELECT PERCENT<br />
* Default: PEAKS TRA SELECT PERCENT<br />
* Default: PEAKS ROT CUTOFF 75<br />
* Default: PEAKS TRA CUTOFF 75<br />
* Default: PEAKS ROT CLUSTER ON<br />
* Default: PEAKS TRA CLUSTER ON<br />
setPEAK_ROTA_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"]) <br />
setPEAK_TRAN_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"])<br />
setPEAK_ROTA_CUTO(float <CUTOFF>)<br />
setPEAK_TRAN_CUTO(float <CUTOFF>) <br />
setPEAK_ROTA_CLUS(bool <CLUSTER>) <br />
setPEAK_TRAN_CLUS(bool <CLUSTER>)<br />
setPEAK_ROTA_DOWN(float <PERCENT>)<br />
<br />
==[[Image:User2.gif|link=]]PERMUTATIONS== <br />
; PERMUTATIONS [ON|OFF]<br />
: Only relevant to [[#SEARCH | SEARCH METHOD FULL]]. Toggle for whether the order of the search set is to be permuted.<br />
* Default: PERMUTATIONS OFF<br />
setPERM(bool <PERMUTATIONS>)<br />
<br />
==[[Image:User2.gif|link=]]PERTURB== <br />
; PERTURB RMS STEP <RMS><br />
: Increment in rms Ångstroms between pdb files to be written. <br />
; PERTURB RMS MAX <MAXRMS><br />
: The structure will be perturbed along each mode until the MAXRMS deviation has been reached.<br />
; PERTURB RMS DIRECTION [FORWARD|BACKWARD|TOFRO] <br />
: The structure is perturbed either forwards or backwards or to-and-fro (FORWARD|BACKWARD|TOFRO) along the eigenvectors of the modes specified.<br />
; PERTURB INCREMENT [RMS| DQ] <br />
: Perturb the structure by rms devitations along the modes, or by set dq increments<br />
; PERTURB DQ <DQ1> ''{DQ <DQ2>…}''<br />
: Alternatively, the DQ factors (as used by the Elnemo server (K. Suhre & Y-H. Sanejouand, NAR 2004 vol 32) ) by which to perturb the atoms along the eigenvectors can be entered directly.<br />
* Default: PERTURB INCREMENT RMS<br />
* Default: PERTURB RMS STEP 0.2<br />
* Default: PERTURB RMS MAXRMS 0.3<br />
* Default: PERTURB RMS DIRECTION TOFRO<br />
setPERT_INCR(str [ "RMS" | "DQ" ])<br />
setPERT_RMS_MAXI(float <MAX>)<br />
setPERT_RMS_DIRE(str [ "FORWARDS" | "BACKWARDS" | "TOFRO" ]) <br />
addPERT_DQ(float <DQ>)<br />
<br />
==[[Image:User2.gif|link=]]PURGE== <br />
; PURGE ROT ENABLE [ON|OFF]<sup>1</sup><br />
; PURGE ROT PERCENT <PERC><sup>2</sup><br />
; PURGE ROT NUMBER <NUM><sup>3</sup><br />
: Purging criteria for rotation function (RF), where PERCENT and NUMBER are alternative selection criteria (''OR'' criteria)<br />
::<sup>1</sup> Toggle for whether to purge the solution list from the RF according to the top solution found. If there are a number of RF searches with different partial solution backgrounds, the PURGE is applied to the total list of peaks. If there is one clearly significant RF solution from one of the backgrounds it acts to purge all the less significant solutions. If there is only one RF (a single partial solution background) the PURGE gives no additional selection over and above the PEAKS command. <br />
::<sup>2</sup> [[Molecular_Replacement#How_to_Select_Peaks | Selection by percent]]. PERC is percentage of the top peak, where the value of the top peak is defined as 100% and the value of the mean is defined as 0%. Note that this criterion is applied subsequent to any selection criteria applied through the [[#PEAKS | PEAKS]] command. If the [[#PEAKS | PEAKS]] selection is by percent, then the percent cutoff given in the PURGE command over-rides that for [[#PEAKS | PEAKS]], so as to rationalize results in the case of only a single RF (single partial solution background.)<br />
::<sup>3</sup> NUM is the number of solutions to retain in purging. If NUMBER is given (non-zero) it overrides the PERCENT option. NUMBER given as zero is the flag for not applying this criterion.<br />
; PURGE TRA ENABLE [ON|OFF]<br />
; PURGE TRA PERCENT <PERC><br />
; PURGE TRA NUMBER <NUM><br />
: As above, but for translation function<br />
; PURGE RNP ENABLE [ON|OFF]<br />
; PURGE RNP PERCENT <PERC><br />
; PURGE RNP NUMBER <NUM><br />
: As above but for refinement, but with the important distinction that PERCENT and NUMBER are concurrent selection criteria (''AND'' criteria)<br />
* Default: PURGE ROT ENABLE ON <br />
* Default: PURGE ROT PERC 75<br />
* Default: PURGE ROT NUM 0<br />
* Default: PURGE TRA ENABLE ON<br />
* Default: PURGE TRA PERC 75<br />
* Default: PURGE TRA NUM 0<br />
* Default: PURGE RNP ENABLE ON<br />
* Default: PURGE RNP PERC 75<br />
* Default: PURGE RNP NUM 0<br />
setPURG_ROTA_ENAB(bool <ENABLE>)<br />
setPURG_TRAN_ENAB(bool <ENABLE>) <br />
setPURG_RNP_ENAB(bool <ENABLE>)<br />
setPURG_ROTA_PERC(float <PERC>) <br />
setPURG_TRAN_PERC(float <PERC>) <br />
setPURG_RNP_PERC(float <PERC>)<br />
setPURG_ROTA_NUMB(float <NUM>) <br />
setPURG_TRAN_NUMB(float <NUM>)<br />
setPURG_TRAN_NUMB(float <NUM>)<br />
setPURG_RNP_NUMB(float <NUM>)<br />
<br />
==[[Image:User2.gif|link=]]RESOLUTION== <br />
; RESOLUTION HIGH <HIRES> <br />
: High resolution limit in Ångstroms. For all data use RESOLUTION 0.1 as RESOLUTION 0 indicates default (ELLG selection)<br />
; RESOLUTION LOW <LORES><br />
: Low resolution limit in Ångstroms.<br />
; RESOLUTION AUTO HIGH <HIRES> <br />
: High resolution limit in Ångstroms for final high resolution refinement in MR_AUTO mode.<br />
* Default for molecular replacement: Set by [[#ELLG | ELLG TARGET]] for structure solution, final refinement uses all data<br />
* Default for experimental phasing: All data used<br />
setRESO_HIGH(float <HIRES>) <br />
setRESO_LOW(float <LORES>)<br />
setRESO_AUTO_HIGH(float <HIRES>) <br />
setRESO(float <HIRES>,float <LORES>)<br />
<br />
==[[Image:User2.gif|link=]]ROTATE== <br />
; ROTATE VOLUME FULL<br />
: Sample all unique angles <br />
; ROTATE VOLUME AROUND EULER <A> <nowiki><B></nowiki> <C> RANGE <RANGE> <br />
: Restrict the search to the region of +/- RANGE degrees around orientation given by EULER<br />
setROTA_VOLU(string ["FULL"|"AROUND"|) <br />
setROTA_EULE(dvect3 <A B C>) <br />
setROTA_RANG(float <RANGE>)<br />
<br />
==[[Image:User2.gif|link=]]SCATTERING==<br />
; SCATTERING TYPE <TYPE> FP=<FP> FDP=<FDP> FIX [ON|OFF|EDGE]<br />
: Measured scattering factors for a given atom type, from a fluorescence scan. FIX EDGE (default) fixes the fdp value if it is away from an edge, but refines it if it is close to an edge, while FIX ON or FIX OFF does not depend on proximity of edge.<br />
; SCATTERING RESTRAINT [ON|OFF]<br />
: use Fdp restraints<br />
; SCATTERING SIGMA <SIGMA><br />
: Fdp restraint sigma used is SIGMA multiplied by initial fdp value<br />
* Default: SCATTERING SIGMA 0.2<br />
* Default: SCATTERING RESTRAINT ON<br />
addSCAT(str <TYPE>,float <FP>,float <FDP, string <FIXFDP>) <br />
setSCAT_REST(bool) <br />
setSCAT_SIGM(float <SIGMA>)<br />
<br />
==[[Image:User2.gif|link=]]SCEDS== <br />
; SCEDS NDOM <NDOM><br />
:Number of domains into which to split the protein<br />
; SCEDS WEIGHT SPHERICITY <WS><br />
: Weight factor for the the Density Test in the SCED Score. The Sphericity Test scores boundaries that divide the protein into more spherical domains more highly.<br />
; SCEDS WEIGHT CONTINUITY <WC><br />
: Weight factor for the the Continuity Test in the SCED Score. The Continuity Test scores boundaries that divide the protein into domains contigous in sequence more highly. <br />
; SCEDS WEIGHT EQUALITY <WE><br />
: Weight factor for the the Equality Test in the SCED Score. The Equality Test scores boundaries that divide the protein more equally more highly.<br />
; SCEDS WEIGHT DENSITY <WD><br />
: Weight factor for the the Equality Test in the SCED Score. The Density Test scores boundaries that divide the protein into domains more densely packed with atoms more highly. <br />
* Default: SCEDS NDOM 2<br />
* Default: SCEDS WEIGHT EQUALITY 1<br />
* Default: SCEDS WEIGHT SPHERICITY 4 <br />
* Default: SCEDS WEIGHT DENSITY 1<br />
* Default: SCEDS WEIGHT CONTINUITY 0<br />
setSCED_NDOM(int <NDOM>) <br />
setSCED_WEIG_SPHE(float <WS>) <br />
setSCED_WEIG_CONT(float <WC>)<br />
setSCED_WEIG_EQUA(float <WE>) <br />
setSCED_WEIG_DENS(float <WD>)<br />
<br />
==[[Image:User2.gif|link=]]TARGET==<br />
; TARGET ROT [FAST | BRUTE]<br />
: Target function for fast rotation searches (2). BRUTE searches all angles on a grid with the full rotation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these rotations with the full rotation likelihood target.<br />
; TARGET TRA [FAST | BRUTE | PHASED]<br />
: Target function for fast translation searches (3). BRUTE searches all positions on a grid with the full translation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these positions with the full translation likelihood target. PHASED selects the "phased translation function", for which a LABIN command should also be given, specifying FMAP, PHMAP and (optionally) FOM.<br />
* Default: TARGET ROT FAST<br />
* Default: TARGET TRA FAST<br />
setTARG_ROTA(str ["FAST"|"BRUTE"])<br />
setTARG_TRAN(str ["FAST"|"BRUTE"|"PHASED"])<br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS NMOL <NMOL><br />
: Number of molecules/molecular assemblies related by single TNCS vector (usually only 2). If the TNCS is a pseudo-tripling of the cell then NMOL=3, a pseudo-quadrupling then NMOL=4 etc.<br />
* Default: TNCS NMOL 2<br />
setTNCS_NMOL(int <NMOL>)<br />
<br><br />
<br />
==[[Image:User2.gif|link=]]TRANSLATION== <br />
; TRANSLATION VOLUME [ <sup>1</sup>FULL | <sup>2</sup>REGION | <sup>3</sup>LINE | <sup>4</sup>AROUND ])<br />
: Search volume for brute force translation function.<br />
: <sup>1</sup> Cheshire cell or Primitive cell volume. <br />
: <sup>2</sup> Search region.<br />
: <sup>3</sup> Search along line. <br />
: <sup>4</sup> Search around a point.<br />
; <sup>1 2 3</sup>TRANSLATION START <X Y Z> <br />
; <sup>1 2 3</sup>TRANSLATION END <X Y Z><br />
: Search within region or line bounded by START and END.<br />
; <sup>4</sup>TRANSLATION POINT <X Y Z><br />
; <sup>4</sup>TRANSLATION RANGE <RANGE><br />
: Search within +/- RANGE Ångstroms (not fractional coordinates, even if the search point is given as fractional coordinates) of a point <X Y Z>.<br />
; TRANSLATION [ORTH | FRAC]<br />
: Coordinates are given in orthogonal or fractional values.<br />
; TRANSLATION PACKING USE [ON | OFF]<br />
: Top translation function peak will be testes for packing.<br />
; TRANSLATION PACKING CUTOFF <PERC><br />
: Percent pairwise packing used for packing function test of top TF peak. Equivalent to PACK CUTOFF <PERC> for packing function. <br />
; TRANSLATION PACKING NUM <NUM><br />
: Number of translation function peaks to test for packing before bailing out of packing test. Set to 0 to pack all translation function peaks (slow for large packing volumes). <br />
* Default: TRANSLATION VOLUME FULL<br />
* Default: TRANSLATION PACK CUTOFF 50<br />
* Default: TRANSLATION PACK NUM 0 (helices - all packing checked)<br />
* Default: TRANSLATION PACK NUM 500 (non-helices)<br />
setTRAN_VOLU(string ["FULL"|"REGION"|"LINE"|"AROUND"])<br />
setTRAN_START(dvect <START>)<br />
setTRAN_END(dvect <END>)<br />
setTRAN_POINT(dvect <POINT>)<br />
setTRAN_RANGE(float <RANGE>)<br />
setTRAN_FRAC(bool <True=FRAC False=ORTH>)<br />
setTRAN_PACK_USE(bool)<br />
setTRAN_PACK_CUTO(float)<br />
<br />
==[[Image:User2.gif|link=]]ZSCORE== <br />
; ZSCORE USE [ON|OFF]<br />
: Use the TFZ tests. Only applicable with [[#SEARCH | SEARCH METHOD FAST]]. (Note Phaser-2.4.0 and below use "ZSCORE SOLVED 0" to turn off the TFZ tests)<br />
; ZSCORE SOLVED <ZSCORE_SOLVED><br />
: Set the minimum TFZ that indicates a definite solution for amalgamating solutions in FAST search method. <br />
;ZSCORE STOP [ON|OFF]<br />
: Stop adding components beyond point where TFZ is below cutoff when adding multiple components in FAST mode. However, FAST mode will always add one component even if TFZ is below cutoff, or two components if starting search with no components input (no input solution).<br />
; ZSCORE HALF [ON|OFF]<br />
: Set the TFZ for amalgamating solutions in the FAST search method to the maximum of ZSCORE_SOLVED and half the maximum TFZ, to accommodate cases of partially correct solutions in very high TFZ cases (e.g. TFZ > 16)<br />
* Default: ZSCORE USE ON<br />
* Default: ZSCORE SOLVED 8<br />
* Default: ZSCORE HALF ON<br />
* Default: ZSCORE STOP ON<br />
setZSCO_USE(bool <True=ON False=OFF>)<br />
setZSCO_SOLV(floatType ZSCORE_SOLVED)<br />
setZSCO_HALF(bool <True=ON False=OFF>)<br />
setZSCO_STOP(bool <True=ON False=OFF>)<br />
<br><br />
<br><br />
<br />
=Expert Keywords=<br />
<br />
==[[Image:Expert.gif|link=]]MACANO== <br />
; MACANO PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for the refinement of SigmaN in the anisotropy correction<br />
; MACANO ANISO [ON|OFF] BINS [ON|OFF] SOLK [ON|OFF] SOLB [ON|OFF] ''{NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}''<br />
: Macrocycle for the custom refinement of SigmaN in the anisotropy correction. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACANO PROTOCOL DEFAULT<br />
setMACA_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACA(bool <ANISO>,bool <BINS>,bool <SOLK>,bool <SOLB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACMR== <br />
; MACMR PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACMR ROT [ON|OFF] TRA [ON|OFF] BFAC [ON|OFF] VRMS [ON|OFF] ''CELL [ON|OFF] LAST [ON|OFF] NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of molecular replacement solutions. Macrocycles are performed in the order in which they are entered. For description of VRMS see the [[FAQ]]. CELL is the scale factor for the unit cell for maps (EM maps). LAST is a flag that refines the parameters for the last component of a solution only, fixing all the others.<br />
; MACMR CHAINS [ON|OFF]<br />
: Split the ensembles into chains for refinement<br />
: Not possible as part of an automated mode<br />
* Default: MACMR PROTOCOL DEFAULT<br />
* Default: MACMR CHAINS OFF<br />
setMACM_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACM(bool <ROT>,bool <TRA>,bool <BFAC>,bool <VRMS>,bool <CELL>,bool <LAST>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
setMACM_CHAI(bool])<br />
<br />
==[[Image:Expert.gif|link=]]MACOCC== <br />
; MACOCC PROTOCOL [ DEFAULT | CUSTOM | OFF | ALL ]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACOCC NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of occupancy for solutions. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACOCC PROTOCOL DEFAULT<br />
setMACO_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACO(int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACGYRE== <br />
; MACGYRE PROTOCOL [ DEFAULT | CUSTOM | OFF | ALL ]<br />
: Protocol for refinement of gyre rotations<br />
; MACGYRE ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] ''ANCHOR [ON|OFF] SIGROT <SIGR> SIGTRA <SIGT> NCYCLE <NCYC> MINIMIZER [ BFGS | NEWTON | DESCENT ]''<br />
: Macrocycle for custom refinement of occupancy for solutions. Macrocycles are performed in the order in which they are entered.<br />
; MACGYRE SIGROT <SIGROT> <br />
; MACGYRE SIGTRA <SIGTRA> <br />
; MACGYRE ANCHOR [ON|OFF]<br />
: Override default values for harmonic restraints for rotation and translation refinement, and whether or not to anchor one fragment (no translation) for all macrocycles<br />
* Default: MACGYRE PROTOCOL DEFAULT<br />
setMACG_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACG(bool <REF>,bool <REF>, bool <REF>)<br />
addMACG_FULL(bool <REF>,bool <REF>,bool<REF>,bool <ANCHOR>,float <SIGROT>,float <SIGTRA>,int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
setMACG_SIGR(bool <SIGROT>)<br />
setMACG_SIGT(bool <SIGTRA>)<br />
setMACG_ANCH(bool <ANCHOR>)<br />
<br />
==[[Image:Expert.gif|link=]]MACSAD== <br />
; MACSAD PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for SAD refinement.<br />
:''n.b. PROTOCOL ALL will crash phaser and is only useful for debugging - see code for details''<br />
; MACSAD XYZ [ON|OFF] OCC [ON|OFF] BFAC [ON|OFF] FDP [ON|OFF] SA [ON|OFF] SB [ON|OFF] SP [ON|OFF] SD [ON|OFF] ''{PK [ON|OFF]} {PB [ON|OFF]} {NCYCLE <NCYC>} MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for SAD refinement. Macrocycles are performed in the order in which they are entered.<br />
*Default: MACSAD PROTOCOL DEFAULT<br />
setMACS_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACS(<br />
bool <XYZ>,bool <OCC>,bool <BFAC>,bool <FDP><br />
bool <SA>,bool <SB>,bool <SP>,bool <SD>,<br />
bool <PK>, bool <PB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACTNCS== <br />
; MACTNCS PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for pseudo-translational NCS refinement.<br />
; MACTNCS ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] ''NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for pseudo-translational NCS refinement. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACTNCS PROTOCOL DEFAULT<br />
setMACT_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACT(bool <ROT>,bool <TRA>,bool <VRMS>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]OCCUPANCY== <br />
; OCCUPANCY WINDOW ELLG <ELLG><br />
: Target eLLG for determining number of residues in window for occupancy refinement. The number of residues in a window will be an odd number. Occupancy refinement will be done for each offset of the refinement window.<br />
; OCCUPANCY WINDOW NRES <NRES><br />
: As an alternative to using the eLLG to define the number of residues in window for occupancy refinement, the number may be input directly. NRES must be an odd number.<br />
; OCCUPANCY WINDOW MAX <NRES><br />
: Maximum number of residues in an occupancy window (determined either by ellg or given as NRES) for which occupancy is refined. Prevents the refinement windows from spanning non-local regions of space.<br />
; OCCUPANCY MIN <MINOCC> MAX <MAXOCC><br />
: Minimum and maximum values of occupancy during refinement.<br />
; OCCUPANCY MERGE [ON/OFF]<br />
: Merge refined occupancies from different window offsets to give final occupancies per residue. If OFF, occupancies from a single window offset will be used, selected using OCCUPANCY OFFSET <N><br />
; OCCUPANCY FRAC <FRAC><br />
: Minimum fraction of the protein for which the occupancy may be set to zero.<br />
; OCCUPANCY OFFSET <N><br />
: If OCCUPANCY MERGE OFF, then <N> defines the single window offset from which final occupancies will be taken<br />
* Default: OCCUPANCY WINDOW ELLG 5<br />
* Default: OCCUPANCY WINDOW MAX 111<br />
* Default: OCCUPANCY MIN 0.01 MAX 1<br />
* Default: OCCUPANCY NCYCLES 1<br />
* Default: OCCUPANCY MERGE ON<br />
* Default: OCCUPANCY FRAC 0.5<br />
* Default: OCCUPANCY OFFSET 0<br />
setOCCU_WIND_ELLG(float <ELLG>)<br />
setOCCU_WIND_NRES(int <NRES>)<br />
setOCCU_WIND_MAX(int <NRES>)<br />
setOCCU_MIN(float <MIN>)<br />
setOCCU_MAX(float <MAX>)<br />
setOCCU_MERG(float <FRAC>)<br />
setOCCU_FRAC(bool)<br />
setOCCU_OFFS(int <N>)<br />
<br />
==[[Image:Expert.gif|link=]]RESCORE== <br />
; RESCORE ROT [ON|OFF]<br />
; RESCORE TRA [ON|OFF]<br />
: Toggle for rescoring of fast rotation function (ROT) or fast translation function (TRA) search peaks. <br />
* Default: RESCORE ROT ON<br />
* Default: RESCORE TRA ON|OFF will depend on whether phaser is running in the mode [[#MODE | MODE MR_AUTO]] with [[#SEARCH | SEARCH METHOD FAST]] or with [[#SEARCH | SEARCH METHOD FULL]], or running the translation function separately [[#MODE | MODE MR_FTF]]. For [[#SEARCH | SEARCH METHOD FAST]] the default also depends on whether or not the expected LLG target [[#ELLG | ELLG TARGET <TARGET>]] value is reached.<br />
setRESC_ROTA(bool)<br />
setRESC_TRAN(bool)<br />
<br />
==[[Image:Expert.gif|link=]]RFACTOR== <br />
; RFACTOR USE [ON|OFF]<br />
: For cases of searching for one ensemble when there is one ensemble in the asymmetric unit, the R-factor for the ensemble at the orientation and position in the input is calculated. If this value is low then MR is not performed in the MR_AUTO job in FAST search mode. Instead, rigid body refinement is performed before exiting. Note that the same R-factor test and cutoff is used for judging success in single-atom molecular replacement (MR_ATOM mode).<br />
; RFACTOR CUTOFF <VALUE><br />
: Rfactor in percent used as cutoff for deciding whether or not the R-factor indicates that MR is not necessary.<br />
* Default: RFACTOR USE ON CUTOFF 35<br />
setRFAC_USE(bool)<br />
setRFAC_CUTO(float <PERCENT>)<br />
<br />
==[[Image:Expert.gif|link=]]SAMPLING==<br />
; SAMPLING ROT <SAMP><br />
; SAMPLING TRA <SAMP><br />
: Sampling of search given in degrees for a rotation search and Ångstroms for a translation search. Sampling for rotation search depends on the mean radius of the Ensemble and the high resolution limit (dmin) of the search.<br />
* Default: SAMP = 2*atan(dmin/(4*meanRadius)) (ROTATION FUNCTION)<br />
* Default: SAMP = dmin/5; (BRUTE TRANSLATION FUNCTION)<br />
* Default: SAMP = dmin/4; (FAST TRANSLATION FUNCTION)<br />
setSAMP_ROTA(float <SAMP>)<br />
setSAMP_TRAN(float <SAMP>)<br />
<br><br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS USE [ON|OFF]<br />
: Use TNCS if present: apply TNCS corrections. (Note: was TNCS IGNORE [ON|OFF] in Phaser-2.4.0)<br />
; TNCS RLIST ADD [ON | OFF]<br />
: Supplement the rotation list used in the translation function with rotations already present in the list of known solutions. New molecules in the same orientation as those in the known search (as occurs with translational ncs) may not have peaks associated with them from the rotation function because the known molecules mask the presence of the ones not yet found. <br />
; TNCS PATT HIRES <hires><br />
: High resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT LORES <lores><br />
: Low resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT PERCENT <percent><br />
: Percent of origin Patterson peak that qualifies as a TNCS vector<br />
; TNCS PATT DISTANCE <distance><br />
: Minimum distance of Patterson peak from origin that qualifies as a TNCS vector<br />
; TNCS TRANSLATION PERTURB [ON | OFF]<br />
: If the TNCS translation vector is on a special position, perturb the vector from the special position before refinement<br />
; TNCS ROTATION RANGE <angle><br />
: Maximum deviation from initial rotation from which to look for rotational deviation. Default uses internally determined value based on resolution of data and size of G-function effective molecular radius. Value of 0 turns rotational refinement off.<br />
; TNCS ROTATION SAMPLING <sampling><br />
: Sampling for rotation search. Default uses internally determined value based on resolution of data and size of G-function effective molecular radius. Value of 0 turns rotational refinement off.<br />
* Default: TNCS USE ON<br />
* Default: TNCS RLIST ADD ON<br />
* Default: TNCS PATT HIRES 5<br />
* Default: TNCS PATT LORES 10<br />
* Default: TNCS PATT PERCENT 20<br />
* Default: TNCS PATT DISTANCE 15 <br />
* Default: TNCS TRANSLATION PERTURB ON<br />
setTNCS_USE(bool)<br />
setTNCS_RLIS_ADD(bool)<br />
setTNCS_PATT_HIRE(float <HIRES>)<br />
setTNCS_PATT_LORE(float <LORES>) <br />
setTNCS_PATT_PERC(float <PERCENT>) <br />
setTNCS_PATT_DIST(float <DISTANCE>)<br />
setTNCS_TRAN_PERT(bool)<br />
setTNCS_ROTA_RANG(float <RANGE>) <br />
setTNCS_ROTA_SAMP(float <SAMPLING>) <br />
<br><br />
<br><br />
<br />
=Developer Keywords=<br />
==[[Image:Developer.gif|link=]]BINS== <br />
; BINS DATA [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the data.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections<br />
; BINS ENSE [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the calaculated structure factos for the ensembles.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections<br />
* Default: BINS DATA MIN 6 MAX 50 WIDTH 500 <br />
* Default: BINS ENSE MIN 6 MAX 1000 WIDTH 1000 <br />
setBINS_DATA_MINI(float <L>)<br />
setBINS_DATA_MAXI(float <H>)<br />
setBINS_DATA_WIDT(float <W>)<br />
setBINS_ENSE_MINI(float <L>)<br />
setBINS_ENSE_MAXI(float <H>)<br />
setBINS_ENSE_WIDT(float <W>)<br />
<br />
==[[Image:Developer.gif|link=]]BFACTOR==<br />
; BFACTOR WILSON RESTRAINT [ON|OFF]<br />
: Toggle to use the Wilson restraint on the isotropic component of the atomic B-factors in SAD phasing.<br />
; BFACTOR SPHERICITY RESTRAINT [ON|OFF] <br />
: Toggle to use the sphericity restraint on the anisotropic B-factors in SAD phasing<br />
; BFACTOR REFINE RESTRAINT [ON|OFF] <br />
: Toggle to use the restraint to zero for the molecular B-factor in molecular replacement.<br />
; BFACTOR WILSON SIGMA <SIGMA><br />
: The sigma of the Wilson restraint.<br />
; BFACTOR SPHERICITY SIGMA <SIGMA><br />
: The sigma of the sphericity restraint.<br />
; BFACTOR REFINE SIGMA <SIGMA><br />
: The sigma of the restraint to zero for the molecular B-factor in molecular replacement.<br />
* Default: BFACTOR WILSON RESTRAINT ON <br />
* Default: BFACTOR SPHERICITY RESTRAINT ON <br />
* Default: BFACTOR REFINE RESTRAINT ON <br />
* Default: BFACTOR WILSON SIGMA 5<br />
* Default: BFACTOR SPHERICITY SIGMA 5<br />
* Default: BFACTOR REFINE SIGMA 6<br />
setBFAC_WILS_REST(bool <True|False>)<br />
setBFAC_SPHE_REST(bool <True|False>)<br />
setBFAC_REFI_REST(bool <True|False>) <br />
setBFAC_WILS_SIGM(float <SIGMA>) <br />
setBFAC_SPHE_SIGM(float <SIGMA>) <br />
setBFAC_REFI_SIGM(float <SIGMA>)<br />
<br />
==[[Image:Developer.gif|link=]]BOXSCALE==<br />
; BOXSCALE <BOXSCALE><br />
: Scale for box for calculating structure factors. The ensembles are put in a box equal to (extent of molecule)*BOXSCALE<br />
* Default: BOXSCALE 4<br />
setBOXS<float <BOXSCALE>)<br />
<br />
==[[Image:Developer.gif|link=]]CELL==<br />
; <span style="color:darkorange">Python Only</span> <br />
: Unit cell dimensions<br />
* Default: Cell read from MTZ file<br />
setCELL(float <A>,float <nowiki><B></nowiki>,float <C>,float <ALPHA>,float <BETA>,float <GAMMA>)<br />
setCELL6(float_array <A B C ALPHA BETA GAMMA>)<br />
<br />
==[[Image:Developer.gif|link=]]COMPOSITION== <br />
; COMPOSITION MIN SOLVENT <PERC><br />
: Minimum solvent to give maximum asu packing volume for automated search copy determination (NUM 0)<br />
* Default: COMPOSITION MIN SOLVENT 0.2<br />
setCOMP_MIN_SOLV(float)<br />
<br />
==[[Image:Developer.gif|link=]]DDM== <br />
; DDM SLIDER <VAL> <br />
: The SLIDER window width is used to smooth the Difference Distance Matrix. <br />
; DDM DISTANCE MIN <VAL> MAX <VAL> STEP <VAL><br />
: The range and step interval, as the fraction of the difference between the lowest and highest DDM values used to step.<br />
; DDM SEPARATION MIN <VAL> MAX <VAL><br />
: Through space separation in Angstroms used.<br />
; DDM SEQUENCE MIN <VAL> MAX <VAL><br />
: The range of sequence separations between matrix pairs.<br />
; DDM JOIN MIN <VAL> MAX <VAL><br />
: The range of lengths of the sequences to join if domain segments are discontinuous in percentages of the polypeptide chain.<br />
* Default: DDM SLIDER 0<br />
* Default: DDM DISTANCE MIN 1 MAX 5 STEP 50<br />
* Default: DDM SEPARATION MIN 7 MAX 14<br />
* Default: DDM SEQUENCE MIN 0 MAX 1<br />
* Default: DDM JOIN MIN 2 MAX 12<br />
setDDM_SLID(int <VAL>) <br />
setDDM_DIST_STEP(int <VAL>) <br />
setDDM_DIST_MINI(int <VAL>) <br />
setDDM_DIST_MAXI(int <VAL>) <br />
setDDM_SEPA_MINI(float <VAL>) <br />
setDDM_SEPA_MAXI(float <VAL>)<br />
setDDM_JOIN_MINI(int <VAL>) <br />
setDDM_JOIN_MAXI(int <VAL>) <br />
setDDM_SEQU_MINI(int <VAL>) <br />
setDDM_SEQU_MAXI(int <VAL>)<br />
<br />
==[[Image:Developer.gif|link=]]ENM== <br />
; ENM OSCILLATORS [ <sup>1</sup>RTB | <sup>2</sup>ALL ] <br />
: Define the way the atoms are used for the elastic network model.<br />
: <sup>1</sup>Use the rotation-translation block method.<br />
: <sup>2</sup>Use all atoms to determine the modes (only for use on very small molecules, less than 250 atoms). <br />
; ENM MAXBLOCKS <MAXBLOCKS><br />
: MAXBLOCKS is the number of rotation-translation blocks for the RTB analysis.<br />
; ENM NRES <NRES><br />
: For the RTB analysis, by default NRES=0 and then it is calculated so that it is as small as it can be without reaching MAXBlocks. <br />
; ENM RADIUS <RADIUS><br />
: Elastic Network Model interaction radius (Angstroms)<br />
; ENM FORCE <FORCE><br />
: Elastic Network Model force constant<br />
* Default: ENM OSCILLATORS RTB MAXBLOCKS 250 NRES 0 RADIUS 5 FORCE 1<br />
setENM_OSCI(str ["RTB"|"CA"|"ALL"])<br />
setENM_RTB_MAXB(float <MAXB>)<br />
setENM_RTB_NRES(float <NRES>) <br />
setENM_RADI(float <RADIUS>) <br />
setENM_FORC(float <FORCE>)<br />
<br />
==[[Image:Developer.gif|link=]]NORMALIZATION==<br />
; <span style="color:darkorange">Scripting Only</span><br />
; NORM EPSFAC WRITE <FILENAME><br />
: The normalization factors that correct for anisotropy in the data are written to BINARY file FILENAME<br />
; NORM EPSFAC READ <FILENAME><br />
: The normalization factors that correct for anisotropy in the data are read from BINARY file FILENAME. Further refinement is automatically turned off.<br />
; <span style="color:darkorange">Python Only</span><br />
The normalization factors that correct for anisotropy in the data, extracted from ResultANO object with getSigmaN(). Anisotropy should subsequently be turned off with setMACA_PROT("OFF").<br />
setNORM_DATA(data_norm <SIGMAN>)<br />
<br />
==[[Image:Developer.gif|link=]]OUTLIER==<br />
; OUTLIER REJECT [ON|OFF]<br />
: Reject low probability data outliers<br />
; OUTLIER PROB <PROB><br />
: Cutoff for rejection of low probablity outliers<br />
* Default: OUTLIER REJECT ON PROB 0.000001<br />
setOUTL_REJE(bool) <br />
setOUTL_PROB(float <PROB>)<br />
<br />
==[[Image:Developer.gif|link=]]PTGROUP== <br />
; PTGROUP COVERAGE <COVERAGE><br />
: Percentage coverage for two sequences to be considered in same pointgroup<br />
; PTGROUP IDENTITY <IDENTITY><br />
: Percentage identity for two sequences to be considered in same pointgroup<br />
; PTGROUP RMSD <RMSD><br />
: Percentage rmsd for two models to be considered in same pointgroup<br />
; PTGROUP TOLERANCE ANGULAR <ANG><br />
: Angular tolerance for pointgroup<br />
; PTGROUP TOLERANCE SPATIAL <DIST><br />
: Spatial tolerance for pointgroup<br />
setPTGR_COVE(float <COVERAGE>) <br />
setPTGR_IDEN(float <IDENTITY>) <br />
setPTGR_RMSD(float <RMSD>) <br />
setPTGR_TOLE_ANGU(float <ANG>) <br />
setPTGR_TOLE_SPAT(float <DIST>)<br />
<br />
==[[Image:Developer.gif|link=]]RESHARPEN== <br />
; RESHARPEN PERCENTAGE <PERC><br />
: Perecentage of the B-factor in the direction of lowest fall-off (in anisotropic data) to add back into the structure factors F_ISO and FWT and FDELWT so as to sharpen the electron density maps<br />
* Default: RESHARPEN PERCENT 100<br />
setRESH_PERC(float <PERCENT>)<br />
<br />
==[[Image:Developer.gif|link=]]SOLPARAMETERS==<br />
; SOLPARAMETERS SIGA FSOL <FSOL> BSOL <BSOL> MIN <MINSIGA><br />
: Babinet solvent parameters for Sigma(A) curves. MINSIGA is the minimum SIGA for Babinet solvent term (low resolution only). The solvent term in the Sigma(A) curve is given by <BR>max(1 - FSOL*exp(-BSOL/(4d^2)),MINSIGA).<br />
; SOLPARAMETERS BULK USE [ON|OFF]<br />
: Toggle for use of solvent mask scaling parameters for ensemble structure factors, applied to Fmask.<br />
; SOLPARAMETERS BULK FSOL <FSOL> BSOL <BSOL> <br />
: Solvent mask scaling parameters for ensemble structure factors, applied to Fmask.<br />
* Default: SOLPARAMETERS SIGA FSOL 1.05 BSOL 501 MIN 0.1<br />
* Default: SOLPARAMETERS SIGA RESTRAINT ON<br />
* Default: SOLPARAMETERS BULK USE OFF<br />
* Default: SOLPARAMETERS BULK FSOL 0.35 BSOL 45<br />
setSOLP_SIGA_FSOL(float <FSOL>) <br />
setSOLP_SIGA_BSOL(float <BSOL>)<br />
setSOLP_SIGA_MIN(float <MINSIGA>)<br />
setSOLP_BULK_USE(bool)<br />
setSOLP_BULK_FSOL(float <FSOL>) <br />
setSOLP_BULK_BSOL(float <BSOL>)<br />
<br />
==[[Image:Developer.gif|link=]]TARGET== <br />
; TARGET ROT FAST TYPE [LERF1 | CROWTHER]<br />
: Target function type for fast rotation searches<br />
; TARGET TRA FAST TYPE [LETF1 | LETF2 | CORRELATION]<br />
: Target function type for fast translation searches<br />
setTARG_ROTA_TYPE(string TYPE)<br />
setTARG_TRAN_TYPE(string TYPE)<br />
<br />
==[[Image:Developer.gif|link=]]TNCS==<br />
; TNCS ROTATION ANGLE <A> <nowiki><B></nowiki> <C><br />
: Input rotational difference between molecules related by the pseudo-translational symmetry vector, specified as rotations in degrees about x, y and z axes. Central value for grid search (RANGE > 0).<br />
; TNCS ROTATION RANGE <A><br />
: Range of angular difference in rotation angles to explore around central angle.<br />
; TNCS ROTATION SAMPLING <A><br />
: Sampling step for rotational grid search.<br />
; TNCS TRA VECTOR <x y z> <br />
: Input pseudo-translational symmetry vector (fractional coordinates). By default the translation is determined from the Patterson.<br />
; TNCS VARIANCE RMSD <num><br />
: Input estimated rms deviation between pseudo-translational symmetry vector related molecules.<br />
; TNCS VARIANCE FRAC <num><br />
: Input estimated fraction of cell content that obeys pseudo-translational symmetry.<br />
; TNCS LINK RESTRAINT [ON | OFF]<br />
: Link the occupancy of atoms related by TNCS in SAD phasing<br />
; TNCS LINK SIGMA <sigma><br />
: Sigma of link restraint of the occupancy of atoms related by TNCS in SAD phasing<br />
* Default: TNCS ROTATION ANGLE 0 0 0<br />
* Default: TNCS ROTATION RANGE -999 (determine from structure size and resolution)<br />
* Default: TNCS ROTATION SAMPLING -999 (determine from structure size and resolution)<br />
* Default: TNCS TRANSLATION VECTOR determined from position of Patterson peak<br />
* Default: TNCS VARIANCE RMSD 0.4 <br />
* Default: TNCS VARIANCE FRAC 1 <br />
* Default: TNCS LINK RESTRAINT ON<br />
* Default: TNCS LINK SIGMA 0.1<br />
setTNCS_ROTA_ANGL(dvect3 <A B C>) <br />
setTNCS_TRAN_VECT(dvect3 <X Y Z>) <br />
setTNCS_VARI_RMSD(float <RMSD>) <br />
setTNCS_VARI_FRAC(float <FRAC>)<br />
setTNCS_LINK_REST(bool)<br />
setTNCS_LINK_SIGM(float <SIGMA>)<br />
; <span style="color:darkorange">Scripting Only</span><br />
; TNCS EPSFAC WRITE <FILENAME><br />
: The normalization factors that correct for tNCS in the data are written to BINARY file FILENAME<br />
; TNCS EPSFAC READ <FILENAME><br />
: The normalization factors that correct for tNCS in the data are read from BINARY file FILENAME. Further refinement is automatically turned off.<br />
; <span style="color:darkorange">Python Only</span><br />
The normalization factors that correct for tNCS in the data, extracted from ResultNCS object with getPtNcs(). tNCS refinement should subsequently be turned off with setMACT_PROT("OFF").<br />
setTNCS(data_tncs <PTNCS>)<br />
<br />
==[[Image:Developer.gif|link=]]TRANSLATION== <br />
; TRANSLATION MAPS [ON | OFF]<br />
: Output maps of fast translation function FSS scoring functions<br />
: Maps take the names <ROOT>.<ensemble>.k.e.map where k is the Known backgound number and e is the Euler angle number for that known background<br />
* Default: TRANSLATION MAPS OFF<br />
setTRAN_MAPS(bool)</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Keywords&diff=2403Keywords2017-01-24T11:35:28Z<p>Airlie: Reverted edits by Airlie (talk) to last revision by Miffy</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
===Phaser Executable===<br />
<br />
The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the [[#MODE | MODE]] keyword. The different modes and the keywords relevant to each mode are described in [[Modes]].<br />
<br />
Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. However, some keywords are meaningful when entered multiple times. The order may or may not be important. <br />
<br />
*[[Image:User1.gif|link=]] [[#Basic Keywords | Basic Keywords]]<br />
<br />
*[[Image:Output.png|link=]] [[#Output Control Keywords | Output Control Keywords]]<br />
<br />
*[[Image:User2.gif|link=]] [[#Advanced Keywords |Advanced Keywords ]]<br />
<br />
*[[Image:Expert.gif|link=]] [[#Expert Keywords | Expert Keywords]]<br />
<br />
*[[Image:Developer.gif|link=]] [[#Developer Keywords | Developer Keywords]]<br />
<br />
<br />
===Python Interface===<br />
<br />
Phaser can be compiled as a python library. The mode is selected by calling the appropriate run-job. Input to the run-job is via input-objects, which are passed to the run-job. Setter function on the input objects are equivalent to the keywords for input to the phaser executable. The different modes and the keywords relevant to each mode are described in [[Modes]]. See [[Python Interface]] for details. <br />
<br />
The python interface uses standard python and cctbx/scitbx variable types.<br />
<br />
str string<br />
float double precision floating point<br />
Miller cctbx::miller::index<int> <br />
dvect3 scitbx::vec3<float> <br />
dmat33 scitbx::mat3<float> <br />
'''type'''_array scitbx::af::shared<'''type'''> arrays<br />
<br />
=Basic Keywords=<br />
==[[Image:User1.gif|link=]]ATOM== <br />
; ATOM CRYSTAL <XTALID> PDB <FILENAME><br />
: Definition of atom positions using a pdb file.<br />
; ATOM CRYSTAL <XTALID> HA <FILENAME><br />
: Definition of atom positions using a ha file (from RANTAN, MLPHARE etc.).<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> <br />
: Minimal definition of atom position. B-factor defaults to isotropic and Wilson B-factor. Use <TYPE>=TX for Ta6Br12 cluster and <TYPE>=XX for all other clusters. Scattering for cluster is spherically averaged. Coordinates of cluster compounds other than Ta6Br12 must be entered with CLUSTER keyword. Ta6Br12 coordinates are in phaser code and do not need to be given with CLUSTER keyword.<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> [ ISOB <ISOB> | ANOU <HH KK LL HK HL KL> | USTAR <HH KK LL HK HL KL>] FIXX [ON|OFF] FIXO [ON|OFF] FIXB [ON|OFF] BSWAP [ON|OFF] LABEL <SITE_NAME><br />
: Full definition of atom position including B-factor.<br />
;ATOM CHANGE BFACTOR WILSON [ON|OFF]<br />
: Reset all atomic B-factors to the Wilson B-factor.<br />
; ATOM CHANGE SCATTERER <SCATTERER><br />
:Reset all atomic scatterers to element (or cluster) type.<br />
setATOM_PDB(str <XTALID>,str <PDB FILENAME>)<br />
setATOM_IOTBX(str <XTALID>,iotbx::pdb::hierarchy::root <iotbx object>)<br />
setATOM_STR(str <XTALID>,str <pdb format string>)<br />
setATOM_HA(str <XTALID>,str <FILENAME>)<br />
addATOM(str <XTALID>,str <TYPE>,<br />
float <X>,float <Y>,float <Z>,float <OCC>)<br />
addATOM_FULL(str <XTALID>,str <TYPE>,bool <ORTH>,<br />
dvect3 <X Y Z>,float <OCC>,bool <ISO>,float <ISOB>,<br />
bool <ANOU>,dmat6 <HH KK LL HK HL KL>,<br />
bool <FIXX>,bool <FIXO>,bool <FIXB>,bool <SWAPB>,<br />
str <SITE_NAME>)<br />
setATOM_CHAN_BFAC_WILS(bool)<br />
setATOM_CHAN_SCAT(bool)<br />
setATOM_CHAN_SCAT_TYPE(str <TYPE>)<br />
<br />
==[[Image:User1.gif|link=]]CLUSTER== <br />
; CLUSTER PDB <PDBFILE><br />
: Sample coordinates for a cluster compound for experimental phasing. Clusters are specified with type XX. Ta6Br12 clusters do not need to have coordinates specified as the coordinates are in the phaser code. To use Ta6Br12 clusters, specify atomtypes/clusters as TX.<br />
setCLUS_PDB(str <PDBFILE>)<br />
addCLUS_PDB(str <ID>, str <PDBFILE>)<br />
<br />
==[[Image:User1.gif|link=]]COMPOSITION== <br />
; COMPOSITION BY [ <sup>1</sup>AVERAGE| <sup>2</sup>SOLVENT| <sup>3</sup>ASU ]<br />
: Alternative ways of defining composition<br />
: <sup>1</sup> AVERAGE solvent fraction for crystals (50%)<br />
: <sup>2</sup> Composition entered by solvent content.<br />
: <sup>3</sup> Explicit description of composition of ASU by sequence or molecular weight<br />
; <sup>2</sup>COMPOSITION PERCENTAGE <SOLVENT><br />
: Specified SOLVENT content<br />
; <sup>3</sup>COMPOSITION PROTEIN [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of protein in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION NUCLEIC [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of nucleic acid in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION ATOM <TYPE> NUMBER <NUM><br />
: Add NUM copies of an atom (usually a heavy atom) to the composition<br />
* Default: COMPOSITION BY ASU<br />
setCOMP_BY(str ["AVERAGE" | "SOLVENT" | "ASU" ])<br />
setCOMP_PERC(float <SOLVENT>)<br />
addCOMP_PROT_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_PROT_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_PROT_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_PROT_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_NUCL_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_NUCL_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_NUCL_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_NUCL_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_ATOM(str <TYPE>,float <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]CRYSTAL== <br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN Fpos =<F+> SIGFpos=<SIG+> Fneg=<F-> SIGFneg=<SIG-><br />
: Columns of MTZ file to read for this (anomalous) dataset<br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN F =<F> SIGF=<SIGF><br />
: Columns of MTZ file to read for this (non-anomalous) dataset. Used for LLG completion in SAD phasing when there is no anomalous signal (single atom MR protocol). Use LABIN for MR.<br />
setCRYS_ANOM_LABI(str <F+>,str <SIGF+>,str <F->,str <SIGF->) <br />
setCRYS_MEAN_LABI(str <F>,str <SIGF>)<br />
<br />
==[[Image:User1.gif|link=]]ENSEMBLE== <br />
; ENSEMBLE <MODLID> [PDB|CIF] <PDBFILE> [RMS <RMS><sup>1</sup> | ID <ID><sup>2</sup> | CARD ON<sup>3</sup>] ''CHAIN "<CHAIN>"<sup>4</sup> MODEL <NUM><sup>5</sup>''<br />
: The names of the PDB/CIF files used to build the ENSEMBLE, and either<br />
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
:: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file (e.g. "REMARK PHASER ENSEMBLE MODEL 1 ID 31.2") containing the superimposed models concatenated in the one file. This syntax enables simple automation of the use of ensembles. The pdb file can be non-standard because the atom list for the different models need not be the same.<br />
:: <sup>4</sup> CHAIN is selected from the pdb file. <br />
:: <sup>5</sup> MODEL number is selected from the pdb file.<br />
; ENSEMBLE <MODLID> HKLIN <MTZFILE> F=<F> PHI=<PHI> EXTENT <EX> <EY> <EZ> RMS <RMS> CENTRE <CX> <CY> <CZ> PROTEIN MW <PMW> NUCLEIC MW <NMW> ''CELL SCALE <SCALE>''<br />
: An ENSEMBLE defined from a map (via an mtz file). The molecular weight of the object the map represents is required for scaling. The effective RMS coordinate error is needed to judge how the map accuracy falls off with resolution. For density obtained from an EM image reconstruction, a good first guess would be to take the resolution where the FSC curve drops below 0.5 and divide by 3. The extent (difference between maximum and minimum x,y,z coordinates of region containing model density) is needed to determine reasonable rotation steps, and the centre is needed to carry out a proper interpolation of the molecular transform. The extent and the centre are both given in Ångstroms. The cell scale factor defaults to 1 and can be refined (for example, if the map is from electron microscopy when the cell scale may be unknown to within a few percent).<br />
; ENSEMBLE <MODLID> ATOM <TYPE> RMS <RMS><br />
: Define an ensemble as a single atom for single atom MR<br />
; ENSEMBLE <MODLID> HELIX <NUM> <br />
: Define an ensemble as a helix with NUM residues<br />
; ENSEMBLE <MODLID> HETATM [ON|OFF]<br />
: Use scattering from HETATM records in pdb file. See [[Molecular_Replacement#Coordinate_Editing | Coordinate Editing ]]<br />
; ENSEMBLE <MODLID> DISABLE CHECK [ON|OFF]<br />
: Toggle to disable checking of deviation between models in an ensemble. '''Use with extreme caution'''. Results of computations are not guaranteed to be sensible.<br />
; ENSEMBLE <MODLID> ESTIMATOR [OEFFNER | OEFFNERHI | OEFFNERLO | CHOTHIALESK ]<br />
: Define the estimator function for converting ID to RMS<br />
; ENSEMBLE <MODLID> PTGRP [COVERAGE | IDENTITY | RMSD | TOLANG | TOLSPC | EULER | SYMM ]<br />
: Define the pointgroup parameters <br />
; ENSEMBLE <MODLID> BINS [MIN <N>| MAX <M>| WIDTH <W> ]<br />
: Define the Fcalc reflection binning parameters <br />
; ENSEMBLE <MODLID> TRACE [PDB|CIF] <PDBFILE><br />
: Define the coordinates used for packing independent of the coordinates used for structure factor calculation<br />
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
:: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file <br />
; ENSEMBLE <MODLID> TRACE SAMPLING MIN <DIST> <br />
: Set the minimum distance for the sampling of packing grid<br />
; ENSEMBLE <MODLID> TRACE SAMPLING TARGET <NUM> <br />
: Set the target for the number of points to sample the smallest molecule to be packed<br />
; ENSEMBLE <MODLID> TRACE SAMPLING RANGE <NUM> <br />
: Target range (TARGET+/-RANGE) for search for hexgrid points in protein volume<br />
; ENSEMBLE <MODLID> TRACE SAMPLING USE [AUTO | ALL | CALPHA | HEXGRID ]<br />
: Sample trace coordinates using all atoms, C-alpha atoms, a hexagonal grid in the atomic volume or use an automatically determined choice<br />
; ENSEMBLE <MODLID> TRACE SAMPLING DISTANCE <DIST> <br />
: Set the distance for the sampling of the hexagonal grid explicitly and do not use TARGET to find default sampling distance<br />
; ENSEMBLE <MODLID> TRACE SAMPLING WANG <WANG> <br />
: Scale factor for the size of the Wang mask generated from an ensemble map<br />
; ENSEMBLE <MODLID> TRACE PDB <PDBFILE> <br />
: Use the given set of coordinates for packing rather than using the coordinates for structure factor calculation<br />
* Default: ENSEMBLE <MODLID> DISABLE CHECK OFF<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING MIN 1.0<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING TARGET 1000<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING RANGE 100<br />
addENSE_PDB_ID(str <MODLID>,str <FILE>,float <ID>) <br />
addENSE_PDB_RMS(str <MODLID>,str <FILE>,float <RMS>) <br />
setENSE_TRAC_SAMP_MIN(MODLID,float <MIN>)<br />
setENSE_TRAC_SAMP_TARG(MODLID,int <TARGET>)<br />
setENSE_TRAC_SAMP_RANG(MODLID,int <RANGE>)<br />
setENSE_TRAC_SAMP_USE(MODLID,str)<br />
setENSE_TRAC_SAMP_DIST(MODLID,float <DIST>)<br />
setENSE_TRAC_SAMP_WANG(MODLID,float <WANG>)r <FILE>,float <RMS>)<br />
addENSE_CARD(str <MODLID>,str <FILE>,bool)<br />
addENSE_MAP(str <MODLID>,str <MTZFILE>,str <F>,str <PHI>,dvect3 <EX EY EZ>,<br />
float <RMS>,dvect3 <CX CY CZ>,float <PMW>,float <NMW>,float <CELL>)<br />
setENSE_DISA_CHEC(bool)<br />
<br />
==[[Image:User1.gif|link=]]HKLIN==<br />
; HKLIN <FILENAME><br />
: The mtz file containing the data<br />
setHKLI(str <FILENAME>)<br />
<br />
==[[Image:User1.gif|link=]]JOBS== <br />
; JOBS <NUM><br />
: Number of processors to use in parallelized sections of code<br />
* Default: JOBS 2<br />
setJOBS(int <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]LABIN== <br />
; LABIN F = <F> SIGF = <SIGF> <br />
: Columns in mtz file. F must be given. SIGF should be given but is optional<br />
; LABIN I = <nowiki><I></nowiki> SIGI = <SIGI> <br />
: Columns in mtz file. I must be given. SIGI should be given but is optional<br />
; LABIN FMAP = <PH> PHMAP = <PHMAP> <br />
: Columns in mtz file. FMAP/PHMAP are weighted coefficients for use in the Phased Translation Function.<br />
; LABIN FMAP = <PH> PHMAP = <PHMAP> FOM = <FOM><br />
: Columns in mtz file. FMAP/PHMAP are unweighted coefficients for use in the Phased Translation Function and FOM the figure of merit for weighting<br />
setLABI_F_SIGF(str <F>,str <SIGF>)<br />
setLABI_I_SIGI(str <nowiki><I></nowiki>,str <SIGI>)<br />
setLABI_PTF(str <FMAP>,str <PHMAP>,str <FOM>)<br />
<br />
''Data should be input to python run-jobs using one data_refl parameter''<br />
''This is extracted from the ResultMR_DAT object after a call to runMR_DAT''<br />
setREFL_DATA(data_ref)<br />
''Example:''<br />
i = InputMR_DAT()<br />
i.setHKLI("*.mtz")<br />
i.setLABI_F_SIGF("F","SIGF")<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputMR_LLG()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.setREFL_DATA(r.getDATA())<br />
''See also: '' [[Python Example Scripts]]<br />
<br />
''Alternatively, reflection arrays can be set using cctbx::af::shared<double>''<br />
setREFL_F_SIGF(float_array <F>,float_array <SIGF>)<br />
setREFL_I_SIGI(float_array <nowiki><I></nowiki>,float_array <SIGI>)<br />
setREFL_PTF(float_array <FMAP>,float_array <PHMAP>,float_array <FOM>)<br />
<br />
==[[Image:User1.gif|link=]]MODE==<br />
; MODE [ ANO | CCA | SCEDS | NMAXYZ | NCS | MR_ELLG | MR_AUTO | MR_GYRE | MR_ATOM | MR_ROT | MR_TRA | MR_RNP | | MR_OCC | MR_PAK | EP_AUTO | EP_SAD]<br />
: The mode of operation of Phaser. The different modes are described in a separate page on [[Keyword Modes]]<br />
ResultANO r = runANO(InputANO)<br />
ResultCCA r = runCCA(InputCCA)<br />
ResultNMA r = runSCEDS(InputNMA)<br />
ResultNMA r = runNMAXYZ(InputNMA)<br />
ResultNCS r = runNCS(InputNCS)<br />
ResultELLG r = runMR_ELLG(InputMR_ELLG)<br />
ResultMR r = runMR_AUTO(InputMR_AUTO)<br />
ResultEP r = runMR_ATOM(InputMR_ATOM)<br />
ResulrMR_RF r = runMR_FRF(InputMR_FRF)<br />
ResultMR_TF r = runMR_FTF(InputMR_FTF)<br />
ResultMR r = runMR_RNP(InputMR_RNP)<br />
ResultGYRE r = runMR_GYRE(InputMR_RNP)<br />
ResultMR r = runMR_OCC(InputMR_OCC)<br />
ResultMR r = runMR_PAK(InputMR_PAK)<br />
ResultEP r = runEP_AUTO(InputEP_AUTO)<br />
ResultEP_SAD r = runEP_SAD(InputEP_SAD)<br />
<br />
==[[Image:User1.gif|link=]]PARTIAL== <br />
; PARTIAL PDB <PDBFILE> [RMSIDENTITY] <RMS_ID><br />
: The partial structure for MR-SAD substructure completion. Note that this must already be correctly placed, as the experimental phasing module will not carry out molecular replacement.<br />
; PARTIAL HKLIN <MTZFILE> [RMS|IDENTITY] <RMS_ID><br />
: The partial electron density for MR-SAD substructure completion.<br />
; PARTIAL LABIN FC=<FC> PHIC=<PHIC><br />
: Column labels for partial electron density for MR-SAD substructure completion.<br />
setPART_PDB(str <PDBFILE>)<br />
setPART_HKLI(str <MTZFILE>) <br />
setPART_LABI_FC(str <FC>)<br />
setPART_LABI_PHIC(str <PHIC>) <br />
setPART_VARI(str ["ID"|"RMS"])<br />
setPART_DEVI(float <RMS_ID>)<br />
<br />
==[[Image:User1.gif|link=]]SEARCH==<br />
; SEARCH ENSEMBLE <MODLID> ''{OR ENSEMBLE <MODLID>}… NUMBER <NUM><sup>*</sup>''<br />
: The ENSEMBLE to be searched for in a rotation search or an automatic search. When multiple ensembles are given using the OR keyword, the search is performed for each ENSEMBLE in turn. When the keyword is entered multiple times, each SEARCH keyword refers to a new component of the structure. If the component is present multiple times the sub-keyword NUMber can be used (rather than entering the same SEARCH keyword NUMber times).<br />
: <sup>*</sup>For automatic determination of search number use NUMBER 0. If the composition is entered, the maximum number will be that defined by the composition, otherwise the maximum number will fill the asymmetric unit to a minimum solvent content of 20%. Searches for new components will continue until the TFZ score is above 8, and terminate if the TFZ score drops below 8 before the placement of the maximum number of components.<br />
; SEARCH METHOD [FULL|FAST]<br />
: Search using the [[Modes#Modes |full search]] or [[Modes#Modes | fast search]] algorithms.<br />
; SEARCH ORDER AUTO [ON|OFF]<br />
: Search in the "best" order as estimated using estimated rms deviation and completeness of models.<br />
; SEARCH PRUNE [ON|OFF]<br />
: For high TFZ solutions that fail the packing test, carry out a sliding-window occupancy refinement and prune residues that refine to low occupancy, in an effort to resolve packing clashes. If this flag is set to true, the flag for keeping high tfz score solutions (see [[#PACK | PACK]]) that don't pack is also set to true (PACK KEEP HIGH TFZ ON).<br />
; SEARCH AMALGAMATE USE [ON|OFF]<br />
: For multiple high TFZ solutions, enable amalgamation into a single solution<br />
; SEARCH BFACTOR <BFAC><br />
: B-factor applied to search molecule (or atom).<br />
; SEARCH OFACTOR <OFAC><br />
: Occupancy factor applied to search molecule (or atom).<br />
* Default: SEARCH METHOD FAST<br />
* Default: SEARCH ORDER AUTO ON<br />
* Default: SEARCH PRUNE ON<br />
* Default: SEARCH AMALGAMATE USE ON<br />
* Default: SEARCH BFACTOR 0<br />
* Default: SEARCH OFACTOR 1<br />
addSEAR_ENSE_NUM(str <MODLID>,int <NUM>) <br />
addSEAR_ENSE_OR_ENSE_NUM(string_array <MODLIDS>,int <NUM>) <br />
setSEAR_METH(str [ "FULL" | "FAST" ])<br />
setSEAR_ORDE_AUTO(bool)<br />
setSEAR_PRUN(bool <PRUNE>)<br />
setSEAR_AMAL_USE(bool <AMAL>)<br />
setSEAR_BFAC(float <BFAC>)<br />
setSEAR_OFAC(float <OFAC>)<br />
<br />
==[[Image:User1.gif|link=]]SGALTERNATIVE==<br />
; SGALTERNATIVE SELECT [<sup>1</sup>ALL| <sup>2</sup>HAND| <sup>3</sup>LIST| <sup>4</sup>NONE]<br />
: Selection of alternative space groups to test in translation functions i.e. those that are in same laue group as that given in [[#SPACEGROUP | SPACEGROUP]]<br />
: <sup>1</sup> Test all possible space groups, <br />
: <sup>2</sup> Test the given space group and its enantiomorph.<br />
: <sup>3</sup> Test the space groups listed with SGALTERNATIVE TEST <SG>.<br />
: <sup>4</sup> Do not test alternative space groups.<br />
; SGALTERNATIVE TEST <SG><br />
: Alternative space groups to test. Multiple test space groups can be entered.<br />
* Default: SGALTERNATIVE SELECT HAND<br />
setSGAL_SELE(str [ "ALL" | "HAND" | "LIST" | "NONE" ]) <br />
addSGAL_TEST(str <SG>)<br />
<br />
==[[Image:User1.gif|link=]]SOLUTION==<br />
; SOLUTION SET <ANNOTATION><br />
: Start new set of solutions <br />
; SOLUTION TEMPLATE <ANNOTATION><br />
: Specifies a template solution against which other solutions in this run will be compared. Given in place of SOLUTION SET. Template rotation and translations given by subsequent SOLUTION 6DIM cards as per SOLUTION SETS.<br />
; SOLUTION 6DIM ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> [ORTH|FRAC] <X> <Y> <Z> ''FIXR [ON|OFF] FIXT [ON|OFF] FIXB [ON|OFF] BFAC <BFAC> MULT <MULT>''<br />
: This keyword is repeated for each known position and orientation of an ENSEMBLE MODLID. A B G are the Euler angles (z-y-z convention) and X Y Z are the translation elements, expressed either in orthogonal Angstroms (ORTH) or fractions of a cell edge (FRAC). The input ensemble is transformed by a rotation around the origin of the coordinate system, followed by a translation. BFAC default to 0, MULT (for multiplicity) defaults to 1.<br />
; SOLUTION ENSEMBLE <MODLID> VRMS DELTA <DELTA> RMSD <RMSD><br />
: Refined RMS variance terms for pdb files (or map) in ensemble MODLID. RMSD is the input RMSD of the job that produced the sol file, DELTA is the shift with respect to this RMSD. If given as part of a solution, these values overwrite the values used for input in the ENSEMBLE keyword (if refined).<br />
; SOLUTION ENSEMBLE <MODLID> CELL SCALE <SCALE><br />
: Refined cell scale factor. Only applicable to ensembles that are maps<br />
; SOLUTION TRIAL ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> RFZ <RFZ><br />
: Rotation List for translation function<br />
; SOLUTION ORIGIN ENSEMBLE <MODLID><br />
: Create solution for ensemble MODLID at the origin<br />
; SOLUTION SPACEGROUP <SG><br />
: Space Group of the solution (if alternative spacegroups searched)<br />
; SOLUTION RESOLUTION <HIRES><br />
: High resolution limit of data used to find/refine this solution<br />
; SOLUTION PACKS <PACKS><br />
: Flag for whether solution has been retained despite failing packing test, due to having high TFZ<br />
setSOLU(mr_solution <SOL>) <br />
addSOLU_SET(str <ANNOTATION>) <br />
addSOLU_TEMPLATE(str <ANNOTATION>) <br />
addSOLU_6DIM_ENSE(str <MODLID>,dvect3 <A B C>,bool <FRAC>,dvect3 <X Y Z>,<br />
float <BFAC>,bool <FIXR>,bool <FIXT>,bool <FIXB>,int <MULT>, 1.0) <br />
addSOLU_ENSE_DRMS(str <MODLID>, float <DRMS>) <br />
addSOLU_ENSE_CELL(str <MODLID>, float <SCALE>)<br />
addSOLU_TRIAL_ENSE(string <MODLID>,dvect3 <A B C>,float <RFZ>)<br />
addSOLU_ORIG_ENSE(string <MODLID>)<br />
setSOLU_SPAC(str <SG>)<br />
setSOLU_RESO(float <HIRES>)<br />
setSOLU_PACK(bool <PACKS>)<br />
<br />
==[[Image:User1.gif|link=]]SPACEGROUP==<br />
; SPACEGROUP <SG><br />
: Space group may be altered from the one on the MTZ file to a space group in the same point group. The space group can be entered in one of three ways<br />
#The Hermann-Mauguin symbol e.g. P212121 or P 21 21 21 (with or without spaces)<br />
#The international tables number, which gives standard setting e.g. 19 <br />
#The Hall symbols e.g. P 2ac 2ab<br />
: '''The space group can also be a subgroup of the merged space group'''. For example, P1 is always allowed. The reflections will be expanded to the symmetry of the given subgroup. This is only a valid approach when the true symmetry is the symmetry of the subgroup and perfect twinning causes the data to merge "perfectly" in the higher symmetry. <br />
:'''A list of the allowed space groups in the same point group as the given space group (or space group read from MTZ file) and allowed subgroups of these is given in the Cell Content Analysis logfile.'''<br />
* Default: Read from MTZ file<br />
setSPAC_NUM(int <NUM>)<br />
setSPAC_NAME(string <HM>)<br />
setSPAC_HALL(string <HALL>)<br />
<br />
==[[Image:User1.gif|link=]]WAVELENGTH== <br />
; WAVELENGTH <LAMBDA> <br />
: The wavelengh at which the SAD dataset was collected<br />
setWAVE(float <LAMBDA>)<br />
<br><br />
<br><br />
<br />
=Output Control Keywords=<br />
==[[Image:Output.png|link=]]DEBUG== <br />
; DEBUG [ON|OFF]<br />
: Extra verbose output for debugging<br />
* Default: DEBUG OFF<br />
setDEBU(bool) <br />
<br />
==[[Image:Output.png|link=]]EIGEN==<br />
; EIGEN WRITE [ON|OFF]<br />
; EIGEN READ <EIGENFILE><br />
: Read or write a file containing the eigenvectors and eigenvalues. If reading, the eigenvalues and eigenvectors of the Hessian are read from the file generated by a previous run, rather than calculated. This option must be used with the job that generated the eigenfile and the job reading the eigenfile must have identical input for the ENM parameters. Use WRITE to control whether or not the eigenfile is written when not using the READ mode.<br />
* Default: EIGEN WRITE ON<br />
setEIGE_WRIT(bool)<br />
setEIGE_READ(str <EIGENFILE>)<br />
<br />
==[[Image:Output.png|link=]]HKLOUT== <br />
; HKLOUT [ON|OFF]<br />
: Flags for output of an mtz file containing the phasing information<br />
* Default: HKLOUT ON<br />
setHKLO(bool) <br />
<br />
==[[Image:Output.png|link=]]KEYWORDS== <br />
; KEYWORDS [ON|OFF]<br />
: Write output Phaser .sol file (.rlist file for rotation function)<br />
* Default: KEYWORDS ON<br />
setKEYW(bool)<br />
<br />
==[[Image:Output.gif|link=]]LLGMAPS==<br />
; LLGMAPS [ON|OFF]<br />
: Write log-likelihood gradient map coefficients to MTZ file<br />
* Default: LLGMAPS OFF<br />
setLLGM(bool <True|False>)<br />
<br />
==[[Image:Output.png|link=]]MUTE== <br />
; MUTE [ON|OFF]<br />
: Toggle for running in silent/mute mode, where no logfile is written to ''standard output''.<br />
* Default: MUTE OFF<br />
setMUTE(bool) <br />
<br />
==[[Image:Output.png|link=]]KILL== <br />
; KILL TIME [MINS]<br />
: Kill Phaser after MINS minutes of CPU have elapsed, provided parallel section is complete<br />
; KILL FILE [FILENAME]<br />
: Kill Phaser if file FILENAME is present, provided parallel section is complete<br />
* Default: KILL TIME 0 ''Phaser runs to completion''<br />
* Detaulf: KILL FILE "" ''Phaser runs to completion''<br />
setKILL_TIME(float) <br />
setKILL_FILE(string)<br />
<br />
==[[Image:Output.png|link=]]OUTPUT== <br />
; OUTPUT LEVEL [SILENT|CONCISE|SUMMARY|LOGFILE|VERBOSE|DEBUG]<br />
: Output level for logfile<br />
; OUTPUT LEVEL [0|1|2|3|4|5]<br />
: Output level for logfile (equivalent to keyword level setting)<br />
* Default: OUTPUT LEVEL LOGFILE<br />
setOUTP_LEVE(string)<br />
setOUTP(enum)<br />
<br />
==[[Image:Output.png|link=]]TITLE==<br />
; TITLE <TITLE><br />
: Title for job<br />
* Default: TITLE [no title given]<br />
setTITL(str <TITLE>)<br />
<br />
==[[Image:Output.png|link=]]TOPFILES== <br />
; TOPFILES <NUM><br />
: Number of top pdbfiles or mtzfiles to write to output.<br />
* Default: TOPFILES 1<br />
setTOPF(int <NUM>) <br />
<br />
==[[Image:Output.png|link=]]ROOT== <br />
; ROOT <FILEROOT><br />
: Root filename for output files (e.g. FILEROOT.log)<br />
* Default: ROOT PHASER<br />
setROOT(string <FILEROOT>)<br />
<br />
==[[Image:Output.png|link=]]VERBOSE== <br />
; VERBOSE [ON|OFF] <br />
: Toggle to send verbose output to log file.<br />
* Default: VERBOSE OFF<br />
setVERB(bool) <br />
<br />
==[[Image:Output.png|link=]]XYZOUT== <br />
; XYZOUT [ON|OFF] ''ENSEMBLE [ON|OFF]<sup>1</sup> PACKING [ON|OFF]<sup>2</sup>''<br />
: Toggle for output coordinate files. <br />
::<sup>1</sup> If the optional ENSEMBLE keyword is ON, then each placed ensemble is written to its own pdb file. The files are named FILEROOT.#.#.pdb with the first # being the solution number and the second # being the number of the placed ensemble (representing a SOLU 6DIM entry in the .sol file). <br />
::<sup>2</sup> If the optional PACKING keyword is ON, then the hexagonal grid used for the packing analysis is output to its own pdb file FILEROOT.pak.pdb<br />
* Default: XYZOUT OFF (Rotation functions)<br />
* Default: XYZOUT ON ENSEMBLE OFF (all other relevant modes)<br />
* Default: XYZOUT ON PACKING OFF (all other relevant modes)<br />
setXYZO(bool) <br />
setXYZO_ENSE(bool)<br />
setXYZO_PACK(bool)<br />
<br><br />
<br><br />
<br />
=Advanced Keywords=<br />
==[[Image:User2.gif|link=]]ELLG==<br />
([[Molecular_Replacement#Should_Phaser_Solve_It.3F|explained here]])<br />
; ELLG TARGET <TARGET><br />
: Target value for expected LLG for determining resolution limits and search order<br />
<!--; ELLG HIRES <HIRES> Internal control only--><br />
* Default: ELLG TARGET 225<br />
setELLG_TARG(float <TARGET>)<br />
<br />
==[[Image:User2.gif|link=]]FORMFACTORS==<br />
; FORMFACTORS [XRAY | ELECTRON | NEUTRON]<br />
: Use scattering factors from x-ray, electron or neutrons<br />
* Default: FORMFACTORS XRAY<br />
setFORM(string XRAY)<br />
<br />
==[[Image:User2.gif|link=]]HAND==<br />
; HAND [ <sup>1</sup>ON| <sup>2</sup>OFF| <sup>3</sup>BOTH]<br />
: Hand of heavy atoms for experimental phasing<br />
: <sup>1</sup>Phase using the other hand of heavy atoms <br />
: <sup>2</sup>Phase using given hand of heavy atoms <br />
: <sup>3</sup>Phase using both hands of heavy atoms<br />
* Default: HAND BOTH<br />
setHAND(str [ "OFF" | "ON" | "BOTH" ])<br />
<br />
==[[Image:User2.gif|link=]]LLGCOMPLETE==<br />
; LLGCOMPLETE COMPLETE [ON|OFF]<br />
: Toggle for structure completion by log-likelihood gradient maps<br />
; LLGCOMPLETE SCATTERER <TYPE> <br />
: Atom/Cluster type(s) to be used for log-likelihood gradient completion. If more than one element is entered for log-likelihood gradient completion, the atom type that gives the highest Z-score for each peak is selected. Type = "RX" is a purely real scatterer and type="AX" is purely anomalous scatterer<br />
; LLGCOMPLETE REAL ON<br />
: Use a purely real scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER RX)<br />
; LLGCOMPLETE ANOMALOUS ON<br />
: Use a purely anomalous scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER AX)<br />
; LLGCOMPLETE CLASH <CLASH> <br />
: Minimum distance between atoms in log-likelihood gradient maps and also the distance used for determining anisotropy of atoms (default determined by resolution, flagged by CLASH=0)<br />
; LLGCOMPLETE SIGMA <Z><br />
: Z-score (sigma) for accepting peaks as new atoms in log-likelihood gradient maps<br />
; LLGCOMPLETE NCYC <NMAX><br />
: Maximum number of cycles of log-likelihood gradient structure completion. By default, NMAX is 50, but this limit should never be reached, because all features in the log-likelihood gradient maps should be assigned well before 50 cycles are finished. This keyword should be used to reduce the number of cycles to 1 or 2.<br />
; LLGCOMPLETE METHOD [IMAGINARY|ATOMTYPE]<br />
: Pick peaks from the imaginary map only or from all the completion atomtype maps.<br />
* Default: LLGCOMPLETE COMPLETE OFF<br />
* Default: LLGCOMPLETE CLASH 0<br />
* Default: LLGCOMPLETE SIGMA 6<br />
* Default: LLGComplete NCYC 50<br />
* Default: LLGComplete METHOD ATOMTYPE<br />
setLLGC_COMP(bool <True|False>) <br />
setLLGC_CLAS(float <CLASH>) <br />
setLLGC_SIGM(float <Z>) <br />
setLLGC_NCYC(int <NMAX>)<br />
setLLGC_METH(str ["IMAGINARY"|"ATOMTYPE"])<br />
<br />
==[[Image:User2.gif|link=]]NMA== <br />
; NMA MODE <M1> ''{MODE <M2>…}'' <br />
: The MODE keyword gives the mode along which to perturb the structure. If multiple modes are entered, the structure is perturbed along all the modes AND combinations of the modes given. There is no limit on the number of modes that can be entered, but the number of pdb files explodes combinatorially. The first 6 modes are the pure rotation and translation modes and do not lead to perturbation of the structure. If the number M is less than 7 then M is interpreted as the first M modes starting at 7, so for example, MODE 5 would give modes 7 8 9 10 11.<br />
; NMA COMBINATION <NMAX><br />
: Controls how many modes are present in any combination.<br />
* Default: NMA MODE 5<br />
* Default: NMA COMBINATION 2<br />
addNMA_MODE(int <MODE>) <br />
setNMA_COMB(int <NMAX>)<br />
<br />
==[[Image:User2.gif|link=]]PACK==<br />
; PACK SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>ALL ]<br />
: <sup>1</sup>Allow up to the PERCENT of sampling points to clash, considering only pairwise clashes <br />
: <sup>2</sup>Allow all solutions (no packing test)<br />
; PACK CUTOFF <PERCENT> <br />
: Limit on total number (or percent) of clashes <br />
; PACK QUICK [ON|OFF]<br />
: Packing check stops when ALLOWED_CLASHES or MAX_CLASHES is reached. However, all clashes are found when the solution has a high Z-score (see [[#ZSCORE | ZSCORE]]).<br />
; PACK COMPACT [ON|OFF]<br />
: Pack ensembles into a compact association (minimize distances between centres of mass for the addition of each component in a solution).<br />
; PACK KEEP HIGH TFZ [ON|OFF]<br />
: Solutions with high tfz (see [[#ZSCORE | ZSCORE]]) but that fail to pack are retained in the solution list. Set to true if SEARCH PRUNE ON (see [[#SEARCH | SEARCH]])<br />
* Default: PACK SELECT PERCENT<br />
* Default: PACK CUTOFF 5<br />
* Default: PACK COMPACT ON<br />
* Default: PACK QUICK ON<br />
* Default: PACK KEEP HIGH TFZ OFF<br />
* Default: PACK CONSERVATION DISTANCE 1,5<br />
setPACK_SELE(str ["PERCENT"|"ALL"]) <br />
setPACK_CUTO(float <ALLOWED_CLASHES>)<br />
setPACK_QUIC(bool)<br />
setPACK_KEEP_HIGH_TFZ(bool)<br />
setPACK_COMP(bool)<br />
<br />
==[[Image:User2.gif|link=]]PEAKS==<br />
; PEAKS TRA SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL] <br />
; PEAKS ROT SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL]<br />
: Peaks for individual rotation functions (ROT) or individual translation functions (TRA) satisfying selection criteria are saved. To be used for subsequent steps, peaks must also satisfy the overall [[#PURGE | PURGE]] selection criteria, so it will usually be appropriate to set only the PURGE criteria (which over-ride the defaults for the PEAKS criteria if not explicitly set). See [[Molecular_Replacement#How_to_Select_Peaks | How to Select Peaks]]<br />
: <sup>1</sup> Select peaks by taking all peaks over CUTOFF percent of the difference between the top peak and the mean value.<br />
: <sup>2</sup> Select peaks by taking all peaks with a Z-score greater than CUTOFF.<br />
: <sup>3</sup> Select peaks by taking top CUTOFF.<br />
: <sup>4</sup> Select all peaks.<br />
; PEAKS ROT CUTOFF <CUTOFF><br />
; PEAKS TRA CUTOFF <CUTOFF><br />
: Cutoff value for the rotation function (ROT) or translation function (TRA) peak selection criteria.<br />
: If selection is by percent and [[#PURGE | PURGE PERCENT]] is changed from the default, then the PEAKS percent value is set to the lower PURGE percent value.<br />
; PEAKS ROT CLUSTER [ON|OFF] <br />
; PEAKS TRA CLUSTER [ON|OFF]<br />
: Toggle selects clustered or unclustered peaks for rotation function (ROT) or translation function (TRA).<br />
; PEAKS ROT DOWN [PERCENT] <br />
: [[#SEARCH | SEARCH METHOD FAST]] only. Percentage to reduce rotation function cutoff if there is no TFZ over the zscore cutoff that determines a true solution (see [[#ZSCORE | ZSCORE]]) in first search.<br />
* Default: PEAKS ROT SELECT PERCENT<br />
* Default: PEAKS TRA SELECT PERCENT<br />
* Default: PEAKS ROT CUTOFF 75<br />
* Default: PEAKS TRA CUTOFF 75<br />
* Default: PEAKS ROT CLUSTER ON<br />
* Default: PEAKS TRA CLUSTER ON<br />
setPEAK_ROTA_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"]) <br />
setPEAK_TRAN_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"])<br />
setPEAK_ROTA_CUTO(float <CUTOFF>)<br />
setPEAK_TRAN_CUTO(float <CUTOFF>) <br />
setPEAK_ROTA_CLUS(bool <CLUSTER>) <br />
setPEAK_TRAN_CLUS(bool <CLUSTER>)<br />
setPEAK_ROTA_DOWN(float <PERCENT>)<br />
<br />
==[[Image:User2.gif|link=]]PERMUTATIONS== <br />
; PERMUTATIONS [ON|OFF]<br />
: Only relevant to [[#SEARCH | SEARCH METHOD FULL]]. Toggle for whether the order of the search set is to be permuted.<br />
* Default: PERMUTATIONS OFF<br />
setPERM(bool <PERMUTATIONS>)<br />
<br />
==[[Image:User2.gif|link=]]PERTURB== <br />
; PERTURB RMS STEP <RMS><br />
: Increment in rms Ångstroms between pdb files to be written. <br />
; PERTURB RMS MAX <MAXRMS><br />
: The structure will be perturbed along each mode until the MAXRMS deviation has been reached.<br />
; PERTURB RMS DIRECTION [FORWARD|BACKWARD|TOFRO] <br />
: The structure is perturbed either forwards or backwards or to-and-fro (FORWARD|BACKWARD|TOFRO) along the eigenvectors of the modes specified.<br />
; PERTURB INCREMENT [RMS| DQ] <br />
: Perturb the structure by rms devitations along the modes, or by set dq increments<br />
; PERTURB DQ <DQ1> ''{DQ <DQ2>…}''<br />
: Alternatively, the DQ factors (as used by the Elnemo server (K. Suhre & Y-H. Sanejouand, NAR 2004 vol 32) ) by which to perturb the atoms along the eigenvectors can be entered directly.<br />
* Default: PERTURB INCREMENT RMS<br />
* Default: PERTURB RMS STEP 0.2<br />
* Default: PERTURB RMS MAXRMS 0.3<br />
* Default: PERTURB RMS DIRECTION TOFRO<br />
setPERT_INCR(str [ "RMS" | "DQ" ])<br />
setPERT_RMS_MAXI(float <MAX>)<br />
setPERT_RMS_DIRE(str [ "FORWARDS" | "BACKWARDS" | "TOFRO" ]) <br />
addPERT_DQ(float <DQ>)<br />
<br />
==[[Image:User2.gif|link=]]PURGE== <br />
; PURGE ROT ENABLE [ON|OFF]<sup>1</sup><br />
; PURGE ROT PERCENT <PERC><sup>2</sup><br />
; PURGE ROT NUMBER <NUM><sup>3</sup><br />
: Purging criteria for rotation function (RF), where PERCENT and NUMBER are alternative selection criteria (''OR'' criteria)<br />
::<sup>1</sup> Toggle for whether to purge the solution list from the RF according to the top solution found. If there are a number of RF searches with different partial solution backgrounds, the PURGE is applied to the total list of peaks. If there is one clearly significant RF solution from one of the backgrounds it acts to purge all the less significant solutions. If there is only one RF (a single partial solution background) the PURGE gives no additional selection over and above the PEAKS command. <br />
::<sup>2</sup> [[Molecular_Replacement#How_to_Select_Peaks | Selection by percent]]. PERC is percentage of the top peak, where the value of the top peak is defined as 100% and the value of the mean is defined as 0%. Note that this criterion is applied subsequent to any selection criteria applied through the [[#PEAKS | PEAKS]] command. If the [[#PEAKS | PEAKS]] selection is by percent, then the percent cutoff given in the PURGE command over-rides that for [[#PEAKS | PEAKS]], so as to rationalize results in the case of only a single RF (single partial solution background.)<br />
::<sup>3</sup> NUM is the number of solutions to retain in purging. If NUMBER is given (non-zero) it overrides the PERCENT option. NUMBER given as zero is the flag for not applying this criterion.<br />
; PURGE TRA ENABLE [ON|OFF]<br />
; PURGE TRA PERCENT <PERC><br />
; PURGE TRA NUMBER <NUM><br />
: As above, but for translation function<br />
; PURGE RNP ENABLE [ON|OFF]<br />
; PURGE RNP PERCENT <PERC><br />
; PURGE RNP NUMBER <NUM><br />
: As above but for refinement, but with the important distinction that PERCENT and NUMBER are concurrent selection criteria (''AND'' criteria)<br />
* Default: PURGE ROT ENABLE ON <br />
* Default: PURGE ROT PERC 75<br />
* Default: PURGE ROT NUM 0<br />
* Default: PURGE TRA ENABLE ON<br />
* Default: PURGE TRA PERC 75<br />
* Default: PURGE TRA NUM 0<br />
* Default: PURGE RNP ENABLE ON<br />
* Default: PURGE RNP PERC 75<br />
* Default: PURGE RNP NUM 0<br />
setPURG_ROTA_ENAB(bool <ENABLE>)<br />
setPURG_TRAN_ENAB(bool <ENABLE>) <br />
setPURG_RNP_ENAB(bool <ENABLE>)<br />
setPURG_ROTA_PERC(float <PERC>) <br />
setPURG_TRAN_PERC(float <PERC>) <br />
setPURG_RNP_PERC(float <PERC>)<br />
setPURG_ROTA_NUMB(float <NUM>) <br />
setPURG_TRAN_NUMB(float <NUM>)<br />
setPURG_TRAN_NUMB(float <NUM>)<br />
setPURG_RNP_NUMB(float <NUM>)<br />
<br />
==[[Image:User2.gif|link=]]RESOLUTION== <br />
; RESOLUTION HIGH <HIRES> <br />
: High resolution limit in Ångstroms. <br />
; RESOLUTION LOW <LORES><br />
: Low resolution limit in Ångstroms.<br />
; RESOLUTION AUTO HIGH <HIRES> <br />
: High resolution limit in Ångstroms for final high resolution refinement in MR_AUTO mode.<br />
* Default for molecular replacement: Set by [[#ELLG | ELLG TARGET]] for structure solution, final refinement uses all data<br />
* Default for experimental phasing: All data used<br />
setRESO_HIGH(float <HIRES>) <br />
setRESO_LOW(float <LORES>)<br />
setRESO_AUTO_HIGH(float <HIRES>) <br />
setRESO(float <HIRES>,float <LORES>)<br />
<br />
==[[Image:User2.gif|link=]]ROTATE== <br />
; ROTATE VOLUME FULL<br />
: Sample all unique angles <br />
; ROTATE VOLUME AROUND EULER <A> <nowiki><B></nowiki> <C> RANGE <RANGE> <br />
: Restrict the search to the region of +/- RANGE degrees around orientation given by EULER<br />
setROTA_VOLU(string ["FULL"|"AROUND"|) <br />
setROTA_EULE(dvect3 <A B C>) <br />
setROTA_RANG(float <RANGE>)<br />
<br />
==[[Image:User2.gif|link=]]SCATTERING==<br />
; SCATTERING TYPE <TYPE> FP=<FP> FDP=<FDP> FIX [ON|OFF|EDGE]<br />
: Measured scattering factors for a given atom type, from a fluorescence scan. FIX EDGE (default) fixes the fdp value if it is away from an edge, but refines it if it is close to an edge, while FIX ON or FIX OFF does not depend on proximity of edge.<br />
; SCATTERING RESTRAINT [ON|OFF]<br />
: use Fdp restraints<br />
; SCATTERING SIGMA <SIGMA><br />
: Fdp restraint sigma used is SIGMA multiplied by initial fdp value<br />
* Default: SCATTERING SIGMA 0.2<br />
* Default: SCATTERING RESTRAINT ON<br />
addSCAT(str <TYPE>,float <FP>,float <FDP, string <FIXFDP>) <br />
setSCAT_REST(bool) <br />
setSCAT_SIGM(float <SIGMA>)<br />
<br />
==[[Image:User2.gif|link=]]SCEDS== <br />
; SCEDS NDOM <NDOM><br />
:Number of domains into which to split the protein<br />
; SCEDS WEIGHT SPHERICITY <WS><br />
: Weight factor for the the Density Test in the SCED Score. The Sphericity Test scores boundaries that divide the protein into more spherical domains more highly.<br />
; SCEDS WEIGHT CONTINUITY <WC><br />
: Weight factor for the the Continuity Test in the SCED Score. The Continuity Test scores boundaries that divide the protein into domains contigous in sequence more highly. <br />
; SCEDS WEIGHT EQUALITY <WE><br />
: Weight factor for the the Equality Test in the SCED Score. The Equality Test scores boundaries that divide the protein more equally more highly.<br />
; SCEDS WEIGHT DENSITY <WD><br />
: Weight factor for the the Equality Test in the SCED Score. The Density Test scores boundaries that divide the protein into domains more densely packed with atoms more highly. <br />
* Default: SCEDS NDOM 2<br />
* Default: SCEDS WEIGHT EQUALITY 1<br />
* Default: SCEDS WEIGHT SPHERICITY 4 <br />
* Default: SCEDS WEIGHT DENSITY 1<br />
* Default: SCEDS WEIGHT CONTINUITY 0<br />
setSCED_NDOM(int <NDOM>) <br />
setSCED_WEIG_SPHE(float <WS>) <br />
setSCED_WEIG_CONT(float <WC>)<br />
setSCED_WEIG_EQUA(float <WE>) <br />
setSCED_WEIG_DENS(float <WD>)<br />
<br />
==[[Image:User2.gif|link=]]TARGET==<br />
; TARGET ROT [FAST | BRUTE]<br />
: Target function for fast rotation searches (2). BRUTE searches all angles on a grid with the full rotation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these rotations with the full rotation likelihood target.<br />
; TARGET TRA [FAST | BRUTE | PHASED]<br />
: Target function for fast translation searches (3). BRUTE searches all positions on a grid with the full translation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these positions with the full translation likelihood target. PHASED selects the "phased translation function", for which a LABIN command should also be given, specifying FMAP, PHMAP and (optionally) FOM.<br />
* Default: TARGET ROT FAST<br />
* Default: TARGET TRA FAST<br />
setTARG_ROTA(str ["FAST"|"BRUTE"])<br />
setTARG_TRAN(str ["FAST"|"BRUTE"|"PHASED"])<br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS NMOL <NMOL><br />
: Number of molecules/molecular assemblies related by single TNCS vector (usually only 2). If the TNCS is a pseudo-tripling of the cell then NMOL=3, a pseudo-quadrupling then NMOL=4 etc.<br />
* Default: TNCS NMOL 2<br />
setTNCS_NMOL(int <NMOL>)<br />
<br><br />
<br />
==[[Image:User2.gif|link=]]TRANSLATION== <br />
; TRANSLATION VOLUME [ <sup>1</sup>FULL | <sup>2</sup>REGION | <sup>3</sup>LINE | <sup>4</sup>AROUND ])<br />
: Search volume for brute force translation function.<br />
: <sup>1</sup> Cheshire cell or Primitive cell volume. <br />
: <sup>2</sup> Search region.<br />
: <sup>3</sup> Search along line. <br />
: <sup>4</sup> Search around a point.<br />
; <sup>1 2 3</sup>TRANSLATION START <X Y Z> <br />
; <sup>1 2 3</sup>TRANSLATION END <X Y Z><br />
: Search within region or line bounded by START and END.<br />
; <sup>4</sup>TRANSLATION POINT <X Y Z><br />
; <sup>4</sup>TRANSLATION RANGE <RANGE><br />
: Search within +/- RANGE Ångstroms (not fractional coordinates, even if the search point is given as fractional coordinates) of a point <X Y Z>.<br />
; TRANSLATION [ORTH | FRAC]<br />
: Coordinates are given in orthogonal or fractional values.<br />
; TRANSLATION PACKING USE [ON | OFF]<br />
: Top translation function peak will be testes for packing.<br />
; TRANSLATION PACKING CUTOFF <PERC><br />
: Percent pairwise packing used for packing function test of top TF peak. Equivalent to PACK CUTOFF <PERC> for packing function. <br />
; TRANSLATION PACKING NUM <NUM><br />
: Number of translation function peaks to test for packing before bailing out of packing test. Set to 0 to pack all translation function peaks (slow for large packing volumes). <br />
* Default: TRANSLATION VOLUME FULL<br />
* Default: TRANSLATION PACK CUTOFF 50<br />
* Default: TRANSLATION PACK NUM 0 (helices - all packing checked)<br />
* Default: TRANSLATION PACK NUM 500 (non-helices)<br />
setTRAN_VOLU(string ["FULL"|"REGION"|"LINE"|"AROUND"])<br />
setTRAN_START(dvect <START>)<br />
setTRAN_END(dvect <END>)<br />
setTRAN_POINT(dvect <POINT>)<br />
setTRAN_RANGE(float <RANGE>)<br />
setTRAN_FRAC(bool <True=FRAC False=ORTH>)<br />
setTRAN_PACK_USE(bool)<br />
setTRAN_PACK_CUTO(float)<br />
<br />
==[[Image:User2.gif|link=]]ZSCORE== <br />
; ZSCORE USE [ON|OFF]<br />
: Use the TFZ tests. Only applicable with [[#SEARCH | SEARCH METHOD FAST]]. (Note Phaser-2.4.0 and below use "ZSCORE SOLVED 0" to turn off the TFZ tests)<br />
; ZSCORE SOLVED <ZSCORE_SOLVED><br />
: Set the minimum TFZ that indicates a definite solution for amalgamating solutions in FAST search method. <br />
;ZSCORE STOP [ON|OFF]<br />
: Stop adding components beyond point where TFZ is below cutoff when adding multiple components in FAST mode. However, FAST mode will always add one component even if TFZ is below cutoff, or two components if starting search with no components input (no input solution).<br />
; ZSCORE HALF [ON|OFF]<br />
: Set the TFZ for amalgamating solutions in the FAST search method to the maximum of ZSCORE_SOLVED and half the maximum TFZ, to accommodate cases of partially correct solutions in very high TFZ cases (e.g. TFZ > 16)<br />
* Default: ZSCORE USE ON<br />
* Default: ZSCORE SOLVED 8<br />
* Default: ZSCORE HALF ON<br />
* Default: ZSCORE STOP ON<br />
setZSCO_USE(bool <True=ON False=OFF>)<br />
setZSCO_SOLV(floatType ZSCORE_SOLVED)<br />
setZSCO_HALF(bool <True=ON False=OFF>)<br />
setZSCO_STOP(bool <True=ON False=OFF>)<br />
<br><br />
<br><br />
<br />
=Expert Keywords=<br />
<br />
==[[Image:Expert.gif|link=]]MACANO== <br />
; MACANO PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for the refinement of SigmaN in the anisotropy correction<br />
; MACANO ANISO [ON|OFF] BINS [ON|OFF] SOLK [ON|OFF] SOLB [ON|OFF] ''{NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}''<br />
: Macrocycle for the custom refinement of SigmaN in the anisotropy correction. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACANO PROTOCOL DEFAULT<br />
setMACA_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACA(bool <ANISO>,bool <BINS>,bool <SOLK>,bool <SOLB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACMR== <br />
; MACMR PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACMR ROT [ON|OFF] TRA [ON|OFF] BFAC [ON|OFF] VRMS [ON|OFF] ''CELL [ON|OFF] LAST [ON|OFF] NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of molecular replacement solutions. Macrocycles are performed in the order in which they are entered. For description of VRMS see the [[FAQ]]. CELL is the scale factor for the unit cell for maps (EM maps). LAST is a flag that refines the parameters for the last component of a solution only, fixing all the others.<br />
; MACMR CHAINS [ON|OFF]<br />
: Split the ensembles into chains for refinement<br />
: Not possible as part of an automated mode<br />
* Default: MACMR PROTOCOL DEFAULT<br />
* Default: MACMR CHAINS OFF<br />
setMACM_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACM(bool <ROT>,bool <TRA>,bool <BFAC>,bool <VRMS>,bool <CELL>,bool <LAST>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
setMACM_CHAI(bool])<br />
<br />
==[[Image:Expert.gif|link=]]MACOCC== <br />
; MACOCC PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACOCC NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of occupancy for solutions. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACOCC PROTOCOL DEFAULT<br />
setMACO_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACO(int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACSAD== <br />
; MACSAD PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for SAD refinement.<br />
:''n.b. PROTOCOL ALL will crash phaser and is only useful for debugging - see code for details''<br />
; MACSAD XYZ [ON|OFF] OCC [ON|OFF] BFAC [ON|OFF] FDP [ON|OFF] SA [ON|OFF] SB [ON|OFF] SP [ON|OFF] SD [ON|OFF] ''{PK [ON|OFF]} {PB [ON|OFF]} {NCYCLE <NCYC>} MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for SAD refinement. Macrocycles are performed in the order in which they are entered.<br />
*Default: MACSAD PROTOCOL DEFAULT<br />
setMACS_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACS(<br />
bool <XYZ>,bool <OCC>,bool <BFAC>,bool <FDP><br />
bool <SA>,bool <SB>,bool <SP>,bool <SD>,<br />
bool <PK>, bool <PB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACTNCS== <br />
; MACTNCS PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for pseudo-translational NCS refinement.<br />
; MACTNCS ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] ''NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for pseudo-translational NCS refinement. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACTNCS PROTOCOL DEFAULT<br />
setMACT_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACT(bool <ROT>,bool <TRA>,bool <VRMS>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]OCCUPANCY== <br />
; OCCUPANCY WINDOW ELLG <ELLG><br />
: Target eLLG for determining number of residues in window for occupancy refinement. The number of residues in a window will be an odd number. Occupancy refinement will be done for each offset of the refinement window.<br />
; OCCUPANCY WINDOW NRES <NRES><br />
: As an alternative to using the eLLG to define the number of residues in window for occupancy refinement, the number may be input directly. NRES must be an odd number.<br />
; OCCUPANCY WINDOW MAX <NRES><br />
: Maximum number of residues in an occupancy window (determined either by ellg or given as NRES) for which occupancy is refined. Prevents the refinement windows from spanning non-local regions of space.<br />
; OCCUPANCY MIN <MINOCC> MAX <MAXOCC><br />
: Minimum and maximum values of occupancy during refinement.<br />
; OCCUPANCY MERGE [ON/OFF]<br />
: Merge refined occupancies from different window offsets to give final occupancies per residue. If OFF, occupancies from a single window offset will be used, selected using OCCUPANCY OFFSET <N><br />
; OCCUPANCY FRAC <FRAC><br />
: Minimum fraction of the protein for which the occupancy may be set to zero.<br />
; OCCUPANCY OFFSET <N><br />
: If OCCUPANCY MERGE OFF, then <N> defines the single window offset from which final occupancies will be taken<br />
* Default: OCCUPANCY WINDOW ELLG 5<br />
* Default: OCCUPANCY WINDOW MAX 111<br />
* Default: OCCUPANCY MIN 0.01 MAX 1<br />
* Default: OCCUPANCY NCYCLES 1<br />
* Default: OCCUPANCY MERGE ON<br />
* Default: OCCUPANCY FRAC 0.5<br />
* Default: OCCUPANCY OFFSET 0<br />
setOCCU_WIND_ELLG(float <ELLG>)<br />
setOCCU_WIND_NRES(int <NRES>)<br />
setOCCU_WIND_MAX(int <NRES>)<br />
setOCCU_MIN(float <MIN>)<br />
setOCCU_MAX(float <MAX>)<br />
setOCCU_MERG(float <FRAC>)<br />
setOCCU_FRAC(bool)<br />
setOCCU_OFFS(int <N>)<br />
<br />
==[[Image:Expert.gif|link=]]RESCORE== <br />
; RESCORE ROT [ON|OFF]<br />
; RESCORE TRA [ON|OFF]<br />
: Toggle for rescoring of fast rotation function (ROT) or fast translation function (TRA) search peaks. <br />
* Default: RESCORE ROT ON<br />
* Default: RESCORE TRA ON|OFF will depend on whether phaser is running in the mode [[#MODE | MODE MR_AUTO]] with [[#SEARCH | SEARCH METHOD FAST]] or with [[#SEARCH | SEARCH METHOD FULL]], or running the translation function separately [[#MODE | MODE MR_FTF]]. For [[#SEARCH | SEARCH METHOD FAST]] the default also depends on whether or not the expected LLG target [[#ELLG | ELLG TARGET <TARGET>]] value is reached.<br />
setRESC_ROTA(bool)<br />
setRESC_TRAN(bool)<br />
<br />
==[[Image:Expert.gif|link=]]RFACTOR== <br />
; RFACTOR USE [ON|OFF]<br />
: For cases of searching for one ensemble when there is one ensemble in the asymmetric unit, the R-factor for the ensemble at the orientation and position in the input is calculated. If this value is low then MR is not performed in the MR_AUTO job in FAST search mode. Instead, rigid body refinement is performed before exiting. Note that the same R-factor test and cutoff is used for judging success in single-atom molecular replacement (MR_ATOM mode).<br />
; RFACTOR CUTOFF <VALUE><br />
: Rfactor in percent used as cutoff for deciding whether or not the R-factor indicates that MR is not necessary.<br />
* Default: RFACTOR USE ON CUTOFF 35<br />
setRFAC_USE(bool)<br />
setRFAC_CUTO(float <PERCENT>)<br />
<br />
==[[Image:Expert.gif|link=]]SAMPLING==<br />
; SAMPLING ROT <SAMP><br />
; SAMPLING TRA <SAMP><br />
: Sampling of search given in degrees for a rotation search and Ångstroms for a translation search. Sampling for rotation search depends on the mean radius of the Ensemble and the high resolution limit (dmin) of the search.<br />
* Default: SAMP = 2*atan(dmin/(4*meanRadius)) (ROTATION FUNCTION)<br />
* Default: SAMP = dmin/5; (BRUTE TRANSLATION FUNCTION)<br />
* Default: SAMP = dmin/4; (FAST TRANSLATION FUNCTION)<br />
setSAMP_ROTA(float <SAMP>)<br />
setSAMP_TRAN(float <SAMP>)<br />
<br><br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS USE [ON|OFF]<br />
: Use TNCS if present: apply TNCS corrections. (Note: was TNCS IGNORE [ON|OFF] in Phaser-2.4.0)<br />
; TNCS RLIST ADD [ON | OFF]<br />
: Supplement the rotation list used in the translation function with rotations already present in the list of known solutions. New molecules in the same orientation as those in the known search (as occurs with translational ncs) may not have peaks associated with them from the rotation function because the known molecules mask the presence of the ones not yet found. <br />
; TNCS PATT HIRES <hires><br />
: High resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT LORES <lores><br />
: Low resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT PERCENT <percent><br />
: Percent of origin Patterson peak that qualifies as a TNCS vector<br />
; TNCS PATT DISTANCE <distance><br />
: Minimum distance of Patterson peak from origin that qualifies as a TNCS vector<br />
; TNCS TRANSLATION PERTURB [ON | OFF]<br />
: If the TNCS translation vector is on a special position, perturb the vector from the special position before refinement<br />
; TNCS ROTATION RANGE <angle><br />
: Maximum deviation from initial rotation from which to look for rotational deviation. Default uses internally determined value based on resolution of data and size of G-function effective molecular radius. Value of 0 turns rotational refinement off.<br />
; TNCS ROTATION SAMPLING <sampling><br />
: Sampling for rotation search. Default uses internally determined value based on resolution of data and size of G-function effective molecular radius. Value of 0 turns rotational refinement off.<br />
* Default: TNCS USE ON<br />
* Default: TNCS RLIST ADD ON<br />
* Default: TNCS PATT HIRES 5<br />
* Default: TNCS PATT LORES 10<br />
* Default: TNCS PATT PERCENT 20<br />
* Default: TNCS PATT DISTANCE 15 <br />
* Default: TNCS TRANSLATION PERTURB ON<br />
setTNCS_USE(bool)<br />
setTNCS_RLIS_ADD(bool)<br />
setTNCS_PATT_HIRE(float <HIRES>)<br />
setTNCS_PATT_LORE(float <LORES>) <br />
setTNCS_PATT_PERC(float <PERCENT>) <br />
setTNCS_PATT_DIST(float <DISTANCE>)<br />
setTNCS_TRAN_PERT(bool)<br />
setTNCS_ROTA_RANG(float <RANGE>) <br />
setTNCS_ROTA_SAMP(float <SAMPLING>) <br />
<br><br />
<br><br />
<br />
=Developer Keywords=<br />
==[[Image:Developer.gif|link=]]BINS== <br />
; BINS DATA [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the data.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections<br />
; BINS ENSE [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the calaculated structure factos for the ensembles.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections<br />
* Default: BINS DATA MIN 6 MAX 50 WIDTH 500 <br />
* Default: BINS ENSE MIN 6 MAX 1000 WIDTH 1000 <br />
setBINS_DATA_MINI(float <L>)<br />
setBINS_DATA_MAXI(float <H>)<br />
setBINS_DATA_WIDT(float <W>)<br />
setBINS_ENSE_MINI(float <L>)<br />
setBINS_ENSE_MAXI(float <H>)<br />
setBINS_ENSE_WIDT(float <W>)<br />
<br />
==[[Image:Developer.gif|link=]]BFACTOR==<br />
; BFACTOR WILSON RESTRAINT [ON|OFF]<br />
: Toggle to use the Wilson restraint on the isotropic component of the atomic B-factors in SAD phasing.<br />
; BFACTOR SPHERICITY RESTRAINT [ON|OFF] <br />
: Toggle to use the sphericity restraint on the anisotropic B-factors in SAD phasing<br />
; BFACTOR REFINE RESTRAINT [ON|OFF] <br />
: Toggle to use the restraint to zero for the molecular B-factor in molecular replacement.<br />
; BFACTOR WILSON SIGMA <SIGMA><br />
: The sigma of the Wilson restraint.<br />
; BFACTOR SPHERICITY SIGMA <SIGMA><br />
: The sigma of the sphericity restraint.<br />
; BFACTOR REFINE SIGMA <SIGMA><br />
: The sigma of the restraint to zero for the molecular B-factor in molecular replacement.<br />
* Default: BFACTOR WILSON RESTRAINT ON <br />
* Default: BFACTOR SPHERICITY RESTRAINT ON <br />
* Default: BFACTOR REFINE RESTRAINT ON <br />
* Default: BFACTOR WILSON SIGMA 5<br />
* Default: BFACTOR SPHERICITY SIGMA 5<br />
* Default: BFACTOR REFINE SIGMA 6<br />
setBFAC_WILS_REST(bool <True|False>)<br />
setBFAC_SPHE_REST(bool <True|False>)<br />
setBFAC_REFI_REST(bool <True|False>) <br />
setBFAC_WILS_SIGM(float <SIGMA>) <br />
setBFAC_SPHE_SIGM(float <SIGMA>) <br />
setBFAC_REFI_SIGM(float <SIGMA>)<br />
<br />
==[[Image:Developer.gif|link=]]BOXSCALE==<br />
; BOXSCALE <BOXSCALE><br />
: Scale for box for calculating structure factors. The ensembles are put in a box equal to (extent of molecule)*BOXSCALE<br />
* Default: BOXSCALE 4<br />
setBOXS<float <BOXSCALE>)<br />
<br />
==[[Image:Developer.gif|link=]]CELL==<br />
; <span style="color:darkorange">Python Only</span> <br />
: Unit cell dimensions<br />
* Default: Cell read from MTZ file<br />
setCELL(float <A>,float <nowiki><B></nowiki>,float <C>,float <ALPHA>,float <BETA>,float <GAMMA>)<br />
setCELL6(float_array <A B C ALPHA BETA GAMMA>)<br />
<br />
==[[Image:Developer.gif|link=]]COMPOSITION== <br />
; COMPOSITION MIN SOLVENT <PERC><br />
: Minimum solvent to give maximum asu packing volume for automated search copy determination (NUM 0)<br />
* Default: COMPOSITION MIN SOLVENT 0.2<br />
setCOMP_MIN_SOLV(float)<br />
<br />
==[[Image:Developer.gif|link=]]DDM== <br />
; DDM SLIDER <VAL> <br />
: The SLIDER window width is used to smooth the Difference Distance Matrix. <br />
; DDM DISTANCE MIN <VAL> MAX <VAL> STEP <VAL><br />
: The range and step interval, as the fraction of the difference between the lowest and highest DDM values used to step.<br />
; DDM SEPARATION MIN <VAL> MAX <VAL><br />
: Through space separation in Angstroms used.<br />
; DDM SEQUENCE MIN <VAL> MAX <VAL><br />
: The range of sequence separations between matrix pairs.<br />
; DDM JOIN MIN <VAL> MAX <VAL><br />
: The range of lengths of the sequences to join if domain segments are discontinuous in percentages of the polypeptide chain.<br />
* Default: DDM SLIDER 0<br />
* Default: DDM DISTANCE MIN 1 MAX 5 STEP 50<br />
* Default: DDM SEPARATION MIN 7 MAX 14<br />
* Default: DDM SEQUENCE MIN 0 MAX 1<br />
* Default: DDM JOIN MIN 2 MAX 12<br />
setDDM_SLID(int <VAL>) <br />
setDDM_DIST_STEP(int <VAL>) <br />
setDDM_DIST_MINI(int <VAL>) <br />
setDDM_DIST_MAXI(int <VAL>) <br />
setDDM_SEPA_MINI(float <VAL>) <br />
setDDM_SEPA_MAXI(float <VAL>)<br />
setDDM_JOIN_MINI(int <VAL>) <br />
setDDM_JOIN_MAXI(int <VAL>) <br />
setDDM_SEQU_MINI(int <VAL>) <br />
setDDM_SEQU_MAXI(int <VAL>)<br />
<br />
==[[Image:Developer.gif|link=]]ENM== <br />
; ENM OSCILLATORS [ <sup>1</sup>RTB | <sup>2</sup>ALL ] <br />
: Define the way the atoms are used for the elastic network model.<br />
: <sup>1</sup>Use the rotation-translation block method.<br />
: <sup>2</sup>Use all atoms to determine the modes (only for use on very small molecules, less than 250 atoms). <br />
; ENM MAXBLOCKS <MAXBLOCKS><br />
: MAXBLOCKS is the number of rotation-translation blocks for the RTB analysis.<br />
; ENM NRES <NRES><br />
: For the RTB analysis, by default NRES=0 and then it is calculated so that it is as small as it can be without reaching MAXBlocks. <br />
; ENM RADIUS <RADIUS><br />
: Elastic Network Model interaction radius (Angstroms)<br />
; ENM FORCE <FORCE><br />
: Elastic Network Model force constant<br />
* Default: ENM OSCILLATORS RTB MAXBLOCKS 250 NRES 0 RADIUS 5 FORCE 1<br />
setENM_OSCI(str ["RTB"|"CA"|"ALL"])<br />
setENM_RTB_MAXB(float <MAXB>)<br />
setENM_RTB_NRES(float <NRES>) <br />
setENM_RADI(float <RADIUS>) <br />
setENM_FORC(float <FORCE>)<br />
<br />
==[[Image:Developer.gif|link=]]NORMALIZATION==<br />
; <span style="color:darkorange">Scripting Only</span><br />
; NORM EPSFAC WRITE <FILENAME><br />
: The normalization factors that correct for anisotropy in the data are written to BINARY file FILENAME<br />
; NORM EPSFAC READ <FILENAME><br />
: The normalization factors that correct for anisotropy in the data are read from BINARY file FILENAME. Further refinement is automatically turned off.<br />
; <span style="color:darkorange">Python Only</span><br />
The normalization factors that correct for anisotropy in the data, extracted from ResultANO object with getSigmaN(). Anisotropy should subsequently be turned off with setMACA_PROT("OFF").<br />
setNORM_DATA(data_norm <SIGMAN>)<br />
<br />
==[[Image:Developer.gif|link=]]OUTLIER==<br />
; OUTLIER REJECT [ON|OFF]<br />
: Reject low probability data outliers<br />
; OUTLIER PROB <PROB><br />
: Cutoff for rejection of low probablity outliers<br />
* Default: OUTLIER REJECT ON PROB 0.000001<br />
setOUTL_REJE(bool) <br />
setOUTL_PROB(float <PROB>)<br />
<br />
==[[Image:Developer.gif|link=]]PTGROUP== <br />
; PTGROUP COVERAGE <COVERAGE><br />
: Percentage coverage for two sequences to be considered in same pointgroup<br />
; PTGROUP IDENTITY <IDENTITY><br />
: Percentage identity for two sequences to be considered in same pointgroup<br />
; PTGROUP RMSD <RMSD><br />
: Percentage rmsd for two models to be considered in same pointgroup<br />
; PTGROUP TOLERANCE ANGULAR <ANG><br />
: Angular tolerance for pointgroup<br />
; PTGROUP TOLERANCE SPATIAL <DIST><br />
: Spatial tolerance for pointgroup<br />
setPTGR_COVE(float <COVERAGE>) <br />
setPTGR_IDEN(float <IDENTITY>) <br />
setPTGR_RMSD(float <RMSD>) <br />
setPTGR_TOLE_ANGU(float <ANG>) <br />
setPTGR_TOLE_SPAT(float <DIST>)<br />
<br />
==[[Image:Developer.gif|link=]]RESHARPEN== <br />
; RESHARPEN PERCENTAGE <PERC><br />
: Perecentage of the B-factor in the direction of lowest fall-off (in anisotropic data) to add back into the structure factors F_ISO and FWT and FDELWT so as to sharpen the electron density maps<br />
* Default: RESHARPEN PERCENT 100<br />
setRESH_PERC(float <PERCENT>)<br />
<br />
==[[Image:Developer.gif|link=]]SOLPARAMETERS==<br />
; SOLPARAMETERS SIGA FSOL <FSOL> BSOL <BSOL> MIN <MINSIGA><br />
: Babinet solvent parameters for Sigma(A) curves. MINSIGA is the minimum SIGA for Babinet solvent term (low resolution only). The solvent term in the Sigma(A) curve is given by <BR>max(1 - FSOL*exp(-BSOL/(4d^2)),MINSIGA).<br />
; SOLPARAMETERS BULK USE [ON|OFF]<br />
: Toggle for use of solvent mask scaling parameters for ensemble structure factors, applied to Fmask.<br />
; SOLPARAMETERS BULK FSOL <FSOL> BSOL <BSOL> <br />
: Solvent mask scaling parameters for ensemble structure factors, applied to Fmask.<br />
* Default: SOLPARAMETERS SIGA FSOL 1.05 BSOL 501 MIN 0.1<br />
* Default: SOLPARAMETERS SIGA RESTRAINT ON<br />
* Default: SOLPARAMETERS BULK USE OFF<br />
* Default: SOLPARAMETERS BULK FSOL 0.35 BSOL 45<br />
setSOLP_SIGA_FSOL(float <FSOL>) <br />
setSOLP_SIGA_BSOL(float <BSOL>)<br />
setSOLP_SIGA_MIN(float <MINSIGA>)<br />
setSOLP_BULK_USE(bool)<br />
setSOLP_BULK_FSOL(float <FSOL>) <br />
setSOLP_BULK_BSOL(float <BSOL>)<br />
<br />
==[[Image:Developer.gif|link=]]TARGET== <br />
; TARGET ROT FAST TYPE [LERF1 | CROWTHER]<br />
: Target function type for fast rotation searches<br />
; TARGET TRA FAST TYPE [LETF1 | LETF2 | CORRELATION]<br />
: Target function type for fast translation searches<br />
setTARG_ROTA_TYPE(string TYPE)<br />
setTARG_TRAN_TYPE(string TYPE)<br />
<br />
==[[Image:Developer.gif|link=]]TNCS==<br />
; TNCS ROTATION ANGLE <A> <nowiki><B></nowiki> <C><br />
: Input rotational difference between molecules related by the pseudo-translational symmetry vector, specified as rotations in degrees about x, y and z axes. Central value for grid search (RANGE > 0).<br />
; TNCS ROTATION RANGE <A><br />
: Range of angular difference in rotation angles to explore around central angle.<br />
; TNCS ROTATION SAMPLING <A><br />
: Sampling step for rotational grid search.<br />
; TNCS TRA VECTOR <x y z> <br />
: Input pseudo-translational symmetry vector (fractional coordinates). By default the translation is determined from the Patterson.<br />
; TNCS VARIANCE RMSD <num><br />
: Input estimated rms deviation between pseudo-translational symmetry vector related molecules.<br />
; TNCS VARIANCE FRAC <num><br />
: Input estimated fraction of cell content that obeys pseudo-translational symmetry.<br />
; TNCS LINK RESTRAINT [ON | OFF]<br />
: Link the occupancy of atoms related by TNCS in SAD phasing<br />
; TNCS LINK SIGMA <sigma><br />
: Sigma of link restraint of the occupancy of atoms related by TNCS in SAD phasing<br />
* Default: TNCS ROTATION ANGLE 0 0 0<br />
* Default: TNCS ROTATION RANGE -999 (determine from structure size and resolution)<br />
* Default: TNCS ROTATION SAMPLING -999 (determine from structure size and resolution)<br />
* Default: TNCS TRANSLATION VECTOR determined from position of Patterson peak<br />
* Default: TNCS VARIANCE RMSD 0.4 <br />
* Default: TNCS VARIANCE FRAC 1 <br />
* Default: TNCS LINK RESTRAINT ON<br />
* Default: TNCS LINK SIGMA 0.1<br />
setTNCS_ROTA_ANGL(dvect3 <A B C>) <br />
setTNCS_TRAN_VECT(dvect3 <X Y Z>) <br />
setTNCS_VARI_RMSD(float <RMSD>) <br />
setTNCS_VARI_FRAC(float <FRAC>)<br />
setTNCS_LINK_REST(bool)<br />
setTNCS_LINK_SIGM(float <SIGMA>)<br />
; <span style="color:darkorange">Scripting Only</span><br />
; TNCS EPSFAC WRITE <FILENAME><br />
: The normalization factors that correct for tNCS in the data are written to BINARY file FILENAME<br />
; TNCS EPSFAC READ <FILENAME><br />
: The normalization factors that correct for tNCS in the data are read from BINARY file FILENAME. Further refinement is automatically turned off.<br />
; <span style="color:darkorange">Python Only</span><br />
The normalization factors that correct for tNCS in the data, extracted from ResultNCS object with getPtNcs(). tNCS refinement should subsequently be turned off with setMACT_PROT("OFF").<br />
setTNCS(data_tncs <PTNCS>)<br />
<br />
==[[Image:Developer.gif|link=]]TRANSLATION== <br />
; TRANSLATION MAPS [ON | OFF]<br />
: Output maps of fast translation function FSS scoring functions<br />
: Maps take the names <ROOT>.<ensemble>.k.e.map where k is the Known backgound number and e is the Euler angle number for that known background<br />
* Default: TRANSLATION MAPS OFF<br />
setTRAN_MAPS(bool)</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Keywords&diff=2402Keywords2017-01-13T17:40:10Z<p>Airlie: /* link=RESOLUTION */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
===Phaser Executable===<br />
<br />
The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the [[#MODE | MODE]] keyword. The different modes and the keywords relevant to each mode are described in [[Modes]].<br />
<br />
Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. However, some keywords are meaningful when entered multiple times. The order may or may not be important. <br />
<br />
*[[Image:User1.gif|link=]] [[#Basic Keywords | Basic Keywords]]<br />
<br />
*[[Image:Output.png|link=]] [[#Output Control Keywords | Output Control Keywords]]<br />
<br />
*[[Image:User2.gif|link=]] [[#Advanced Keywords |Advanced Keywords ]]<br />
<br />
*[[Image:Expert.gif|link=]] [[#Expert Keywords | Expert Keywords]]<br />
<br />
*[[Image:Developer.gif|link=]] [[#Developer Keywords | Developer Keywords]]<br />
<br />
<br />
===Python Interface===<br />
<br />
Phaser can be compiled as a python library. The mode is selected by calling the appropriate run-job. Input to the run-job is via input-objects, which are passed to the run-job. Setter function on the input objects are equivalent to the keywords for input to the phaser executable. The different modes and the keywords relevant to each mode are described in [[Modes]]. See [[Python Interface]] for details. <br />
<br />
The python interface uses standard python and cctbx/scitbx variable types.<br />
<br />
str string<br />
float double precision floating point<br />
Miller cctbx::miller::index<int> <br />
dvect3 scitbx::vec3<float> <br />
dmat33 scitbx::mat3<float> <br />
'''type'''_array scitbx::af::shared<'''type'''> arrays<br />
<br />
=Basic Keywords=<br />
==[[Image:User1.gif|link=]]ATOM== <br />
; ATOM CRYSTAL <XTALID> PDB <FILENAME><br />
: Definition of atom positions using a pdb file.<br />
; ATOM CRYSTAL <XTALID> HA <FILENAME><br />
: Definition of atom positions using a ha file (from RANTAN, MLPHARE etc.).<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> <br />
: Minimal definition of atom position. B-factor defaults to isotropic and Wilson B-factor. Use <TYPE>=TX for Ta6Br12 cluster and <TYPE>=XX for all other clusters. Scattering for cluster is spherically averaged. Coordinates of cluster compounds other than Ta6Br12 must be entered with CLUSTER keyword. Ta6Br12 coordinates are in phaser code and do not need to be given with CLUSTER keyword.<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> [ ISOB <ISOB> | ANOU <HH KK LL HK HL KL> | USTAR <HH KK LL HK HL KL>] FIXX [ON|OFF] FIXO [ON|OFF] FIXB [ON|OFF] BSWAP [ON|OFF] LABEL <SITE_NAME><br />
: Full definition of atom position including B-factor.<br />
;ATOM CHANGE BFACTOR WILSON [ON|OFF]<br />
: Reset all atomic B-factors to the Wilson B-factor.<br />
; ATOM CHANGE SCATTERER <SCATTERER><br />
:Reset all atomic scatterers to element (or cluster) type.<br />
setATOM_PDB(str <XTALID>,str <PDB FILENAME>)<br />
setATOM_IOTBX(str <XTALID>,iotbx::pdb::hierarchy::root <iotbx object>)<br />
setATOM_STR(str <XTALID>,str <pdb format string>)<br />
setATOM_HA(str <XTALID>,str <FILENAME>)<br />
addATOM(str <XTALID>,str <TYPE>,<br />
float <X>,float <Y>,float <Z>,float <OCC>)<br />
addATOM_FULL(str <XTALID>,str <TYPE>,bool <ORTH>,<br />
dvect3 <X Y Z>,float <OCC>,bool <ISO>,float <ISOB>,<br />
bool <ANOU>,dmat6 <HH KK LL HK HL KL>,<br />
bool <FIXX>,bool <FIXO>,bool <FIXB>,bool <SWAPB>,<br />
str <SITE_NAME>)<br />
setATOM_CHAN_BFAC_WILS(bool)<br />
setATOM_CHAN_SCAT(bool)<br />
setATOM_CHAN_SCAT_TYPE(str <TYPE>)<br />
<br />
==[[Image:User1.gif|link=]]CLUSTER== <br />
; CLUSTER PDB <PDBFILE><br />
: Sample coordinates for a cluster compound for experimental phasing. Clusters are specified with type XX. Ta6Br12 clusters do not need to have coordinates specified as the coordinates are in the phaser code. To use Ta6Br12 clusters, specify atomtypes/clusters as TX.<br />
setCLUS_PDB(str <PDBFILE>)<br />
addCLUS_PDB(str <ID>, str <PDBFILE>)<br />
<br />
==[[Image:User1.gif|link=]]COMPOSITION== <br />
; COMPOSITION BY [ <sup>1</sup>AVERAGE| <sup>2</sup>SOLVENT| <sup>3</sup>ASU ]<br />
: Alternative ways of defining composition<br />
: <sup>1</sup> AVERAGE solvent fraction for crystals (50%)<br />
: <sup>2</sup> Composition entered by solvent content.<br />
: <sup>3</sup> Explicit description of composition of ASU by sequence or molecular weight<br />
; <sup>2</sup>COMPOSITION PERCENTAGE <SOLVENT><br />
: Specified SOLVENT content<br />
; <sup>3</sup>COMPOSITION PROTEIN [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of protein in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION NUCLEIC [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of nucleic acid in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION ATOM <TYPE> NUMBER <NUM><br />
: Add NUM copies of an atom (usually a heavy atom) to the composition<br />
* Default: COMPOSITION BY ASU<br />
setCOMP_BY(str ["AVERAGE" | "SOLVENT" | "ASU" ])<br />
setCOMP_PERC(float <SOLVENT>)<br />
addCOMP_PROT_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_PROT_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_PROT_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_PROT_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_NUCL_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_NUCL_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_NUCL_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_NUCL_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_ATOM(str <TYPE>,float <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]CRYSTAL== <br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN Fpos =<F+> SIGFpos=<SIG+> Fneg=<F-> SIGFneg=<SIG-><br />
: Columns of MTZ file to read for this (anomalous) dataset<br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN F =<F> SIGF=<SIGF><br />
: Columns of MTZ file to read for this (non-anomalous) dataset. Used for LLG completion in SAD phasing when there is no anomalous signal (single atom MR protocol). Use LABIN for MR.<br />
setCRYS_ANOM_LABI(str <F+>,str <SIGF+>,str <F->,str <SIGF->) <br />
setCRYS_MEAN_LABI(str <F>,str <SIGF>)<br />
<br />
==[[Image:User1.gif|link=]]ENSEMBLE== <br />
; ENSEMBLE <MODLID> [PDB|CIF] <PDBFILE> [RMS <RMS><sup>1</sup> | ID <ID><sup>2</sup> | CARD ON<sup>3</sup>] ''CHAIN "<CHAIN>"<sup>4</sup> MODEL <NUM><sup>5</sup>''<br />
: The names of the PDB/CIF files used to build the ENSEMBLE, and either<br />
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
:: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file (e.g. "REMARK PHASER ENSEMBLE MODEL 1 ID 31.2") containing the superimposed models concatenated in the one file. This syntax enables simple automation of the use of ensembles. The pdb file can be non-standard because the atom list for the different models need not be the same.<br />
:: <sup>4</sup> CHAIN is selected from the pdb file. <br />
:: <sup>5</sup> MODEL number is selected from the pdb file.<br />
; ENSEMBLE <MODLID> HKLIN <MTZFILE> F=<F> PHI=<PHI> EXTENT <EX> <EY> <EZ> RMS <RMS> CENTRE <CX> <CY> <CZ> PROTEIN MW <PMW> NUCLEIC MW <NMW> ''CELL SCALE <SCALE>''<br />
: An ENSEMBLE defined from a map (via an mtz file). The molecular weight of the object the map represents is required for scaling. The effective RMS coordinate error is needed to judge how the map accuracy falls off with resolution. For density obtained from an EM image reconstruction, a good first guess would be to take the resolution where the FSC curve drops below 0.5 and divide by 3. The extent (difference between maximum and minimum x,y,z coordinates of region containing model density) is needed to determine reasonable rotation steps, and the centre is needed to carry out a proper interpolation of the molecular transform. The extent and the centre are both given in Ångstroms. The cell scale factor defaults to 1 and can be refined (for example, if the map is from electron microscopy when the cell scale may be unknown to within a few percent).<br />
; ENSEMBLE <MODLID> ATOM <TYPE> RMS <RMS><br />
: Define an ensemble as a single atom for single atom MR<br />
; ENSEMBLE <MODLID> HELIX <NUM> <br />
: Define an ensemble as a helix with NUM residues<br />
; ENSEMBLE <MODLID> HETATM [ON|OFF]<br />
: Use scattering from HETATM records in pdb file. See [[Molecular_Replacement#Coordinate_Editing | Coordinate Editing ]]<br />
; ENSEMBLE <MODLID> DISABLE CHECK [ON|OFF]<br />
: Toggle to disable checking of deviation between models in an ensemble. '''Use with extreme caution'''. Results of computations are not guaranteed to be sensible.<br />
; ENSEMBLE <MODLID> ESTIMATOR [OEFFNER | OEFFNERHI | OEFFNERLO | CHOTHIALESK ]<br />
: Define the estimator function for converting ID to RMS<br />
; ENSEMBLE <MODLID> PTGRP [COVERAGE | IDENTITY | RMSD | TOLANG | TOLSPC | EULER | SYMM ]<br />
: Define the pointgroup parameters <br />
; ENSEMBLE <MODLID> BINS [MIN <N>| MAX <M>| WIDTH <W> ]<br />
: Define the Fcalc reflection binning parameters <br />
; ENSEMBLE <MODLID> TRACE [PDB|CIF] <PDBFILE><br />
: Define the coordinates used for packing independent of the coordinates used for structure factor calculation<br />
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
:: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file <br />
; ENSEMBLE <MODLID> TRACE SAMPLING MIN <DIST> <br />
: Set the minimum distance for the sampling of packing grid<br />
; ENSEMBLE <MODLID> TRACE SAMPLING TARGET <NUM> <br />
: Set the target for the number of points to sample the smallest molecule to be packed<br />
; ENSEMBLE <MODLID> TRACE SAMPLING RANGE <NUM> <br />
: Target range (TARGET+/-RANGE) for search for hexgrid points in protein volume<br />
; ENSEMBLE <MODLID> TRACE SAMPLING USE [AUTO | ALL | CALPHA | HEXGRID ]<br />
: Sample trace coordinates using all atoms, C-alpha atoms, a hexagonal grid in the atomic volume or use an automatically determined choice<br />
; ENSEMBLE <MODLID> TRACE SAMPLING DISTANCE <DIST> <br />
: Set the distance for the sampling of the hexagonal grid explicitly and do not use TARGET to find default sampling distance<br />
; ENSEMBLE <MODLID> TRACE SAMPLING WANG <WANG> <br />
: Scale factor for the size of the Wang mask generated from an ensemble map<br />
; ENSEMBLE <MODLID> TRACE PDB <PDBFILE> <br />
: Use the given set of coordinates for packing rather than using the coordinates for structure factor calculation<br />
* Default: ENSEMBLE <MODLID> DISABLE CHECK OFF<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING MIN 1.0<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING TARGET 1000<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING RANGE 100<br />
addENSE_PDB_ID(str <MODLID>,str <FILE>,float <ID>) <br />
addENSE_PDB_RMS(str <MODLID>,str <FILE>,float <RMS>) <br />
setENSE_TRAC_SAMP_MIN(MODLID,float <MIN>)<br />
setENSE_TRAC_SAMP_TARG(MODLID,int <TARGET>)<br />
setENSE_TRAC_SAMP_RANG(MODLID,int <RANGE>)<br />
setENSE_TRAC_SAMP_USE(MODLID,str)<br />
setENSE_TRAC_SAMP_DIST(MODLID,float <DIST>)<br />
setENSE_TRAC_SAMP_WANG(MODLID,float <WANG>)r <FILE>,float <RMS>)<br />
addENSE_CARD(str <MODLID>,str <FILE>,bool)<br />
addENSE_MAP(str <MODLID>,str <MTZFILE>,str <F>,str <PHI>,dvect3 <EX EY EZ>,<br />
float <RMS>,dvect3 <CX CY CZ>,float <PMW>,float <NMW>,float <CELL>)<br />
setENSE_DISA_CHEC(bool)<br />
<br />
==[[Image:User1.gif|link=]]HKLIN==<br />
; HKLIN <FILENAME><br />
: The mtz file containing the data<br />
setHKLI(str <FILENAME>)<br />
<br />
==[[Image:User1.gif|link=]]JOBS== <br />
; JOBS <NUM><br />
: Number of processors to use in parallelized sections of code<br />
* Default: JOBS 2<br />
setJOBS(int <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]LABIN== <br />
; LABIN F = <F> SIGF = <SIGF> <br />
: Columns in mtz file. F must be given. SIGF should be given but is optional<br />
; LABIN I = <nowiki><I></nowiki> SIGI = <SIGI> <br />
: Columns in mtz file. I must be given. SIGI should be given but is optional<br />
; LABIN FMAP = <PH> PHMAP = <PHMAP> <br />
: Columns in mtz file. FMAP/PHMAP are weighted coefficients for use in the Phased Translation Function.<br />
; LABIN FMAP = <PH> PHMAP = <PHMAP> FOM = <FOM><br />
: Columns in mtz file. FMAP/PHMAP are unweighted coefficients for use in the Phased Translation Function and FOM the figure of merit for weighting<br />
setLABI_F_SIGF(str <F>,str <SIGF>)<br />
setLABI_I_SIGI(str <nowiki><I></nowiki>,str <SIGI>)<br />
setLABI_PTF(str <FMAP>,str <PHMAP>,str <FOM>)<br />
<br />
''Data should be input to python run-jobs using one data_refl parameter''<br />
''This is extracted from the ResultMR_DAT object after a call to runMR_DAT''<br />
setREFL_DATA(data_ref)<br />
''Example:''<br />
i = InputMR_DAT()<br />
i.setHKLI("*.mtz")<br />
i.setLABI_F_SIGF("F","SIGF")<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputMR_LLG()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.setREFL_DATA(r.getDATA())<br />
''See also: '' [[Python Example Scripts]]<br />
<br />
''Alternatively, reflection arrays can be set using cctbx::af::shared<double>''<br />
setREFL_F_SIGF(float_array <F>,float_array <SIGF>)<br />
setREFL_I_SIGI(float_array <nowiki><I></nowiki>,float_array <SIGI>)<br />
setREFL_PTF(float_array <FMAP>,float_array <PHMAP>,float_array <FOM>)<br />
<br />
==[[Image:User1.gif|link=]]MODE==<br />
; MODE [ ANO | CCA | SCEDS | NMAXYZ | NCS | MR_ELLG | MR_AUTO | MR_GYRE | MR_ATOM | MR_ROT | MR_TRA | MR_RNP | | MR_OCC | MR_PAK | EP_AUTO | EP_SAD]<br />
: The mode of operation of Phaser. The different modes are described in a separate page on [[Keyword Modes]]<br />
ResultANO r = runANO(InputANO)<br />
ResultCCA r = runCCA(InputCCA)<br />
ResultNMA r = runSCEDS(InputNMA)<br />
ResultNMA r = runNMAXYZ(InputNMA)<br />
ResultNCS r = runNCS(InputNCS)<br />
ResultELLG r = runMR_ELLG(InputMR_ELLG)<br />
ResultMR r = runMR_AUTO(InputMR_AUTO)<br />
ResultEP r = runMR_ATOM(InputMR_ATOM)<br />
ResulrMR_RF r = runMR_FRF(InputMR_FRF)<br />
ResultMR_TF r = runMR_FTF(InputMR_FTF)<br />
ResultMR r = runMR_RNP(InputMR_RNP)<br />
ResultGYRE r = runMR_GYRE(InputMR_RNP)<br />
ResultMR r = runMR_OCC(InputMR_OCC)<br />
ResultMR r = runMR_PAK(InputMR_PAK)<br />
ResultEP r = runEP_AUTO(InputEP_AUTO)<br />
ResultEP_SAD r = runEP_SAD(InputEP_SAD)<br />
<br />
==[[Image:User1.gif|link=]]PARTIAL== <br />
; PARTIAL PDB <PDBFILE> [RMSIDENTITY] <RMS_ID><br />
: The partial structure for MR-SAD substructure completion. Note that this must already be correctly placed, as the experimental phasing module will not carry out molecular replacement.<br />
; PARTIAL HKLIN <MTZFILE> [RMS|IDENTITY] <RMS_ID><br />
: The partial electron density for MR-SAD substructure completion.<br />
; PARTIAL LABIN FC=<FC> PHIC=<PHIC><br />
: Column labels for partial electron density for MR-SAD substructure completion.<br />
setPART_PDB(str <PDBFILE>)<br />
setPART_HKLI(str <MTZFILE>) <br />
setPART_LABI_FC(str <FC>)<br />
setPART_LABI_PHIC(str <PHIC>) <br />
setPART_VARI(str ["ID"|"RMS"])<br />
setPART_DEVI(float <RMS_ID>)<br />
<br />
==[[Image:User1.gif|link=]]SEARCH==<br />
; SEARCH ENSEMBLE <MODLID> ''{OR ENSEMBLE <MODLID>}… NUMBER <NUM><sup>*</sup>''<br />
: The ENSEMBLE to be searched for in a rotation search or an automatic search. When multiple ensembles are given using the OR keyword, the search is performed for each ENSEMBLE in turn. When the keyword is entered multiple times, each SEARCH keyword refers to a new component of the structure. If the component is present multiple times the sub-keyword NUMber can be used (rather than entering the same SEARCH keyword NUMber times).<br />
: <sup>*</sup>For automatic determination of search number use NUMBER 0. If the composition is entered, the maximum number will be that defined by the composition, otherwise the maximum number will fill the asymmetric unit to a minimum solvent content of 20%. Searches for new components will continue until the TFZ score is above 8, and terminate if the TFZ score drops below 8 before the placement of the maximum number of components.<br />
; SEARCH METHOD [FULL|FAST]<br />
: Search using the [[Modes#Modes |full search]] or [[Modes#Modes | fast search]] algorithms.<br />
; SEARCH ORDER AUTO [ON|OFF]<br />
: Search in the "best" order as estimated using estimated rms deviation and completeness of models.<br />
; SEARCH PRUNE [ON|OFF]<br />
: For high TFZ solutions that fail the packing test, carry out a sliding-window occupancy refinement and prune residues that refine to low occupancy, in an effort to resolve packing clashes. If this flag is set to true, the flag for keeping high tfz score solutions (see [[#PACK | PACK]]) that don't pack is also set to true (PACK KEEP HIGH TFZ ON).<br />
; SEARCH AMALGAMATE USE [ON|OFF]<br />
: For multiple high TFZ solutions, enable amalgamation into a single solution<br />
; SEARCH BFACTOR <BFAC><br />
: B-factor applied to search molecule (or atom).<br />
; SEARCH OFACTOR <OFAC><br />
: Occupancy factor applied to search molecule (or atom).<br />
* Default: SEARCH METHOD FAST<br />
* Default: SEARCH ORDER AUTO ON<br />
* Default: SEARCH PRUNE ON<br />
* Default: SEARCH AMALGAMATE USE ON<br />
* Default: SEARCH BFACTOR 0<br />
* Default: SEARCH OFACTOR 1<br />
addSEAR_ENSE_NUM(str <MODLID>,int <NUM>) <br />
addSEAR_ENSE_OR_ENSE_NUM(string_array <MODLIDS>,int <NUM>) <br />
setSEAR_METH(str [ "FULL" | "FAST" ])<br />
setSEAR_ORDE_AUTO(bool)<br />
setSEAR_PRUN(bool <PRUNE>)<br />
setSEAR_AMAL_USE(bool <AMAL>)<br />
setSEAR_BFAC(float <BFAC>)<br />
setSEAR_OFAC(float <OFAC>)<br />
<br />
==[[Image:User1.gif|link=]]SGALTERNATIVE==<br />
; SGALTERNATIVE SELECT [<sup>1</sup>ALL| <sup>2</sup>HAND| <sup>3</sup>LIST| <sup>4</sup>NONE]<br />
: Selection of alternative space groups to test in translation functions i.e. those that are in same laue group as that given in [[#SPACEGROUP | SPACEGROUP]]<br />
: <sup>1</sup> Test all possible space groups, <br />
: <sup>2</sup> Test the given space group and its enantiomorph.<br />
: <sup>3</sup> Test the space groups listed with SGALTERNATIVE TEST <SG>.<br />
: <sup>4</sup> Do not test alternative space groups.<br />
; SGALTERNATIVE TEST <SG><br />
: Alternative space groups to test. Multiple test space groups can be entered.<br />
* Default: SGALTERNATIVE SELECT HAND<br />
setSGAL_SELE(str [ "ALL" | "HAND" | "LIST" | "NONE" ]) <br />
addSGAL_TEST(str <SG>)<br />
<br />
==[[Image:User1.gif|link=]]SOLUTION==<br />
; SOLUTION SET <ANNOTATION><br />
: Start new set of solutions <br />
; SOLUTION TEMPLATE <ANNOTATION><br />
: Specifies a template solution against which other solutions in this run will be compared. Given in place of SOLUTION SET. Template rotation and translations given by subsequent SOLUTION 6DIM cards as per SOLUTION SETS.<br />
; SOLUTION 6DIM ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> [ORTH|FRAC] <X> <Y> <Z> ''FIXR [ON|OFF] FIXT [ON|OFF] FIXB [ON|OFF] BFAC <BFAC> MULT <MULT>''<br />
: This keyword is repeated for each known position and orientation of an ENSEMBLE MODLID. A B G are the Euler angles (z-y-z convention) and X Y Z are the translation elements, expressed either in orthogonal Angstroms (ORTH) or fractions of a cell edge (FRAC). The input ensemble is transformed by a rotation around the origin of the coordinate system, followed by a translation. BFAC default to 0, MULT (for multiplicity) defaults to 1.<br />
; SOLUTION ENSEMBLE <MODLID> VRMS DELTA <DELTA> RMSD <RMSD><br />
: Refined RMS variance terms for pdb files (or map) in ensemble MODLID. RMSD is the input RMSD of the job that produced the sol file, DELTA is the shift with respect to this RMSD. If given as part of a solution, these values overwrite the values used for input in the ENSEMBLE keyword (if refined).<br />
; SOLUTION ENSEMBLE <MODLID> CELL SCALE <SCALE><br />
: Refined cell scale factor. Only applicable to ensembles that are maps<br />
; SOLUTION TRIAL ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> RF <RF> RFZ <RFZ><br />
: Rotation List for translation function<br />
; SOLUTION ORIGIN ENSEMBLE <MODLID><br />
: Create solution for ensemble MODLID at the origin<br />
; SOLUTION SPACEGROUP <SG><br />
: Space Group of the solution (if alternative spacegroups searched)<br />
; SOLUTION RESOLUTION <HIRES><br />
: High resolution limit of data used to find/refine this solution<br />
; SOLUTION PACKS <PACKS><br />
: Flag for whether solution has been retained despite failing packing test, due to having high TFZ<br />
setSOLU(mr_solution <SOL>) <br />
addSOLU_SET(str <ANNOTATION>) <br />
addSOLU_TEMPLATE(str <ANNOTATION>) <br />
addSOLU_6DIM_ENSE(str <MODLID>,dvect3 <A B C>,bool <FRAC>,dvect3 <X Y Z>,<br />
float <BFAC>,bool <FIXR>,bool <FIXT>,bool <FIXB>,int <MULT>, 1.0) <br />
addSOLU_ENSE_DRMS(str <MODLID>, float <DRMS>) <br />
addSOLU_ENSE_CELL(str <MODLID>, float <SCALE>)<br />
addSOLU_TRIAL_ENSE(string <MODLID>,dvect3 <A B C>,float <RF>, float <RFZ>)<br />
addSOLU_ORIG_ENSE(string <MODLID>)<br />
setSOLU_SPAC(str <SG>)<br />
setSOLU_RESO(float <HIRES>)<br />
setSOLU_PACK(bool <PACKS>)<br />
<br />
==[[Image:User1.gif|link=]]SPACEGROUP==<br />
; SPACEGROUP <SG><br />
: Space group may be altered from the one on the MTZ file to a space group in the same point group. The space group can be entered in one of three ways<br />
#The Hermann-Mauguin symbol e.g. P212121 or P 21 21 21 (with or without spaces)<br />
#The international tables number, which gives standard setting e.g. 19 <br />
#The Hall symbols e.g. P 2ac 2ab<br />
: '''The space group can also be a subgroup of the merged space group'''. For example, P1 is always allowed. The reflections will be expanded to the symmetry of the given subgroup. This is only a valid approach when the true symmetry is the symmetry of the subgroup and perfect twinning causes the data to merge "perfectly" in the higher symmetry. <br />
:'''A list of the allowed space groups in the same point group as the given space group (or space group read from MTZ file) and allowed subgroups of these is given in the Cell Content Analysis logfile.'''<br />
* Default: Read from MTZ file<br />
setSPAC_NUM(int <NUM>)<br />
setSPAC_NAME(string <HM>)<br />
setSPAC_HALL(string <HALL>)<br />
<br />
==[[Image:User1.gif|link=]]WAVELENGTH== <br />
; WAVELENGTH <LAMBDA> <br />
: The wavelengh at which the SAD dataset was collected<br />
setWAVE(float <LAMBDA>)<br />
<br><br />
<br><br />
<br />
=Output Control Keywords=<br />
==[[Image:Output.png|link=]]DEBUG== <br />
; DEBUG [ON|OFF]<br />
: Extra verbose output for debugging<br />
* Default: DEBUG OFF<br />
setDEBU(bool) <br />
<br />
==[[Image:Output.png|link=]]EIGEN==<br />
; EIGEN WRITE [ON|OFF]<br />
; EIGEN READ <EIGENFILE><br />
: Read or write a file containing the eigenvectors and eigenvalues. If reading, the eigenvalues and eigenvectors of the Hessian are read from the file generated by a previous run, rather than calculated. This option must be used with the job that generated the eigenfile and the job reading the eigenfile must have identical input for the ENM parameters. Use WRITE to control whether or not the eigenfile is written when not using the READ mode.<br />
* Default: EIGEN WRITE ON<br />
setEIGE_WRIT(bool)<br />
setEIGE_READ(str <EIGENFILE>)<br />
<br />
==[[Image:Output.png|link=]]HKLOUT== <br />
; HKLOUT [ON|OFF]<br />
: Flags for output of an mtz file containing the phasing information<br />
* Default: HKLOUT ON<br />
setHKLO(bool) <br />
<br />
==[[Image:Output.png|link=]]KEYWORDS== <br />
; KEYWORDS [ON|OFF]<br />
: Write output Phaser .sol file (.rlist file for rotation function)<br />
* Default: KEYWORDS ON<br />
setKEYW(bool)<br />
<br />
==[[Image:Output.gif|link=]]LLGMAPS==<br />
; LLGMAPS [ON|OFF]<br />
: Write log-likelihood gradient map coefficients to MTZ file<br />
* Default: LLGMAPS OFF<br />
setLLGM(bool <True|False>)<br />
<br />
==[[Image:Output.png|link=]]MUTE== <br />
; MUTE [ON|OFF]<br />
: Toggle for running in silent/mute mode, where no logfile is written to ''standard output''.<br />
* Default: MUTE OFF<br />
setMUTE(bool) <br />
<br />
==[[Image:Output.png|link=]]KILL== <br />
; KILL TIME [MINS]<br />
: Kill Phaser after MINS minutes of CPU have elapsed, provided parallel section is complete<br />
; KILL FILE [FILENAME]<br />
: Kill Phaser if file FILENAME is present, provided parallel section is complete<br />
* Default: KILL TIME 0 ''Phaser runs to completion''<br />
* Detaulf: KILL FILE "" ''Phaser runs to completion''<br />
setKILL_TIME(float) <br />
setKILL_FILE(string)<br />
<br />
==[[Image:Output.png|link=]]OUTPUT== <br />
; OUTPUT LEVEL [SILENT|CONCISE|SUMMARY|LOGFILE|VERBOSE|DEBUG]<br />
: Output level for logfile<br />
; OUTPUT LEVEL [0|1|2|3|4|5]<br />
: Output level for logfile (equivalent to keyword level setting)<br />
* Default: OUTPUT LEVEL LOGFILE<br />
setOUTP_LEVE(string)<br />
setOUTP(enum)<br />
<br />
==[[Image:Output.png|link=]]TITLE==<br />
; TITLE <TITLE><br />
: Title for job<br />
* Default: TITLE [no title given]<br />
setTITL(str <TITLE>)<br />
<br />
==[[Image:Output.png|link=]]TOPFILES== <br />
; TOPFILES <NUM><br />
: Number of top pdbfiles or mtzfiles to write to output.<br />
* Default: TOPFILES 1<br />
setTOPF(int <NUM>) <br />
<br />
==[[Image:Output.png|link=]]ROOT== <br />
; ROOT <FILEROOT><br />
: Root filename for output files (e.g. FILEROOT.log)<br />
* Default: ROOT PHASER<br />
setROOT(string <FILEROOT>)<br />
<br />
==[[Image:Output.png|link=]]VERBOSE== <br />
; VERBOSE [ON|OFF] <br />
: Toggle to send verbose output to log file.<br />
* Default: VERBOSE OFF<br />
setVERB(bool) <br />
<br />
==[[Image:Output.png|link=]]XYZOUT== <br />
; XYZOUT [ON|OFF] ''ENSEMBLE [ON|OFF]<sup>1</sup> PACKING [ON|OFF]<sup>2</sup>''<br />
: Toggle for output coordinate files. <br />
::<sup>1</sup> If the optional ENSEMBLE keyword is ON, then each placed ensemble is written to its own pdb file. The files are named FILEROOT.#.#.pdb with the first # being the solution number and the second # being the number of the placed ensemble (representing a SOLU 6DIM entry in the .sol file). <br />
::<sup>2</sup> If the optional PACKING keyword is ON, then the hexagonal grid used for the packing analysis is output to its own pdb file FILEROOT.pak.pdb<br />
* Default: XYZOUT OFF (Rotation functions)<br />
* Default: XYZOUT ON ENSEMBLE OFF (all other relevant modes)<br />
* Default: XYZOUT ON PACKING OFF (all other relevant modes)<br />
setXYZO(bool) <br />
setXYZO_ENSE(bool)<br />
setXYZO_PACK(bool)<br />
<br><br />
<br><br />
<br />
=Advanced Keywords=<br />
==[[Image:User2.gif|link=]]ELLG==<br />
([[Molecular_Replacement#Should_Phaser_Solve_It.3F|explained here]])<br />
; ELLG TARGET <TARGET><br />
: Target value for expected LLG for determining resolution limits and search order<br />
<!--; ELLG HIRES <HIRES> Internal control only--><br />
* Default: ELLG TARGET 225<br />
setELLG_TARG(float <TARGET>)<br />
<br />
==[[Image:User2.gif|link=]]FORMFACTORS==<br />
; FORMFACTORS [XRAY | ELECTRON | NEUTRON]<br />
: Use scattering factors from x-ray, electron or neutrons<br />
* Default: FORMFACTORS XRAY<br />
setFORM(string XRAY)<br />
<br />
==[[Image:User2.gif|link=]]HAND==<br />
; HAND [ <sup>1</sup>ON| <sup>2</sup>OFF| <sup>3</sup>BOTH]<br />
: Hand of heavy atoms for experimental phasing<br />
: <sup>1</sup>Phase using the other hand of heavy atoms <br />
: <sup>2</sup>Phase using given hand of heavy atoms <br />
: <sup>3</sup>Phase using both hands of heavy atoms<br />
* Default: HAND BOTH<br />
setHAND(str [ "OFF" | "ON" | "BOTH" ])<br />
<br />
==[[Image:User2.gif|link=]]LLGCOMPLETE==<br />
; LLGCOMPLETE COMPLETE [ON|OFF]<br />
: Toggle for structure completion by log-likelihood gradient maps<br />
; LLGCOMPLETE SCATTERER <TYPE> <br />
: Atom/Cluster type(s) to be used for log-likelihood gradient completion. If more than one element is entered for log-likelihood gradient completion, the atom type that gives the highest Z-score for each peak is selected. Type = "RX" is a purely real scatterer and type="AX" is purely anomalous scatterer<br />
; LLGCOMPLETE REAL ON<br />
: Use a purely real scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER RX)<br />
; LLGCOMPLETE ANOMALOUS ON<br />
: Use a purely anomalous scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER AX)<br />
; LLGCOMPLETE CLASH <CLASH> <br />
: Minimum distance between atoms in log-likelihood gradient maps and also the distance used for determining anisotropy of atoms (default determined by resolution, flagged by CLASH=0)<br />
; LLGCOMPLETE SIGMA <Z><br />
: Z-score (sigma) for accepting peaks as new atoms in log-likelihood gradient maps<br />
; LLGCOMPLETE NCYC <NMAX><br />
: Maximum number of cycles of log-likelihood gradient structure completion. By default, NMAX is 50, but this limit should never be reached, because all features in the log-likelihood gradient maps should be assigned well before 50 cycles are finished. This keyword should be used to reduce the number of cycles to 1 or 2.<br />
; LLGCOMPLETE METHOD [IMAGINARY|ATOMTYPE]<br />
: Pick peaks from the imaginary map only or from all the completion atomtype maps.<br />
* Default: LLGCOMPLETE COMPLETE OFF<br />
* Default: LLGCOMPLETE CLASH 0<br />
* Default: LLGCOMPLETE SIGMA 6<br />
* Default: LLGComplete NCYC 50<br />
* Default: LLGComplete METHOD ATOMTYPE<br />
setLLGC_COMP(bool <True|False>) <br />
setLLGC_CLAS(float <CLASH>) <br />
setLLGC_SIGM(float <Z>) <br />
setLLGC_NCYC(int <NMAX>)<br />
setLLGC_METH(str ["IMAGINARY"|"ATOMTYPE"])<br />
<br />
==[[Image:User2.gif|link=]]NMA== <br />
; NMA MODE <M1> ''{MODE <M2>…}'' <br />
: The MODE keyword gives the mode along which to perturb the structure. If multiple modes are entered, the structure is perturbed along all the modes AND combinations of the modes given. There is no limit on the number of modes that can be entered, but the number of pdb files explodes combinatorially. The first 6 modes are the pure rotation and translation modes and do not lead to perturbation of the structure. If the number M is less than 7 then M is interpreted as the first M modes starting at 7, so for example, MODE 5 would give modes 7 8 9 10 11.<br />
; NMA COMBINATION <NMAX><br />
: Controls how many modes are present in any combination.<br />
* Default: NMA MODE 5<br />
* Default: NMA COMBINATION 2<br />
addNMA_MODE(int <MODE>) <br />
setNMA_COMB(int <NMAX>)<br />
<br />
==[[Image:User2.gif|link=]]PACK==<br />
; PACK SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>ALL ]<br />
: <sup>1</sup>Allow up to the PERCENT of sampling points to clash, considering only pairwise clashes <br />
: <sup>2</sup>Allow all solutions (no packing test)<br />
; PACK CUTOFF <PERCENT> <br />
: Limit on total number (or percent) of clashes <br />
; PACK QUICK [ON|OFF]<br />
: Packing check stops when ALLOWED_CLASHES or MAX_CLASHES is reached. However, all clashes are found when the solution has a high Z-score (see [[#ZSCORE | ZSCORE]]).<br />
; PACK COMPACT [ON|OFF]<br />
: Pack ensembles into a compact association (minimize distances between centres of mass for the addition of each component in a solution).<br />
; PACK KEEP HIGH TFZ [ON|OFF]<br />
: Solutions with high tfz (see [[#ZSCORE | ZSCORE]]) but that fail to pack are retained in the solution list. Set to true if SEARCH PRUNE ON (see [[#SEARCH | SEARCH]])<br />
* Default: PACK SELECT PERCENT<br />
* Default: PACK CUTOFF 5<br />
* Default: PACK COMPACT ON<br />
* Default: PACK QUICK ON<br />
* Default: PACK KEEP HIGH TFZ OFF<br />
* Default: PACK CONSERVATION DISTANCE 1,5<br />
setPACK_SELE(str ["PERCENT"|"ALL"]) <br />
setPACK_CUTO(float <ALLOWED_CLASHES>)<br />
setPACK_QUIC(bool)<br />
setPACK_KEEP_HIGH_TFZ(bool)<br />
setPACK_COMP(bool)<br />
<br />
==[[Image:User2.gif|link=]]PEAKS==<br />
; PEAKS TRA SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL] <br />
; PEAKS ROT SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL]<br />
: Peaks for individual rotation functions (ROT) or individual translation functions (TRA) satisfying selection criteria are saved. To be used for subsequent steps, peaks must also satisfy the overall [[#PURGE | PURGE]] selection criteria, so it will usually be appropriate to set only the PURGE criteria (which over-ride the defaults for the PEAKS criteria if not explicitly set). See [[Molecular_Replacement#How_to_Select_Peaks | How to Select Peaks]]<br />
: <sup>1</sup> Select peaks by taking all peaks over CUTOFF percent of the difference between the top peak and the mean value.<br />
: <sup>2</sup> Select peaks by taking all peaks with a Z-score greater than CUTOFF.<br />
: <sup>3</sup> Select peaks by taking top CUTOFF.<br />
: <sup>4</sup> Select all peaks.<br />
; PEAKS ROT CUTOFF <CUTOFF><br />
; PEAKS TRA CUTOFF <CUTOFF><br />
: Cutoff value for the rotation function (ROT) or translation function (TRA) peak selection criteria.<br />
: If selection is by percent and [[#PURGE | PURGE PERCENT]] is changed from the default, then the PEAKS percent value is set to the lower PURGE percent value.<br />
; PEAKS ROT CLUSTER [ON|OFF] <br />
; PEAKS TRA CLUSTER [ON|OFF]<br />
: Toggle selects clustered or unclustered peaks for rotation function (ROT) or translation function (TRA).<br />
; PEAKS ROT DOWN [PERCENT] <br />
: [[#SEARCH | SEARCH METHOD FAST]] only. Percentage to reduce rotation function cutoff if there is no TFZ over the zscore cutoff that determines a true solution (see [[#ZSCORE | ZSCORE]]) in first search.<br />
* Default: PEAKS ROT SELECT PERCENT<br />
* Default: PEAKS TRA SELECT PERCENT<br />
* Default: PEAKS ROT CUTOFF 75<br />
* Default: PEAKS TRA CUTOFF 75<br />
* Default: PEAKS ROT CLUSTER ON<br />
* Default: PEAKS TRA CLUSTER ON<br />
setPEAK_ROTA_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"]) <br />
setPEAK_TRAN_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"])<br />
setPEAK_ROTA_CUTO(float <CUTOFF>)<br />
setPEAK_TRAN_CUTO(float <CUTOFF>) <br />
setPEAK_ROTA_CLUS(bool <CLUSTER>) <br />
setPEAK_TRAN_CLUS(bool <CLUSTER>)<br />
setPEAK_ROTA_DOWN(float <PERCENT>)<br />
<br />
==[[Image:User2.gif|link=]]PERMUTATIONS== <br />
; PERMUTATIONS [ON|OFF]<br />
: Only relevant to [[#SEARCH | SEARCH METHOD FULL]]. Toggle for whether the order of the search set is to be permuted.<br />
* Default: PERMUTATIONS OFF<br />
setPERM(bool <PERMUTATIONS>)<br />
<br />
==[[Image:User2.gif|link=]]PERTURB== <br />
; PERTURB RMS STEP <RMS><br />
: Increment in rms Ångstroms between pdb files to be written. <br />
; PERTURB RMS MAX <MAXRMS><br />
: The structure will be perturbed along each mode until the MAXRMS deviation has been reached.<br />
; PERTURB RMS DIRECTION [FORWARD|BACKWARD|TOFRO] <br />
: The structure is perturbed either forwards or backwards or to-and-fro (FORWARD|BACKWARD|TOFRO) along the eigenvectors of the modes specified.<br />
; PERTURB INCREMENT [RMS| DQ] <br />
: Perturb the structure by rms devitations along the modes, or by set dq increments<br />
; PERTURB DQ <DQ1> ''{DQ <DQ2>…}''<br />
: Alternatively, the DQ factors (as used by the Elnemo server (K. Suhre & Y-H. Sanejouand, NAR 2004 vol 32) ) by which to perturb the atoms along the eigenvectors can be entered directly.<br />
* Default: PERTURB INCREMENT RMS<br />
* Default: PERTURB RMS STEP 0.2<br />
* Default: PERTURB RMS MAXRMS 0.3<br />
* Default: PERTURB RMS DIRECTION TOFRO<br />
setPERT_INCR(str [ "RMS" | "DQ" ])<br />
setPERT_RMS_MAXI(float <MAX>)<br />
setPERT_RMS_DIRE(str [ "FORWARDS" | "BACKWARDS" | "TOFRO" ]) <br />
addPERT_DQ(float <DQ>)<br />
<br />
==[[Image:User2.gif|link=]]PURGE== <br />
; PURGE ROT ENABLE [ON|OFF]<sup>1</sup><br />
; PURGE ROT PERCENT <PERC><sup>2</sup><br />
; PURGE ROT NUMBER <NUM><sup>3</sup><br />
: Purging criteria for rotation function (RF), where PERCENT and NUMBER are alternative selection criteria (''OR'' criteria)<br />
::<sup>1</sup> Toggle for whether to purge the solution list from the RF according to the top solution found. If there are a number of RF searches with different partial solution backgrounds, the PURGE is applied to the total list of peaks. If there is one clearly significant RF solution from one of the backgrounds it acts to purge all the less significant solutions. If there is only one RF (a single partial solution background) the PURGE gives no additional selection over and above the PEAKS command. <br />
::<sup>2</sup> [[Molecular_Replacement#How_to_Select_Peaks | Selection by percent]]. PERC is percentage of the top peak, where the value of the top peak is defined as 100% and the value of the mean is defined as 0%. Note that this criterion is applied subsequent to any selection criteria applied through the [[#PEAKS | PEAKS]] command. If the [[#PEAKS | PEAKS]] selection is by percent, then the percent cutoff given in the PURGE command over-rides that for [[#PEAKS | PEAKS]], so as to rationalize results in the case of only a single RF (single partial solution background.)<br />
::<sup>3</sup> NUM is the number of solutions to retain in purging. If NUMBER is given (non-zero) it overrides the PERCENT option. NUMBER given as zero is the flag for not applying this criterion.<br />
; PURGE TRA ENABLE [ON|OFF]<br />
; PURGE TRA PERCENT <PERC><br />
; PURGE TRA NUMBER <NUM><br />
: As above, but for translation function<br />
; PURGE RNP ENABLE [ON|OFF]<br />
; PURGE RNP PERCENT <PERC><br />
; PURGE RNP NUMBER <NUM><br />
: As above but for refinement, but with the important distinction that PERCENT and NUMBER are concurrent selection criteria (''AND'' criteria)<br />
* Default: PURGE ROT ENABLE ON <br />
* Default: PURGE ROT PERC 75<br />
* Default: PURGE ROT NUM 0<br />
* Default: PURGE TRA ENABLE ON<br />
* Default: PURGE TRA PERC 75<br />
* Default: PURGE TRA NUM 0<br />
* Default: PURGE RNP ENABLE ON<br />
* Default: PURGE RNP PERC 75<br />
* Default: PURGE RNP NUM 0<br />
setPURG_ROTA_ENAB(bool <ENABLE>)<br />
setPURG_TRAN_ENAB(bool <ENABLE>) <br />
setPURG_RNP_ENAB(bool <ENABLE>)<br />
setPURG_ROTA_PERC(float <PERC>) <br />
setPURG_TRAN_PERC(float <PERC>) <br />
setPURG_RNP_PERC(float <PERC>)<br />
setPURG_ROTA_NUMB(float <NUM>) <br />
setPURG_TRAN_NUMB(float <NUM>)<br />
setPURG_TRAN_NUMB(float <NUM>)<br />
setPURG_RNP_NUMB(float <NUM>)<br />
<br />
==[[Image:User2.gif|link=]]RESOLUTION== <br />
; RESOLUTION HIGH <HIRES> <br />
: High resolution limit in Ångstroms. For all data use RESOLUTION 0.1 as RESOLUTION 0 indicates default (ELLG selection)<br />
; RESOLUTION LOW <LORES><br />
: Low resolution limit in Ångstroms.<br />
; RESOLUTION AUTO HIGH <HIRES> <br />
: High resolution limit in Ångstroms for final high resolution refinement in MR_AUTO mode.<br />
* Default for molecular replacement: Set by [[#ELLG | ELLG TARGET]] for structure solution, final refinement uses all data<br />
* Default for experimental phasing: All data used<br />
setRESO_HIGH(float <HIRES>) <br />
setRESO_LOW(float <LORES>)<br />
setRESO_AUTO_HIGH(float <HIRES>) <br />
setRESO(float <HIRES>,float <LORES>)<br />
<br />
==[[Image:User2.gif|link=]]ROTATE== <br />
; ROTATE VOLUME FULL<br />
: Sample all unique angles <br />
; ROTATE VOLUME AROUND EULER <A> <nowiki><B></nowiki> <C> RANGE <RANGE> <br />
: Restrict the search to the region of +/- RANGE degrees around orientation given by EULER<br />
setROTA_VOLU(string ["FULL"|"AROUND"|) <br />
setROTA_EULE(dvect3 <A B C>) <br />
setROTA_RANG(float <RANGE>)<br />
<br />
==[[Image:User2.gif|link=]]SCATTERING==<br />
; SCATTERING TYPE <TYPE> FP=<FP> FDP=<FDP> FIX [ON|OFF|EDGE]<br />
: Measured scattering factors for a given atom type, from a fluorescence scan. FIX EDGE (default) fixes the fdp value if it is away from an edge, but refines it if it is close to an edge, while FIX ON or FIX OFF does not depend on proximity of edge.<br />
; SCATTERING RESTRAINT [ON|OFF]<br />
: use Fdp restraints<br />
; SCATTERING SIGMA <SIGMA><br />
: Fdp restraint sigma used is SIGMA multiplied by initial fdp value<br />
* Default: SCATTERING SIGMA 0.2<br />
* Default: SCATTERING RESTRAINT ON<br />
addSCAT(str <TYPE>,float <FP>,float <FDP, string <FIXFDP>) <br />
setSCAT_REST(bool) <br />
setSCAT_SIGM(float <SIGMA>)<br />
<br />
==[[Image:User2.gif|link=]]SCEDS== <br />
; SCEDS NDOM <NDOM><br />
:Number of domains into which to split the protein<br />
; SCEDS WEIGHT SPHERICITY <WS><br />
: Weight factor for the the Density Test in the SCED Score. The Sphericity Test scores boundaries that divide the protein into more spherical domains more highly.<br />
; SCEDS WEIGHT CONTINUITY <WC><br />
: Weight factor for the the Continuity Test in the SCED Score. The Continuity Test scores boundaries that divide the protein into domains contigous in sequence more highly. <br />
; SCEDS WEIGHT EQUALITY <WE><br />
: Weight factor for the the Equality Test in the SCED Score. The Equality Test scores boundaries that divide the protein more equally more highly.<br />
; SCEDS WEIGHT DENSITY <WD><br />
: Weight factor for the the Equality Test in the SCED Score. The Density Test scores boundaries that divide the protein into domains more densely packed with atoms more highly. <br />
* Default: SCEDS NDOM 2<br />
* Default: SCEDS WEIGHT EQUALITY 1<br />
* Default: SCEDS WEIGHT SPHERICITY 4 <br />
* Default: SCEDS WEIGHT DENSITY 1<br />
* Default: SCEDS WEIGHT CONTINUITY 0<br />
setSCED_NDOM(int <NDOM>) <br />
setSCED_WEIG_SPHE(float <WS>) <br />
setSCED_WEIG_CONT(float <WC>)<br />
setSCED_WEIG_EQUA(float <WE>) <br />
setSCED_WEIG_DENS(float <WD>)<br />
<br />
==[[Image:User2.gif|link=]]TARGET==<br />
; TARGET ROT [FAST | BRUTE]<br />
: Target function for fast rotation searches (2). BRUTE searches all angles on a grid with the full rotation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these rotations with the full rotation likelihood target.<br />
; TARGET TRA [FAST | BRUTE | PHASED]<br />
: Target function for fast translation searches (3). BRUTE searches all positions on a grid with the full translation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these positions with the full translation likelihood target. PHASED selects the "phased translation function", for which a LABIN command should also be given, specifying FMAP, PHMAP and (optionally) FOM.<br />
* Default: TARGET ROT FAST<br />
* Default: TARGET TRA FAST<br />
setTARG_ROTA(str ["FAST"|"BRUTE"])<br />
setTARG_TRAN(str ["FAST"|"BRUTE"|"PHASED"])<br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS NMOL <NMOL><br />
: Number of molecules/molecular assemblies related by single TNCS vector (usually only 2). If the TNCS is a pseudo-tripling of the cell then NMOL=3, a pseudo-quadrupling then NMOL=4 etc.<br />
* Default: TNCS NMOL 2<br />
setTNCS_NMOL(int <NMOL>)<br />
<br><br />
<br />
==[[Image:User2.gif|link=]]TRANSLATION== <br />
; TRANSLATION VOLUME [ <sup>1</sup>FULL | <sup>2</sup>REGION | <sup>3</sup>LINE | <sup>4</sup>AROUND ])<br />
: Search volume for brute force translation function.<br />
: <sup>1</sup> Cheshire cell or Primitive cell volume. <br />
: <sup>2</sup> Search region.<br />
: <sup>3</sup> Search along line. <br />
: <sup>4</sup> Search around a point.<br />
; <sup>1 2 3</sup>TRANSLATION START <X Y Z> <br />
; <sup>1 2 3</sup>TRANSLATION END <X Y Z><br />
: Search within region or line bounded by START and END.<br />
; <sup>4</sup>TRANSLATION POINT <X Y Z><br />
; <sup>4</sup>TRANSLATION RANGE <RANGE><br />
: Search within +/- RANGE Ångstroms (not fractional coordinates, even if the search point is given as fractional coordinates) of a point <X Y Z>.<br />
; TRANSLATION [ORTH | FRAC]<br />
: Coordinates are given in orthogonal or fractional values.<br />
; TRANSLATION PACKING USE [ON | OFF]<br />
: Top translation function peak will be testes for packing.<br />
; TRANSLATION PACKING CUTOFF <PERC><br />
: Percent pairwise packing used for packing function test of top TF peak. Equivalent to PACK CUTOFF <PERC> for packing function. <br />
; TRANSLATION PACKING NUM <NUM><br />
: Number of translation function peaks to test for packing before bailing out of packing test. Set to 0 to pack all translation function peaks (slow for large packing volumes). <br />
* Default: TRANSLATION VOLUME FULL<br />
* Default: TRANSLATION PACK CUTOFF 50<br />
* Default: TRANSLATION PACK NUM 0 (helices - all packing checked)<br />
* Default: TRANSLATION PACK NUM 500 (non-helices)<br />
setTRAN_VOLU(string ["FULL"|"REGION"|"LINE"|"AROUND"])<br />
setTRAN_START(dvect <START>)<br />
setTRAN_END(dvect <END>)<br />
setTRAN_POINT(dvect <POINT>)<br />
setTRAN_RANGE(float <RANGE>)<br />
setTRAN_FRAC(bool <True=FRAC False=ORTH>)<br />
setTRAN_PACK_USE(bool)<br />
setTRAN_PACK_CUTO(float)<br />
<br />
==[[Image:User2.gif|link=]]ZSCORE== <br />
; ZSCORE USE [ON|OFF]<br />
: Use the TFZ tests. Only applicable with [[#SEARCH | SEARCH METHOD FAST]]. (Note Phaser-2.4.0 and below use "ZSCORE SOLVED 0" to turn off the TFZ tests)<br />
; ZSCORE SOLVED <ZSCORE_SOLVED><br />
: Set the minimum TFZ that indicates a definite solution for amalgamating solutions in FAST search method. <br />
;ZSCORE STOP [ON|OFF]<br />
: Stop adding components beyond point where TFZ is below cutoff when adding multiple components in FAST mode. However, FAST mode will always add one component even if TFZ is below cutoff, or two components if starting search with no components input (no input solution).<br />
; ZSCORE HALF [ON|OFF]<br />
: Set the TFZ for amalgamating solutions in the FAST search method to the maximum of ZSCORE_SOLVED and half the maximum TFZ, to accommodate cases of partially correct solutions in very high TFZ cases (e.g. TFZ > 16)<br />
* Default: ZSCORE USE ON<br />
* Default: ZSCORE SOLVED 8<br />
* Default: ZSCORE HALF ON<br />
* Default: ZSCORE STOP ON<br />
setZSCO_USE(bool <True=ON False=OFF>)<br />
setZSCO_SOLV(floatType ZSCORE_SOLVED)<br />
setZSCO_HALF(bool <True=ON False=OFF>)<br />
setZSCO_STOP(bool <True=ON False=OFF>)<br />
<br><br />
<br><br />
<br />
=Expert Keywords=<br />
<br />
==[[Image:Expert.gif|link=]]MACANO== <br />
; MACANO PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for the refinement of SigmaN in the anisotropy correction<br />
; MACANO ANISO [ON|OFF] BINS [ON|OFF] SOLK [ON|OFF] SOLB [ON|OFF] ''{NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}''<br />
: Macrocycle for the custom refinement of SigmaN in the anisotropy correction. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACANO PROTOCOL DEFAULT<br />
setMACA_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACA(bool <ANISO>,bool <BINS>,bool <SOLK>,bool <SOLB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACMR== <br />
; MACMR PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACMR ROT [ON|OFF] TRA [ON|OFF] BFAC [ON|OFF] VRMS [ON|OFF] ''CELL [ON|OFF] LAST [ON|OFF] NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of molecular replacement solutions. Macrocycles are performed in the order in which they are entered. For description of VRMS see the [[FAQ]]. CELL is the scale factor for the unit cell for maps (EM maps). LAST is a flag that refines the parameters for the last component of a solution only, fixing all the others.<br />
; MACMR CHAINS [ON|OFF]<br />
: Split the ensembles into chains for refinement<br />
: Not possible as part of an automated mode<br />
* Default: MACMR PROTOCOL DEFAULT<br />
* Default: MACMR CHAINS OFF<br />
setMACM_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACM(bool <ROT>,bool <TRA>,bool <BFAC>,bool <VRMS>,bool <CELL>,bool <LAST>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
setMACM_CHAI(bool])<br />
<br />
==[[Image:Expert.gif|link=]]MACOCC== <br />
; MACOCC PROTOCOL [ DEFAULT | CUSTOM | OFF | ALL ]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACOCC NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of occupancy for solutions. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACOCC PROTOCOL DEFAULT<br />
setMACO_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACO(int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACGYRE== <br />
; MACGYRE PROTOCOL [ DEFAULT | CUSTOM | OFF | ALL ]<br />
: Protocol for refinement of gyre rotations<br />
; MACGYRE ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] ''ANCHOR [ON|OFF] SIGROT <SIGR> SIGTRA <SIGT> NCYCLE <NCYC> MINIMIZER [ BFGS | NEWTON | DESCENT ]''<br />
: Macrocycle for custom refinement of occupancy for solutions. Macrocycles are performed in the order in which they are entered.<br />
; MACGYRE SIGROT <SIGROT> <br />
; MACGYRE SIGTRA <SIGTRA> <br />
; MACGYRE ANCHOR [ON|OFF]<br />
: Override default values for harmonic restraints for rotation and translation refinement, and whether or not to anchor one fragment (no translation) for all macrocycles<br />
* Default: MACGYRE PROTOCOL DEFAULT<br />
setMACG_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACG(bool <REF>,bool <REF>, bool <REF>)<br />
addMACG_FULL(bool <REF>,bool <REF>,bool<REF>,bool <ANCHOR>,float <SIGROT>,float <SIGTRA>,int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
setMACG_SIGR(bool <SIGROT>)<br />
setMACG_SIGT(bool <SIGTRA>)<br />
setMACG_ANCH(bool <ANCHOR>)<br />
<br />
==[[Image:Expert.gif|link=]]MACSAD== <br />
; MACSAD PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for SAD refinement.<br />
:''n.b. PROTOCOL ALL will crash phaser and is only useful for debugging - see code for details''<br />
; MACSAD XYZ [ON|OFF] OCC [ON|OFF] BFAC [ON|OFF] FDP [ON|OFF] SA [ON|OFF] SB [ON|OFF] SP [ON|OFF] SD [ON|OFF] ''{PK [ON|OFF]} {PB [ON|OFF]} {NCYCLE <NCYC>} MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for SAD refinement. Macrocycles are performed in the order in which they are entered.<br />
*Default: MACSAD PROTOCOL DEFAULT<br />
setMACS_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACS(<br />
bool <XYZ>,bool <OCC>,bool <BFAC>,bool <FDP><br />
bool <SA>,bool <SB>,bool <SP>,bool <SD>,<br />
bool <PK>, bool <PB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACTNCS== <br />
; MACTNCS PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for pseudo-translational NCS refinement.<br />
; MACTNCS ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] ''NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for pseudo-translational NCS refinement. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACTNCS PROTOCOL DEFAULT<br />
setMACT_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACT(bool <ROT>,bool <TRA>,bool <VRMS>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]OCCUPANCY== <br />
; OCCUPANCY WINDOW ELLG <ELLG><br />
: Target eLLG for determining number of residues in window for occupancy refinement. The number of residues in a window will be an odd number. Occupancy refinement will be done for each offset of the refinement window.<br />
; OCCUPANCY WINDOW NRES <NRES><br />
: As an alternative to using the eLLG to define the number of residues in window for occupancy refinement, the number may be input directly. NRES must be an odd number.<br />
; OCCUPANCY WINDOW MAX <NRES><br />
: Maximum number of residues in an occupancy window (determined either by ellg or given as NRES) for which occupancy is refined. Prevents the refinement windows from spanning non-local regions of space.<br />
; OCCUPANCY MIN <MINOCC> MAX <MAXOCC><br />
: Minimum and maximum values of occupancy during refinement.<br />
; OCCUPANCY MERGE [ON/OFF]<br />
: Merge refined occupancies from different window offsets to give final occupancies per residue. If OFF, occupancies from a single window offset will be used, selected using OCCUPANCY OFFSET <N><br />
; OCCUPANCY FRAC <FRAC><br />
: Minimum fraction of the protein for which the occupancy may be set to zero.<br />
; OCCUPANCY OFFSET <N><br />
: If OCCUPANCY MERGE OFF, then <N> defines the single window offset from which final occupancies will be taken<br />
* Default: OCCUPANCY WINDOW ELLG 5<br />
* Default: OCCUPANCY WINDOW MAX 111<br />
* Default: OCCUPANCY MIN 0.01 MAX 1<br />
* Default: OCCUPANCY NCYCLES 1<br />
* Default: OCCUPANCY MERGE ON<br />
* Default: OCCUPANCY FRAC 0.5<br />
* Default: OCCUPANCY OFFSET 0<br />
setOCCU_WIND_ELLG(float <ELLG>)<br />
setOCCU_WIND_NRES(int <NRES>)<br />
setOCCU_WIND_MAX(int <NRES>)<br />
setOCCU_MIN(float <MIN>)<br />
setOCCU_MAX(float <MAX>)<br />
setOCCU_MERG(float <FRAC>)<br />
setOCCU_FRAC(bool)<br />
setOCCU_OFFS(int <N>)<br />
<br />
==[[Image:Expert.gif|link=]]RESCORE== <br />
; RESCORE ROT [ON|OFF]<br />
; RESCORE TRA [ON|OFF]<br />
: Toggle for rescoring of fast rotation function (ROT) or fast translation function (TRA) search peaks. <br />
* Default: RESCORE ROT ON<br />
* Default: RESCORE TRA ON|OFF will depend on whether phaser is running in the mode [[#MODE | MODE MR_AUTO]] with [[#SEARCH | SEARCH METHOD FAST]] or with [[#SEARCH | SEARCH METHOD FULL]], or running the translation function separately [[#MODE | MODE MR_FTF]]. For [[#SEARCH | SEARCH METHOD FAST]] the default also depends on whether or not the expected LLG target [[#ELLG | ELLG TARGET <TARGET>]] value is reached.<br />
setRESC_ROTA(bool)<br />
setRESC_TRAN(bool)<br />
<br />
==[[Image:Expert.gif|link=]]RFACTOR== <br />
; RFACTOR USE [ON|OFF]<br />
: For cases of searching for one ensemble when there is one ensemble in the asymmetric unit, the R-factor for the ensemble at the orientation and position in the input is calculated. If this value is low then MR is not performed in the MR_AUTO job in FAST search mode. Instead, rigid body refinement is performed before exiting. Note that the same R-factor test and cutoff is used for judging success in single-atom molecular replacement (MR_ATOM mode).<br />
; RFACTOR CUTOFF <VALUE><br />
: Rfactor in percent used as cutoff for deciding whether or not the R-factor indicates that MR is not necessary.<br />
* Default: RFACTOR USE ON CUTOFF 35<br />
setRFAC_USE(bool)<br />
setRFAC_CUTO(float <PERCENT>)<br />
<br />
==[[Image:Expert.gif|link=]]SAMPLING==<br />
; SAMPLING ROT <SAMP><br />
; SAMPLING TRA <SAMP><br />
: Sampling of search given in degrees for a rotation search and Ångstroms for a translation search. Sampling for rotation search depends on the mean radius of the Ensemble and the high resolution limit (dmin) of the search.<br />
* Default: SAMP = 2*atan(dmin/(4*meanRadius)) (ROTATION FUNCTION)<br />
* Default: SAMP = dmin/5; (BRUTE TRANSLATION FUNCTION)<br />
* Default: SAMP = dmin/4; (FAST TRANSLATION FUNCTION)<br />
setSAMP_ROTA(float <SAMP>)<br />
setSAMP_TRAN(float <SAMP>)<br />
<br><br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS USE [ON|OFF]<br />
: Use TNCS if present: apply TNCS corrections. (Note: was TNCS IGNORE [ON|OFF] in Phaser-2.4.0)<br />
; TNCS RLIST ADD [ON | OFF]<br />
: Supplement the rotation list used in the translation function with rotations already present in the list of known solutions. New molecules in the same orientation as those in the known search (as occurs with translational ncs) may not have peaks associated with them from the rotation function because the known molecules mask the presence of the ones not yet found. <br />
; TNCS PATT HIRES <hires><br />
: High resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT LORES <lores><br />
: Low resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT PERCENT <percent><br />
: Percent of origin Patterson peak that qualifies as a TNCS vector<br />
; TNCS PATT DISTANCE <distance><br />
: Minimum distance of Patterson peak from origin that qualifies as a TNCS vector<br />
; TNCS TRANSLATION PERTURB [ON | OFF]<br />
: If the TNCS translation vector is on a special position, perturb the vector from the special position before refinement<br />
; TNCS ROTATION RANGE <angle><br />
: Maximum deviation from initial rotation from which to look for rotational deviation. Default uses internally determined value based on resolution of data and size of G-function effective molecular radius. Value of 0 turns rotational refinement off.<br />
; TNCS ROTATION SAMPLING <sampling><br />
: Sampling for rotation search. Default uses internally determined value based on resolution of data and size of G-function effective molecular radius. Value of 0 turns rotational refinement off.<br />
* Default: TNCS USE ON<br />
* Default: TNCS RLIST ADD ON<br />
* Default: TNCS PATT HIRES 5<br />
* Default: TNCS PATT LORES 10<br />
* Default: TNCS PATT PERCENT 20<br />
* Default: TNCS PATT DISTANCE 15 <br />
* Default: TNCS TRANSLATION PERTURB ON<br />
setTNCS_USE(bool)<br />
setTNCS_RLIS_ADD(bool)<br />
setTNCS_PATT_HIRE(float <HIRES>)<br />
setTNCS_PATT_LORE(float <LORES>) <br />
setTNCS_PATT_PERC(float <PERCENT>) <br />
setTNCS_PATT_DIST(float <DISTANCE>)<br />
setTNCS_TRAN_PERT(bool)<br />
setTNCS_ROTA_RANG(float <RANGE>) <br />
setTNCS_ROTA_SAMP(float <SAMPLING>) <br />
<br><br />
<br><br />
<br />
=Developer Keywords=<br />
==[[Image:Developer.gif|link=]]BINS== <br />
; BINS DATA [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the data.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections<br />
; BINS ENSE [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the calaculated structure factos for the ensembles.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections<br />
* Default: BINS DATA MIN 6 MAX 50 WIDTH 500 <br />
* Default: BINS ENSE MIN 6 MAX 1000 WIDTH 1000 <br />
setBINS_DATA_MINI(float <L>)<br />
setBINS_DATA_MAXI(float <H>)<br />
setBINS_DATA_WIDT(float <W>)<br />
setBINS_ENSE_MINI(float <L>)<br />
setBINS_ENSE_MAXI(float <H>)<br />
setBINS_ENSE_WIDT(float <W>)<br />
<br />
==[[Image:Developer.gif|link=]]BFACTOR==<br />
; BFACTOR WILSON RESTRAINT [ON|OFF]<br />
: Toggle to use the Wilson restraint on the isotropic component of the atomic B-factors in SAD phasing.<br />
; BFACTOR SPHERICITY RESTRAINT [ON|OFF] <br />
: Toggle to use the sphericity restraint on the anisotropic B-factors in SAD phasing<br />
; BFACTOR REFINE RESTRAINT [ON|OFF] <br />
: Toggle to use the restraint to zero for the molecular B-factor in molecular replacement.<br />
; BFACTOR WILSON SIGMA <SIGMA><br />
: The sigma of the Wilson restraint.<br />
; BFACTOR SPHERICITY SIGMA <SIGMA><br />
: The sigma of the sphericity restraint.<br />
; BFACTOR REFINE SIGMA <SIGMA><br />
: The sigma of the restraint to zero for the molecular B-factor in molecular replacement.<br />
* Default: BFACTOR WILSON RESTRAINT ON <br />
* Default: BFACTOR SPHERICITY RESTRAINT ON <br />
* Default: BFACTOR REFINE RESTRAINT ON <br />
* Default: BFACTOR WILSON SIGMA 5<br />
* Default: BFACTOR SPHERICITY SIGMA 5<br />
* Default: BFACTOR REFINE SIGMA 6<br />
setBFAC_WILS_REST(bool <True|False>)<br />
setBFAC_SPHE_REST(bool <True|False>)<br />
setBFAC_REFI_REST(bool <True|False>) <br />
setBFAC_WILS_SIGM(float <SIGMA>) <br />
setBFAC_SPHE_SIGM(float <SIGMA>) <br />
setBFAC_REFI_SIGM(float <SIGMA>)<br />
<br />
==[[Image:Developer.gif|link=]]BOXSCALE==<br />
; BOXSCALE <BOXSCALE><br />
: Scale for box for calculating structure factors. The ensembles are put in a box equal to (extent of molecule)*BOXSCALE<br />
* Default: BOXSCALE 4<br />
setBOXS<float <BOXSCALE>)<br />
<br />
==[[Image:Developer.gif|link=]]CELL==<br />
; <span style="color:darkorange">Python Only</span> <br />
: Unit cell dimensions<br />
* Default: Cell read from MTZ file<br />
setCELL(float <A>,float <nowiki><B></nowiki>,float <C>,float <ALPHA>,float <BETA>,float <GAMMA>)<br />
setCELL6(float_array <A B C ALPHA BETA GAMMA>)<br />
<br />
==[[Image:Developer.gif|link=]]COMPOSITION== <br />
; COMPOSITION MIN SOLVENT <PERC><br />
: Minimum solvent to give maximum asu packing volume for automated search copy determination (NUM 0)<br />
* Default: COMPOSITION MIN SOLVENT 0.2<br />
setCOMP_MIN_SOLV(float)<br />
<br />
==[[Image:Developer.gif|link=]]DDM== <br />
; DDM SLIDER <VAL> <br />
: The SLIDER window width is used to smooth the Difference Distance Matrix. <br />
; DDM DISTANCE MIN <VAL> MAX <VAL> STEP <VAL><br />
: The range and step interval, as the fraction of the difference between the lowest and highest DDM values used to step.<br />
; DDM SEPARATION MIN <VAL> MAX <VAL><br />
: Through space separation in Angstroms used.<br />
; DDM SEQUENCE MIN <VAL> MAX <VAL><br />
: The range of sequence separations between matrix pairs.<br />
; DDM JOIN MIN <VAL> MAX <VAL><br />
: The range of lengths of the sequences to join if domain segments are discontinuous in percentages of the polypeptide chain.<br />
* Default: DDM SLIDER 0<br />
* Default: DDM DISTANCE MIN 1 MAX 5 STEP 50<br />
* Default: DDM SEPARATION MIN 7 MAX 14<br />
* Default: DDM SEQUENCE MIN 0 MAX 1<br />
* Default: DDM JOIN MIN 2 MAX 12<br />
setDDM_SLID(int <VAL>) <br />
setDDM_DIST_STEP(int <VAL>) <br />
setDDM_DIST_MINI(int <VAL>) <br />
setDDM_DIST_MAXI(int <VAL>) <br />
setDDM_SEPA_MINI(float <VAL>) <br />
setDDM_SEPA_MAXI(float <VAL>)<br />
setDDM_JOIN_MINI(int <VAL>) <br />
setDDM_JOIN_MAXI(int <VAL>) <br />
setDDM_SEQU_MINI(int <VAL>) <br />
setDDM_SEQU_MAXI(int <VAL>)<br />
<br />
==[[Image:Developer.gif|link=]]ENM== <br />
; ENM OSCILLATORS [ <sup>1</sup>RTB | <sup>2</sup>ALL ] <br />
: Define the way the atoms are used for the elastic network model.<br />
: <sup>1</sup>Use the rotation-translation block method.<br />
: <sup>2</sup>Use all atoms to determine the modes (only for use on very small molecules, less than 250 atoms). <br />
; ENM MAXBLOCKS <MAXBLOCKS><br />
: MAXBLOCKS is the number of rotation-translation blocks for the RTB analysis.<br />
; ENM NRES <NRES><br />
: For the RTB analysis, by default NRES=0 and then it is calculated so that it is as small as it can be without reaching MAXBlocks. <br />
; ENM RADIUS <RADIUS><br />
: Elastic Network Model interaction radius (Angstroms)<br />
; ENM FORCE <FORCE><br />
: Elastic Network Model force constant<br />
* Default: ENM OSCILLATORS RTB MAXBLOCKS 250 NRES 0 RADIUS 5 FORCE 1<br />
setENM_OSCI(str ["RTB"|"CA"|"ALL"])<br />
setENM_RTB_MAXB(float <MAXB>)<br />
setENM_RTB_NRES(float <NRES>) <br />
setENM_RADI(float <RADIUS>) <br />
setENM_FORC(float <FORCE>)<br />
<br />
==[[Image:Developer.gif|link=]]NORMALIZATION==<br />
; <span style="color:darkorange">Scripting Only</span><br />
; NORM EPSFAC WRITE <FILENAME><br />
: The normalization factors that correct for anisotropy in the data are written to BINARY file FILENAME<br />
; NORM EPSFAC READ <FILENAME><br />
: The normalization factors that correct for anisotropy in the data are read from BINARY file FILENAME. Further refinement is automatically turned off.<br />
; <span style="color:darkorange">Python Only</span><br />
The normalization factors that correct for anisotropy in the data, extracted from ResultANO object with getSigmaN(). Anisotropy should subsequently be turned off with setMACA_PROT("OFF").<br />
setNORM_DATA(data_norm <SIGMAN>)<br />
<br />
==[[Image:Developer.gif|link=]]OUTLIER==<br />
; OUTLIER REJECT [ON|OFF]<br />
: Reject low probability data outliers<br />
; OUTLIER PROB <PROB><br />
: Cutoff for rejection of low probablity outliers<br />
* Default: OUTLIER REJECT ON PROB 0.000001<br />
setOUTL_REJE(bool) <br />
setOUTL_PROB(float <PROB>)<br />
<br />
==[[Image:Developer.gif|link=]]PTGROUP== <br />
; PTGROUP COVERAGE <COVERAGE><br />
: Percentage coverage for two sequences to be considered in same pointgroup<br />
; PTGROUP IDENTITY <IDENTITY><br />
: Percentage identity for two sequences to be considered in same pointgroup<br />
; PTGROUP RMSD <RMSD><br />
: Percentage rmsd for two models to be considered in same pointgroup<br />
; PTGROUP TOLERANCE ANGULAR <ANG><br />
: Angular tolerance for pointgroup<br />
; PTGROUP TOLERANCE SPATIAL <DIST><br />
: Spatial tolerance for pointgroup<br />
setPTGR_COVE(float <COVERAGE>) <br />
setPTGR_IDEN(float <IDENTITY>) <br />
setPTGR_RMSD(float <RMSD>) <br />
setPTGR_TOLE_ANGU(float <ANG>) <br />
setPTGR_TOLE_SPAT(float <DIST>)<br />
<br />
==[[Image:Developer.gif|link=]]RESHARPEN== <br />
; RESHARPEN PERCENTAGE <PERC><br />
: Perecentage of the B-factor in the direction of lowest fall-off (in anisotropic data) to add back into the structure factors F_ISO and FWT and FDELWT so as to sharpen the electron density maps<br />
* Default: RESHARPEN PERCENT 100<br />
setRESH_PERC(float <PERCENT>)<br />
<br />
==[[Image:Developer.gif|link=]]SOLPARAMETERS==<br />
; SOLPARAMETERS SIGA FSOL <FSOL> BSOL <BSOL> MIN <MINSIGA><br />
: Babinet solvent parameters for Sigma(A) curves. MINSIGA is the minimum SIGA for Babinet solvent term (low resolution only). The solvent term in the Sigma(A) curve is given by <BR>max(1 - FSOL*exp(-BSOL/(4d^2)),MINSIGA).<br />
; SOLPARAMETERS BULK USE [ON|OFF]<br />
: Toggle for use of solvent mask scaling parameters for ensemble structure factors, applied to Fmask.<br />
; SOLPARAMETERS BULK FSOL <FSOL> BSOL <BSOL> <br />
: Solvent mask scaling parameters for ensemble structure factors, applied to Fmask.<br />
* Default: SOLPARAMETERS SIGA FSOL 1.05 BSOL 501 MIN 0.1<br />
* Default: SOLPARAMETERS SIGA RESTRAINT ON<br />
* Default: SOLPARAMETERS BULK USE OFF<br />
* Default: SOLPARAMETERS BULK FSOL 0.35 BSOL 45<br />
setSOLP_SIGA_FSOL(float <FSOL>) <br />
setSOLP_SIGA_BSOL(float <BSOL>)<br />
setSOLP_SIGA_MIN(float <MINSIGA>)<br />
setSOLP_BULK_USE(bool)<br />
setSOLP_BULK_FSOL(float <FSOL>) <br />
setSOLP_BULK_BSOL(float <BSOL>)<br />
<br />
==[[Image:Developer.gif|link=]]TARGET== <br />
; TARGET ROT FAST TYPE [LERF1 | CROWTHER]<br />
: Target function type for fast rotation searches<br />
; TARGET TRA FAST TYPE [LETF1 | LETF2 | CORRELATION]<br />
: Target function type for fast translation searches<br />
setTARG_ROTA_TYPE(string TYPE)<br />
setTARG_TRAN_TYPE(string TYPE)<br />
<br />
==[[Image:Developer.gif|link=]]TNCS==<br />
; TNCS ROTATION ANGLE <A> <nowiki><B></nowiki> <C><br />
: Input rotational difference between molecules related by the pseudo-translational symmetry vector, specified as rotations in degrees about x, y and z axes. Central value for grid search (RANGE > 0).<br />
; TNCS ROTATION RANGE <A><br />
: Range of angular difference in rotation angles to explore around central angle.<br />
; TNCS ROTATION SAMPLING <A><br />
: Sampling step for rotational grid search.<br />
; TNCS TRA VECTOR <x y z> <br />
: Input pseudo-translational symmetry vector (fractional coordinates). By default the translation is determined from the Patterson.<br />
; TNCS VARIANCE RMSD <num><br />
: Input estimated rms deviation between pseudo-translational symmetry vector related molecules.<br />
; TNCS VARIANCE FRAC <num><br />
: Input estimated fraction of cell content that obeys pseudo-translational symmetry.<br />
; TNCS LINK RESTRAINT [ON | OFF]<br />
: Link the occupancy of atoms related by TNCS in SAD phasing<br />
; TNCS LINK SIGMA <sigma><br />
: Sigma of link restraint of the occupancy of atoms related by TNCS in SAD phasing<br />
* Default: TNCS ROTATION ANGLE 0 0 0<br />
* Default: TNCS ROTATION RANGE -999 (determine from structure size and resolution)<br />
* Default: TNCS ROTATION SAMPLING -999 (determine from structure size and resolution)<br />
* Default: TNCS TRANSLATION VECTOR determined from position of Patterson peak<br />
* Default: TNCS VARIANCE RMSD 0.4 <br />
* Default: TNCS VARIANCE FRAC 1 <br />
* Default: TNCS LINK RESTRAINT ON<br />
* Default: TNCS LINK SIGMA 0.1<br />
setTNCS_ROTA_ANGL(dvect3 <A B C>) <br />
setTNCS_TRAN_VECT(dvect3 <X Y Z>) <br />
setTNCS_VARI_RMSD(float <RMSD>) <br />
setTNCS_VARI_FRAC(float <FRAC>)<br />
setTNCS_LINK_REST(bool)<br />
setTNCS_LINK_SIGM(float <SIGMA>)<br />
; <span style="color:darkorange">Scripting Only</span><br />
; TNCS EPSFAC WRITE <FILENAME><br />
: The normalization factors that correct for tNCS in the data are written to BINARY file FILENAME<br />
; TNCS EPSFAC READ <FILENAME><br />
: The normalization factors that correct for tNCS in the data are read from BINARY file FILENAME. Further refinement is automatically turned off.<br />
; <span style="color:darkorange">Python Only</span><br />
The normalization factors that correct for tNCS in the data, extracted from ResultNCS object with getPtNcs(). tNCS refinement should subsequently be turned off with setMACT_PROT("OFF").<br />
setTNCS(data_tncs <PTNCS>)<br />
<br />
==[[Image:Developer.gif|link=]]TRANSLATION== <br />
; TRANSLATION MAPS [ON | OFF]<br />
: Output maps of fast translation function FSS scoring functions<br />
: Maps take the names <ROOT>.<ensemble>.k.e.map where k is the Known backgound number and e is the Euler angle number for that known background<br />
* Default: TRANSLATION MAPS OFF<br />
setTRAN_MAPS(bool)</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Keywords&diff=2401Keywords2017-01-09T19:10:15Z<p>Airlie: /* link=SOLUTION */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
===Phaser Executable===<br />
<br />
The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the [[#MODE | MODE]] keyword. The different modes and the keywords relevant to each mode are described in [[Modes]].<br />
<br />
Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. However, some keywords are meaningful when entered multiple times. The order may or may not be important. <br />
<br />
*[[Image:User1.gif|link=]] [[#Basic Keywords | Basic Keywords]]<br />
<br />
*[[Image:Output.png|link=]] [[#Output Control Keywords | Output Control Keywords]]<br />
<br />
*[[Image:User2.gif|link=]] [[#Advanced Keywords |Advanced Keywords ]]<br />
<br />
*[[Image:Expert.gif|link=]] [[#Expert Keywords | Expert Keywords]]<br />
<br />
*[[Image:Developer.gif|link=]] [[#Developer Keywords | Developer Keywords]]<br />
<br />
<br />
===Python Interface===<br />
<br />
Phaser can be compiled as a python library. The mode is selected by calling the appropriate run-job. Input to the run-job is via input-objects, which are passed to the run-job. Setter function on the input objects are equivalent to the keywords for input to the phaser executable. The different modes and the keywords relevant to each mode are described in [[Modes]]. See [[Python Interface]] for details. <br />
<br />
The python interface uses standard python and cctbx/scitbx variable types.<br />
<br />
str string<br />
float double precision floating point<br />
Miller cctbx::miller::index<int> <br />
dvect3 scitbx::vec3<float> <br />
dmat33 scitbx::mat3<float> <br />
'''type'''_array scitbx::af::shared<'''type'''> arrays<br />
<br />
=Basic Keywords=<br />
==[[Image:User1.gif|link=]]ATOM== <br />
; ATOM CRYSTAL <XTALID> PDB <FILENAME><br />
: Definition of atom positions using a pdb file.<br />
; ATOM CRYSTAL <XTALID> HA <FILENAME><br />
: Definition of atom positions using a ha file (from RANTAN, MLPHARE etc.).<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> <br />
: Minimal definition of atom position. B-factor defaults to isotropic and Wilson B-factor. Use <TYPE>=TX for Ta6Br12 cluster and <TYPE>=XX for all other clusters. Scattering for cluster is spherically averaged. Coordinates of cluster compounds other than Ta6Br12 must be entered with CLUSTER keyword. Ta6Br12 coordinates are in phaser code and do not need to be given with CLUSTER keyword.<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> [ ISOB <ISOB> | ANOU <HH KK LL HK HL KL> | USTAR <HH KK LL HK HL KL>] FIXX [ON|OFF] FIXO [ON|OFF] FIXB [ON|OFF] BSWAP [ON|OFF] LABEL <SITE_NAME><br />
: Full definition of atom position including B-factor.<br />
;ATOM CHANGE BFACTOR WILSON [ON|OFF]<br />
: Reset all atomic B-factors to the Wilson B-factor.<br />
; ATOM CHANGE SCATTERER <SCATTERER><br />
:Reset all atomic scatterers to element (or cluster) type.<br />
setATOM_PDB(str <XTALID>,str <PDB FILENAME>)<br />
setATOM_IOTBX(str <XTALID>,iotbx::pdb::hierarchy::root <iotbx object>)<br />
setATOM_STR(str <XTALID>,str <pdb format string>)<br />
setATOM_HA(str <XTALID>,str <FILENAME>)<br />
addATOM(str <XTALID>,str <TYPE>,<br />
float <X>,float <Y>,float <Z>,float <OCC>)<br />
addATOM_FULL(str <XTALID>,str <TYPE>,bool <ORTH>,<br />
dvect3 <X Y Z>,float <OCC>,bool <ISO>,float <ISOB>,<br />
bool <ANOU>,dmat6 <HH KK LL HK HL KL>,<br />
bool <FIXX>,bool <FIXO>,bool <FIXB>,bool <SWAPB>,<br />
str <SITE_NAME>)<br />
setATOM_CHAN_BFAC_WILS(bool)<br />
setATOM_CHAN_SCAT(bool)<br />
setATOM_CHAN_SCAT_TYPE(str <TYPE>)<br />
<br />
==[[Image:User1.gif|link=]]CLUSTER== <br />
; CLUSTER PDB <PDBFILE><br />
: Sample coordinates for a cluster compound for experimental phasing. Clusters are specified with type XX. Ta6Br12 clusters do not need to have coordinates specified as the coordinates are in the phaser code. To use Ta6Br12 clusters, specify atomtypes/clusters as TX.<br />
setCLUS_PDB(str <PDBFILE>)<br />
addCLUS_PDB(str <ID>, str <PDBFILE>)<br />
<br />
==[[Image:User1.gif|link=]]COMPOSITION== <br />
; COMPOSITION BY [ <sup>1</sup>AVERAGE| <sup>2</sup>SOLVENT| <sup>3</sup>ASU ]<br />
: Alternative ways of defining composition<br />
: <sup>1</sup> AVERAGE solvent fraction for crystals (50%)<br />
: <sup>2</sup> Composition entered by solvent content.<br />
: <sup>3</sup> Explicit description of composition of ASU by sequence or molecular weight<br />
; <sup>2</sup>COMPOSITION PERCENTAGE <SOLVENT><br />
: Specified SOLVENT content<br />
; <sup>3</sup>COMPOSITION PROTEIN [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of protein in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION NUCLEIC [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of nucleic acid in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION ATOM <TYPE> NUMBER <NUM><br />
: Add NUM copies of an atom (usually a heavy atom) to the composition<br />
* Default: COMPOSITION BY ASU<br />
setCOMP_BY(str ["AVERAGE" | "SOLVENT" | "ASU" ])<br />
setCOMP_PERC(float <SOLVENT>)<br />
addCOMP_PROT_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_PROT_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_PROT_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_PROT_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_NUCL_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_NUCL_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_NUCL_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_NUCL_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_ATOM(str <TYPE>,float <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]CRYSTAL== <br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN Fpos =<F+> SIGFpos=<SIG+> Fneg=<F-> SIGFneg=<SIG-><br />
: Columns of MTZ file to read for this (anomalous) dataset<br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN F =<F> SIGF=<SIGF><br />
: Columns of MTZ file to read for this (non-anomalous) dataset. Used for LLG completion in SAD phasing when there is no anomalous signal (single atom MR protocol). Use LABIN for MR.<br />
setCRYS_ANOM_LABI(str <F+>,str <SIGF+>,str <F->,str <SIGF->) <br />
setCRYS_MEAN_LABI(str <F>,str <SIGF>)<br />
<br />
==[[Image:User1.gif|link=]]ENSEMBLE== <br />
; ENSEMBLE <MODLID> [PDB|CIF] <PDBFILE> [RMS <RMS><sup>1</sup> | ID <ID><sup>2</sup> | CARD ON<sup>3</sup>] ''CHAIN "<CHAIN>"<sup>4</sup> MODEL <NUM><sup>5</sup>''<br />
: The names of the PDB/CIF files used to build the ENSEMBLE, and either<br />
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
:: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file (e.g. "REMARK PHASER ENSEMBLE MODEL 1 ID 31.2") containing the superimposed models concatenated in the one file. This syntax enables simple automation of the use of ensembles. The pdb file can be non-standard because the atom list for the different models need not be the same.<br />
:: <sup>4</sup> CHAIN is selected from the pdb file. <br />
:: <sup>5</sup> MODEL number is selected from the pdb file.<br />
; ENSEMBLE <MODLID> HKLIN <MTZFILE> F=<F> PHI=<PHI> EXTENT <EX> <EY> <EZ> RMS <RMS> CENTRE <CX> <CY> <CZ> PROTEIN MW <PMW> NUCLEIC MW <NMW> ''CELL SCALE <SCALE>''<br />
: An ENSEMBLE defined from a map (via an mtz file). The molecular weight of the object the map represents is required for scaling. The effective RMS coordinate error is needed to judge how the map accuracy falls off with resolution. For density obtained from an EM image reconstruction, a good first guess would be to take the resolution where the FSC curve drops below 0.5 and divide by 3. The extent (difference between maximum and minimum x,y,z coordinates of region containing model density) is needed to determine reasonable rotation steps, and the centre is needed to carry out a proper interpolation of the molecular transform. The extent and the centre are both given in Ångstroms. The cell scale factor defaults to 1 and can be refined (for example, if the map is from electron microscopy when the cell scale may be unknown to within a few percent).<br />
; ENSEMBLE <MODLID> ATOM <TYPE> RMS <RMS><br />
: Define an ensemble as a single atom for single atom MR<br />
; ENSEMBLE <MODLID> HELIX <NUM> <br />
: Define an ensemble as a helix with NUM residues<br />
; ENSEMBLE <MODLID> HETATM [ON|OFF]<br />
: Use scattering from HETATM records in pdb file. See [[Molecular_Replacement#Coordinate_Editing | Coordinate Editing ]]<br />
; ENSEMBLE <MODLID> DISABLE CHECK [ON|OFF]<br />
: Toggle to disable checking of deviation between models in an ensemble. '''Use with extreme caution'''. Results of computations are not guaranteed to be sensible.<br />
; ENSEMBLE <MODLID> ESTIMATOR [OEFFNER | OEFFNERHI | OEFFNERLO | CHOTHIALESK ]<br />
: Define the estimator function for converting ID to RMS<br />
; ENSEMBLE <MODLID> PTGRP [COVERAGE | IDENTITY | RMSD | TOLANG | TOLSPC | EULER | SYMM ]<br />
: Define the pointgroup parameters <br />
; ENSEMBLE <MODLID> BINS [MIN <N>| MAX <M>| WIDTH <W> ]<br />
: Define the Fcalc reflection binning parameters <br />
; ENSEMBLE <MODLID> TRACE [PDB|CIF] <PDBFILE><br />
: Define the coordinates used for packing independent of the coordinates used for structure factor calculation<br />
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
:: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file <br />
; ENSEMBLE <MODLID> TRACE SAMPLING MIN <DIST> <br />
: Set the minimum distance for the sampling of packing grid<br />
; ENSEMBLE <MODLID> TRACE SAMPLING TARGET <NUM> <br />
: Set the target for the number of points to sample the smallest molecule to be packed<br />
; ENSEMBLE <MODLID> TRACE SAMPLING RANGE <NUM> <br />
: Target range (TARGET+/-RANGE) for search for hexgrid points in protein volume<br />
; ENSEMBLE <MODLID> TRACE SAMPLING USE [AUTO | ALL | CALPHA | HEXGRID ]<br />
: Sample trace coordinates using all atoms, C-alpha atoms, a hexagonal grid in the atomic volume or use an automatically determined choice<br />
; ENSEMBLE <MODLID> TRACE SAMPLING DISTANCE <DIST> <br />
: Set the distance for the sampling of the hexagonal grid explicitly and do not use TARGET to find default sampling distance<br />
; ENSEMBLE <MODLID> TRACE SAMPLING WANG <WANG> <br />
: Scale factor for the size of the Wang mask generated from an ensemble map<br />
; ENSEMBLE <MODLID> TRACE PDB <PDBFILE> <br />
: Use the given set of coordinates for packing rather than using the coordinates for structure factor calculation<br />
* Default: ENSEMBLE <MODLID> DISABLE CHECK OFF<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING MIN 1.0<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING TARGET 1000<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING RANGE 100<br />
addENSE_PDB_ID(str <MODLID>,str <FILE>,float <ID>) <br />
addENSE_PDB_RMS(str <MODLID>,str <FILE>,float <RMS>) <br />
setENSE_TRAC_SAMP_MIN(MODLID,float <MIN>)<br />
setENSE_TRAC_SAMP_TARG(MODLID,int <TARGET>)<br />
setENSE_TRAC_SAMP_RANG(MODLID,int <RANGE>)<br />
setENSE_TRAC_SAMP_USE(MODLID,str)<br />
setENSE_TRAC_SAMP_DIST(MODLID,float <DIST>)<br />
setENSE_TRAC_SAMP_WANG(MODLID,float <WANG>)r <FILE>,float <RMS>)<br />
addENSE_CARD(str <MODLID>,str <FILE>,bool)<br />
addENSE_MAP(str <MODLID>,str <MTZFILE>,str <F>,str <PHI>,dvect3 <EX EY EZ>,<br />
float <RMS>,dvect3 <CX CY CZ>,float <PMW>,float <NMW>,float <CELL>)<br />
setENSE_DISA_CHEC(bool)<br />
<br />
==[[Image:User1.gif|link=]]HKLIN==<br />
; HKLIN <FILENAME><br />
: The mtz file containing the data<br />
setHKLI(str <FILENAME>)<br />
<br />
==[[Image:User1.gif|link=]]JOBS== <br />
; JOBS <NUM><br />
: Number of processors to use in parallelized sections of code<br />
* Default: JOBS 2<br />
setJOBS(int <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]LABIN== <br />
; LABIN F = <F> SIGF = <SIGF> <br />
: Columns in mtz file. F must be given. SIGF should be given but is optional<br />
; LABIN I = <nowiki><I></nowiki> SIGI = <SIGI> <br />
: Columns in mtz file. I must be given. SIGI should be given but is optional<br />
; LABIN FMAP = <PH> PHMAP = <PHMAP> <br />
: Columns in mtz file. FMAP/PHMAP are weighted coefficients for use in the Phased Translation Function.<br />
; LABIN FMAP = <PH> PHMAP = <PHMAP> FOM = <FOM><br />
: Columns in mtz file. FMAP/PHMAP are unweighted coefficients for use in the Phased Translation Function and FOM the figure of merit for weighting<br />
setLABI_F_SIGF(str <F>,str <SIGF>)<br />
setLABI_I_SIGI(str <nowiki><I></nowiki>,str <SIGI>)<br />
setLABI_PTF(str <FMAP>,str <PHMAP>,str <FOM>)<br />
<br />
''Data should be input to python run-jobs using one data_refl parameter''<br />
''This is extracted from the ResultMR_DAT object after a call to runMR_DAT''<br />
setREFL_DATA(data_ref)<br />
''Example:''<br />
i = InputMR_DAT()<br />
i.setHKLI("*.mtz")<br />
i.setLABI_F_SIGF("F","SIGF")<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputMR_LLG()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.setREFL_DATA(r.getDATA())<br />
''See also: '' [[Python Example Scripts]]<br />
<br />
''Alternatively, reflection arrays can be set using cctbx::af::shared<double>''<br />
setREFL_F_SIGF(float_array <F>,float_array <SIGF>)<br />
setREFL_I_SIGI(float_array <nowiki><I></nowiki>,float_array <SIGI>)<br />
setREFL_PTF(float_array <FMAP>,float_array <PHMAP>,float_array <FOM>)<br />
<br />
==[[Image:User1.gif|link=]]MODE==<br />
; MODE [ ANO | CCA | SCEDS | NMAXYZ | NCS | MR_ELLG | MR_AUTO | MR_GYRE | MR_ATOM | MR_ROT | MR_TRA | MR_RNP | | MR_OCC | MR_PAK | EP_AUTO | EP_SAD]<br />
: The mode of operation of Phaser. The different modes are described in a separate page on [[Keyword Modes]]<br />
ResultANO r = runANO(InputANO)<br />
ResultCCA r = runCCA(InputCCA)<br />
ResultNMA r = runSCEDS(InputNMA)<br />
ResultNMA r = runNMAXYZ(InputNMA)<br />
ResultNCS r = runNCS(InputNCS)<br />
ResultELLG r = runMR_ELLG(InputMR_ELLG)<br />
ResultMR r = runMR_AUTO(InputMR_AUTO)<br />
ResultEP r = runMR_ATOM(InputMR_ATOM)<br />
ResulrMR_RF r = runMR_FRF(InputMR_FRF)<br />
ResultMR_TF r = runMR_FTF(InputMR_FTF)<br />
ResultMR r = runMR_RNP(InputMR_RNP)<br />
ResultGYRE r = runMR_GYRE(InputMR_RNP)<br />
ResultMR r = runMR_OCC(InputMR_OCC)<br />
ResultMR r = runMR_PAK(InputMR_PAK)<br />
ResultEP r = runEP_AUTO(InputEP_AUTO)<br />
ResultEP_SAD r = runEP_SAD(InputEP_SAD)<br />
<br />
==[[Image:User1.gif|link=]]PARTIAL== <br />
; PARTIAL PDB <PDBFILE> [RMSIDENTITY] <RMS_ID><br />
: The partial structure for MR-SAD substructure completion. Note that this must already be correctly placed, as the experimental phasing module will not carry out molecular replacement.<br />
; PARTIAL HKLIN <MTZFILE> [RMS|IDENTITY] <RMS_ID><br />
: The partial electron density for MR-SAD substructure completion.<br />
; PARTIAL LABIN FC=<FC> PHIC=<PHIC><br />
: Column labels for partial electron density for MR-SAD substructure completion.<br />
setPART_PDB(str <PDBFILE>)<br />
setPART_HKLI(str <MTZFILE>) <br />
setPART_LABI_FC(str <FC>)<br />
setPART_LABI_PHIC(str <PHIC>) <br />
setPART_VARI(str ["ID"|"RMS"])<br />
setPART_DEVI(float <RMS_ID>)<br />
<br />
==[[Image:User1.gif|link=]]SEARCH==<br />
; SEARCH ENSEMBLE <MODLID> ''{OR ENSEMBLE <MODLID>}… NUMBER <NUM><sup>*</sup>''<br />
: The ENSEMBLE to be searched for in a rotation search or an automatic search. When multiple ensembles are given using the OR keyword, the search is performed for each ENSEMBLE in turn. When the keyword is entered multiple times, each SEARCH keyword refers to a new component of the structure. If the component is present multiple times the sub-keyword NUMber can be used (rather than entering the same SEARCH keyword NUMber times).<br />
: <sup>*</sup>For automatic determination of search number use NUMBER 0. If the composition is entered, the maximum number will be that defined by the composition, otherwise the maximum number will fill the asymmetric unit to a minimum solvent content of 20%. Searches for new components will continue until the TFZ score is above 8, and terminate if the TFZ score drops below 8 before the placement of the maximum number of components.<br />
; SEARCH METHOD [FULL|FAST]<br />
: Search using the [[Modes#Modes |full search]] or [[Modes#Modes | fast search]] algorithms.<br />
; SEARCH ORDER AUTO [ON|OFF]<br />
: Search in the "best" order as estimated using estimated rms deviation and completeness of models.<br />
; SEARCH PRUNE [ON|OFF]<br />
: For high TFZ solutions that fail the packing test, carry out a sliding-window occupancy refinement and prune residues that refine to low occupancy, in an effort to resolve packing clashes. If this flag is set to true, the flag for keeping high tfz score solutions (see [[#PACK | PACK]]) that don't pack is also set to true (PACK KEEP HIGH TFZ ON).<br />
; SEARCH AMALGAMATE USE [ON|OFF]<br />
: For multiple high TFZ solutions, enable amalgamation into a single solution<br />
; SEARCH BFACTOR <BFAC><br />
: B-factor applied to search molecule (or atom).<br />
; SEARCH OFACTOR <OFAC><br />
: Occupancy factor applied to search molecule (or atom).<br />
* Default: SEARCH METHOD FAST<br />
* Default: SEARCH ORDER AUTO ON<br />
* Default: SEARCH PRUNE ON<br />
* Default: SEARCH AMALGAMATE USE ON<br />
* Default: SEARCH BFACTOR 0<br />
* Default: SEARCH OFACTOR 1<br />
addSEAR_ENSE_NUM(str <MODLID>,int <NUM>) <br />
addSEAR_ENSE_OR_ENSE_NUM(string_array <MODLIDS>,int <NUM>) <br />
setSEAR_METH(str [ "FULL" | "FAST" ])<br />
setSEAR_ORDE_AUTO(bool)<br />
setSEAR_PRUN(bool <PRUNE>)<br />
setSEAR_AMAL_USE(bool <AMAL>)<br />
setSEAR_BFAC(float <BFAC>)<br />
setSEAR_OFAC(float <OFAC>)<br />
<br />
==[[Image:User1.gif|link=]]SGALTERNATIVE==<br />
; SGALTERNATIVE SELECT [<sup>1</sup>ALL| <sup>2</sup>HAND| <sup>3</sup>LIST| <sup>4</sup>NONE]<br />
: Selection of alternative space groups to test in translation functions i.e. those that are in same laue group as that given in [[#SPACEGROUP | SPACEGROUP]]<br />
: <sup>1</sup> Test all possible space groups, <br />
: <sup>2</sup> Test the given space group and its enantiomorph.<br />
: <sup>3</sup> Test the space groups listed with SGALTERNATIVE TEST <SG>.<br />
: <sup>4</sup> Do not test alternative space groups.<br />
; SGALTERNATIVE TEST <SG><br />
: Alternative space groups to test. Multiple test space groups can be entered.<br />
* Default: SGALTERNATIVE SELECT HAND<br />
setSGAL_SELE(str [ "ALL" | "HAND" | "LIST" | "NONE" ]) <br />
addSGAL_TEST(str <SG>)<br />
<br />
==[[Image:User1.gif|link=]]SOLUTION==<br />
; SOLUTION SET <ANNOTATION><br />
: Start new set of solutions <br />
; SOLUTION TEMPLATE <ANNOTATION><br />
: Specifies a template solution against which other solutions in this run will be compared. Given in place of SOLUTION SET. Template rotation and translations given by subsequent SOLUTION 6DIM cards as per SOLUTION SETS.<br />
; SOLUTION 6DIM ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> [ORTH|FRAC] <X> <Y> <Z> ''FIXR [ON|OFF] FIXT [ON|OFF] FIXB [ON|OFF] BFAC <BFAC> MULT <MULT>''<br />
: This keyword is repeated for each known position and orientation of an ENSEMBLE MODLID. A B G are the Euler angles (z-y-z convention) and X Y Z are the translation elements, expressed either in orthogonal Angstroms (ORTH) or fractions of a cell edge (FRAC). The input ensemble is transformed by a rotation around the origin of the coordinate system, followed by a translation. BFAC default to 0, MULT (for multiplicity) defaults to 1.<br />
; SOLUTION ENSEMBLE <MODLID> VRMS DELTA <DELTA> RMSD <RMSD><br />
: Refined RMS variance terms for pdb files (or map) in ensemble MODLID. RMSD is the input RMSD of the job that produced the sol file, DELTA is the shift with respect to this RMSD. If given as part of a solution, these values overwrite the values used for input in the ENSEMBLE keyword (if refined).<br />
; SOLUTION ENSEMBLE <MODLID> CELL SCALE <SCALE><br />
: Refined cell scale factor. Only applicable to ensembles that are maps<br />
; SOLUTION TRIAL ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> RF <RF> RFZ <RFZ><br />
: Rotation List for translation function<br />
; SOLUTION ORIGIN ENSEMBLE <MODLID><br />
: Create solution for ensemble MODLID at the origin<br />
; SOLUTION SPACEGROUP <SG><br />
: Space Group of the solution (if alternative spacegroups searched)<br />
; SOLUTION RESOLUTION <HIRES><br />
: High resolution limit of data used to find/refine this solution<br />
; SOLUTION PACKS <PACKS><br />
: Flag for whether solution has been retained despite failing packing test, due to having high TFZ<br />
setSOLU(mr_solution <SOL>) <br />
addSOLU_SET(str <ANNOTATION>) <br />
addSOLU_TEMPLATE(str <ANNOTATION>) <br />
addSOLU_6DIM_ENSE(str <MODLID>,dvect3 <A B C>,bool <FRAC>,dvect3 <X Y Z>,<br />
float <BFAC>,bool <FIXR>,bool <FIXT>,bool <FIXB>,int <MULT>, 1.0) <br />
addSOLU_ENSE_DRMS(str <MODLID>, float <DRMS>) <br />
addSOLU_ENSE_CELL(str <MODLID>, float <SCALE>)<br />
addSOLU_TRIAL_ENSE(string <MODLID>,dvect3 <A B C>,float <RF>, float <RFZ>)<br />
addSOLU_ORIG_ENSE(string <MODLID>)<br />
setSOLU_SPAC(str <SG>)<br />
setSOLU_RESO(float <HIRES>)<br />
setSOLU_PACK(bool <PACKS>)<br />
<br />
==[[Image:User1.gif|link=]]SPACEGROUP==<br />
; SPACEGROUP <SG><br />
: Space group may be altered from the one on the MTZ file to a space group in the same point group. The space group can be entered in one of three ways<br />
#The Hermann-Mauguin symbol e.g. P212121 or P 21 21 21 (with or without spaces)<br />
#The international tables number, which gives standard setting e.g. 19 <br />
#The Hall symbols e.g. P 2ac 2ab<br />
: '''The space group can also be a subgroup of the merged space group'''. For example, P1 is always allowed. The reflections will be expanded to the symmetry of the given subgroup. This is only a valid approach when the true symmetry is the symmetry of the subgroup and perfect twinning causes the data to merge "perfectly" in the higher symmetry. <br />
:'''A list of the allowed space groups in the same point group as the given space group (or space group read from MTZ file) and allowed subgroups of these is given in the Cell Content Analysis logfile.'''<br />
* Default: Read from MTZ file<br />
setSPAC_NUM(int <NUM>)<br />
setSPAC_NAME(string <HM>)<br />
setSPAC_HALL(string <HALL>)<br />
<br />
==[[Image:User1.gif|link=]]WAVELENGTH== <br />
; WAVELENGTH <LAMBDA> <br />
: The wavelengh at which the SAD dataset was collected<br />
setWAVE(float <LAMBDA>)<br />
<br><br />
<br><br />
<br />
=Output Control Keywords=<br />
==[[Image:Output.png|link=]]DEBUG== <br />
; DEBUG [ON|OFF]<br />
: Extra verbose output for debugging<br />
* Default: DEBUG OFF<br />
setDEBU(bool) <br />
<br />
==[[Image:Output.png|link=]]EIGEN==<br />
; EIGEN WRITE [ON|OFF]<br />
; EIGEN READ <EIGENFILE><br />
: Read or write a file containing the eigenvectors and eigenvalues. If reading, the eigenvalues and eigenvectors of the Hessian are read from the file generated by a previous run, rather than calculated. This option must be used with the job that generated the eigenfile and the job reading the eigenfile must have identical input for the ENM parameters. Use WRITE to control whether or not the eigenfile is written when not using the READ mode.<br />
* Default: EIGEN WRITE ON<br />
setEIGE_WRIT(bool)<br />
setEIGE_READ(str <EIGENFILE>)<br />
<br />
==[[Image:Output.png|link=]]HKLOUT== <br />
; HKLOUT [ON|OFF]<br />
: Flags for output of an mtz file containing the phasing information<br />
* Default: HKLOUT ON<br />
setHKLO(bool) <br />
<br />
==[[Image:Output.png|link=]]KEYWORDS== <br />
; KEYWORDS [ON|OFF]<br />
: Write output Phaser .sol file (.rlist file for rotation function)<br />
* Default: KEYWORDS ON<br />
setKEYW(bool)<br />
<br />
==[[Image:Output.gif|link=]]LLGMAPS==<br />
; LLGMAPS [ON|OFF]<br />
: Write log-likelihood gradient map coefficients to MTZ file<br />
* Default: LLGMAPS OFF<br />
setLLGM(bool <True|False>)<br />
<br />
==[[Image:Output.png|link=]]MUTE== <br />
; MUTE [ON|OFF]<br />
: Toggle for running in silent/mute mode, where no logfile is written to ''standard output''.<br />
* Default: MUTE OFF<br />
setMUTE(bool) <br />
<br />
==[[Image:Output.png|link=]]KILL== <br />
; KILL TIME [MINS]<br />
: Kill Phaser after MINS minutes of CPU have elapsed, provided parallel section is complete<br />
; KILL FILE [FILENAME]<br />
: Kill Phaser if file FILENAME is present, provided parallel section is complete<br />
* Default: KILL TIME 0 ''Phaser runs to completion''<br />
* Detaulf: KILL FILE "" ''Phaser runs to completion''<br />
setKILL_TIME(float) <br />
setKILL_FILE(string)<br />
<br />
==[[Image:Output.png|link=]]OUTPUT== <br />
; OUTPUT LEVEL [SILENT|CONCISE|SUMMARY|LOGFILE|VERBOSE|DEBUG]<br />
: Output level for logfile<br />
; OUTPUT LEVEL [0|1|2|3|4|5]<br />
: Output level for logfile (equivalent to keyword level setting)<br />
* Default: OUTPUT LEVEL LOGFILE<br />
setOUTP_LEVE(string)<br />
setOUTP(enum)<br />
<br />
==[[Image:Output.png|link=]]TITLE==<br />
; TITLE <TITLE><br />
: Title for job<br />
* Default: TITLE [no title given]<br />
setTITL(str <TITLE>)<br />
<br />
==[[Image:Output.png|link=]]TOPFILES== <br />
; TOPFILES <NUM><br />
: Number of top pdbfiles or mtzfiles to write to output.<br />
* Default: TOPFILES 1<br />
setTOPF(int <NUM>) <br />
<br />
==[[Image:Output.png|link=]]ROOT== <br />
; ROOT <FILEROOT><br />
: Root filename for output files (e.g. FILEROOT.log)<br />
* Default: ROOT PHASER<br />
setROOT(string <FILEROOT>)<br />
<br />
==[[Image:Output.png|link=]]VERBOSE== <br />
; VERBOSE [ON|OFF] <br />
: Toggle to send verbose output to log file.<br />
* Default: VERBOSE OFF<br />
setVERB(bool) <br />
<br />
==[[Image:Output.png|link=]]XYZOUT== <br />
; XYZOUT [ON|OFF] ''ENSEMBLE [ON|OFF]<sup>1</sup> PACKING [ON|OFF]<sup>2</sup>''<br />
: Toggle for output coordinate files. <br />
::<sup>1</sup> If the optional ENSEMBLE keyword is ON, then each placed ensemble is written to its own pdb file. The files are named FILEROOT.#.#.pdb with the first # being the solution number and the second # being the number of the placed ensemble (representing a SOLU 6DIM entry in the .sol file). <br />
::<sup>2</sup> If the optional PACKING keyword is ON, then the hexagonal grid used for the packing analysis is output to its own pdb file FILEROOT.pak.pdb<br />
* Default: XYZOUT OFF (Rotation functions)<br />
* Default: XYZOUT ON ENSEMBLE OFF (all other relevant modes)<br />
* Default: XYZOUT ON PACKING OFF (all other relevant modes)<br />
setXYZO(bool) <br />
setXYZO_ENSE(bool)<br />
setXYZO_PACK(bool)<br />
<br><br />
<br><br />
<br />
=Advanced Keywords=<br />
==[[Image:User2.gif|link=]]ELLG==<br />
([[Molecular_Replacement#Should_Phaser_Solve_It.3F|explained here]])<br />
; ELLG TARGET <TARGET><br />
: Target value for expected LLG for determining resolution limits and search order<br />
<!--; ELLG HIRES <HIRES> Internal control only--><br />
* Default: ELLG TARGET 225<br />
setELLG_TARG(float <TARGET>)<br />
<br />
==[[Image:User2.gif|link=]]FORMFACTORS==<br />
; FORMFACTORS [XRAY | ELECTRON | NEUTRON]<br />
: Use scattering factors from x-ray, electron or neutrons<br />
* Default: FORMFACTORS XRAY<br />
setFORM(string XRAY)<br />
<br />
==[[Image:User2.gif|link=]]HAND==<br />
; HAND [ <sup>1</sup>ON| <sup>2</sup>OFF| <sup>3</sup>BOTH]<br />
: Hand of heavy atoms for experimental phasing<br />
: <sup>1</sup>Phase using the other hand of heavy atoms <br />
: <sup>2</sup>Phase using given hand of heavy atoms <br />
: <sup>3</sup>Phase using both hands of heavy atoms<br />
* Default: HAND BOTH<br />
setHAND(str [ "OFF" | "ON" | "BOTH" ])<br />
<br />
==[[Image:User2.gif|link=]]LLGCOMPLETE==<br />
; LLGCOMPLETE COMPLETE [ON|OFF]<br />
: Toggle for structure completion by log-likelihood gradient maps<br />
; LLGCOMPLETE SCATTERER <TYPE> <br />
: Atom/Cluster type(s) to be used for log-likelihood gradient completion. If more than one element is entered for log-likelihood gradient completion, the atom type that gives the highest Z-score for each peak is selected. Type = "RX" is a purely real scatterer and type="AX" is purely anomalous scatterer<br />
; LLGCOMPLETE REAL ON<br />
: Use a purely real scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER RX)<br />
; LLGCOMPLETE ANOMALOUS ON<br />
: Use a purely anomalous scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER AX)<br />
; LLGCOMPLETE CLASH <CLASH> <br />
: Minimum distance between atoms in log-likelihood gradient maps and also the distance used for determining anisotropy of atoms (default determined by resolution, flagged by CLASH=0)<br />
; LLGCOMPLETE SIGMA <Z><br />
: Z-score (sigma) for accepting peaks as new atoms in log-likelihood gradient maps<br />
; LLGCOMPLETE NCYC <NMAX><br />
: Maximum number of cycles of log-likelihood gradient structure completion. By default, NMAX is 50, but this limit should never be reached, because all features in the log-likelihood gradient maps should be assigned well before 50 cycles are finished. This keyword should be used to reduce the number of cycles to 1 or 2.<br />
; LLGCOMPLETE METHOD [IMAGINARY|ATOMTYPE]<br />
: Pick peaks from the imaginary map only or from all the completion atomtype maps.<br />
* Default: LLGCOMPLETE COMPLETE OFF<br />
* Default: LLGCOMPLETE CLASH 0<br />
* Default: LLGCOMPLETE SIGMA 6<br />
* Default: LLGComplete NCYC 50<br />
* Default: LLGComplete METHOD ATOMTYPE<br />
setLLGC_COMP(bool <True|False>) <br />
setLLGC_CLAS(float <CLASH>) <br />
setLLGC_SIGM(float <Z>) <br />
setLLGC_NCYC(int <NMAX>)<br />
setLLGC_METH(str ["IMAGINARY"|"ATOMTYPE"])<br />
<br />
==[[Image:User2.gif|link=]]NMA== <br />
; NMA MODE <M1> ''{MODE <M2>…}'' <br />
: The MODE keyword gives the mode along which to perturb the structure. If multiple modes are entered, the structure is perturbed along all the modes AND combinations of the modes given. There is no limit on the number of modes that can be entered, but the number of pdb files explodes combinatorially. The first 6 modes are the pure rotation and translation modes and do not lead to perturbation of the structure. If the number M is less than 7 then M is interpreted as the first M modes starting at 7, so for example, MODE 5 would give modes 7 8 9 10 11.<br />
; NMA COMBINATION <NMAX><br />
: Controls how many modes are present in any combination.<br />
* Default: NMA MODE 5<br />
* Default: NMA COMBINATION 2<br />
addNMA_MODE(int <MODE>) <br />
setNMA_COMB(int <NMAX>)<br />
<br />
==[[Image:User2.gif|link=]]PACK==<br />
; PACK SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>ALL ]<br />
: <sup>1</sup>Allow up to the PERCENT of sampling points to clash, considering only pairwise clashes <br />
: <sup>2</sup>Allow all solutions (no packing test)<br />
; PACK CUTOFF <PERCENT> <br />
: Limit on total number (or percent) of clashes <br />
; PACK QUICK [ON|OFF]<br />
: Packing check stops when ALLOWED_CLASHES or MAX_CLASHES is reached. However, all clashes are found when the solution has a high Z-score (see [[#ZSCORE | ZSCORE]]).<br />
; PACK COMPACT [ON|OFF]<br />
: Pack ensembles into a compact association (minimize distances between centres of mass for the addition of each component in a solution).<br />
; PACK KEEP HIGH TFZ [ON|OFF]<br />
: Solutions with high tfz (see [[#ZSCORE | ZSCORE]]) but that fail to pack are retained in the solution list. Set to true if SEARCH PRUNE ON (see [[#SEARCH | SEARCH]])<br />
* Default: PACK SELECT PERCENT<br />
* Default: PACK CUTOFF 5<br />
* Default: PACK COMPACT ON<br />
* Default: PACK QUICK ON<br />
* Default: PACK KEEP HIGH TFZ OFF<br />
* Default: PACK CONSERVATION DISTANCE 1,5<br />
setPACK_SELE(str ["PERCENT"|"ALL"]) <br />
setPACK_CUTO(float <ALLOWED_CLASHES>)<br />
setPACK_QUIC(bool)<br />
setPACK_KEEP_HIGH_TFZ(bool)<br />
setPACK_COMP(bool)<br />
<br />
==[[Image:User2.gif|link=]]PEAKS==<br />
; PEAKS TRA SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL] <br />
; PEAKS ROT SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL]<br />
: Peaks for individual rotation functions (ROT) or individual translation functions (TRA) satisfying selection criteria are saved. To be used for subsequent steps, peaks must also satisfy the overall [[#PURGE | PURGE]] selection criteria, so it will usually be appropriate to set only the PURGE criteria (which over-ride the defaults for the PEAKS criteria if not explicitly set). See [[Molecular_Replacement#How_to_Select_Peaks | How to Select Peaks]]<br />
: <sup>1</sup> Select peaks by taking all peaks over CUTOFF percent of the difference between the top peak and the mean value.<br />
: <sup>2</sup> Select peaks by taking all peaks with a Z-score greater than CUTOFF.<br />
: <sup>3</sup> Select peaks by taking top CUTOFF.<br />
: <sup>4</sup> Select all peaks.<br />
; PEAKS ROT CUTOFF <CUTOFF><br />
; PEAKS TRA CUTOFF <CUTOFF><br />
: Cutoff value for the rotation function (ROT) or translation function (TRA) peak selection criteria.<br />
: If selection is by percent and [[#PURGE | PURGE PERCENT]] is changed from the default, then the PEAKS percent value is set to the lower PURGE percent value.<br />
; PEAKS ROT CLUSTER [ON|OFF] <br />
; PEAKS TRA CLUSTER [ON|OFF]<br />
: Toggle selects clustered or unclustered peaks for rotation function (ROT) or translation function (TRA).<br />
; PEAKS ROT DOWN [PERCENT] <br />
: [[#SEARCH | SEARCH METHOD FAST]] only. Percentage to reduce rotation function cutoff if there is no TFZ over the zscore cutoff that determines a true solution (see [[#ZSCORE | ZSCORE]]) in first search.<br />
* Default: PEAKS ROT SELECT PERCENT<br />
* Default: PEAKS TRA SELECT PERCENT<br />
* Default: PEAKS ROT CUTOFF 75<br />
* Default: PEAKS TRA CUTOFF 75<br />
* Default: PEAKS ROT CLUSTER ON<br />
* Default: PEAKS TRA CLUSTER ON<br />
setPEAK_ROTA_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"]) <br />
setPEAK_TRAN_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"])<br />
setPEAK_ROTA_CUTO(float <CUTOFF>)<br />
setPEAK_TRAN_CUTO(float <CUTOFF>) <br />
setPEAK_ROTA_CLUS(bool <CLUSTER>) <br />
setPEAK_TRAN_CLUS(bool <CLUSTER>)<br />
setPEAK_ROTA_DOWN(float <PERCENT>)<br />
<br />
==[[Image:User2.gif|link=]]PERMUTATIONS== <br />
; PERMUTATIONS [ON|OFF]<br />
: Only relevant to [[#SEARCH | SEARCH METHOD FULL]]. Toggle for whether the order of the search set is to be permuted.<br />
* Default: PERMUTATIONS OFF<br />
setPERM(bool <PERMUTATIONS>)<br />
<br />
==[[Image:User2.gif|link=]]PERTURB== <br />
; PERTURB RMS STEP <RMS><br />
: Increment in rms Ångstroms between pdb files to be written. <br />
; PERTURB RMS MAX <MAXRMS><br />
: The structure will be perturbed along each mode until the MAXRMS deviation has been reached.<br />
; PERTURB RMS DIRECTION [FORWARD|BACKWARD|TOFRO] <br />
: The structure is perturbed either forwards or backwards or to-and-fro (FORWARD|BACKWARD|TOFRO) along the eigenvectors of the modes specified.<br />
; PERTURB INCREMENT [RMS| DQ] <br />
: Perturb the structure by rms devitations along the modes, or by set dq increments<br />
; PERTURB DQ <DQ1> ''{DQ <DQ2>…}''<br />
: Alternatively, the DQ factors (as used by the Elnemo server (K. Suhre & Y-H. Sanejouand, NAR 2004 vol 32) ) by which to perturb the atoms along the eigenvectors can be entered directly.<br />
* Default: PERTURB INCREMENT RMS<br />
* Default: PERTURB RMS STEP 0.2<br />
* Default: PERTURB RMS MAXRMS 0.3<br />
* Default: PERTURB RMS DIRECTION TOFRO<br />
setPERT_INCR(str [ "RMS" | "DQ" ])<br />
setPERT_RMS_MAXI(float <MAX>)<br />
setPERT_RMS_DIRE(str [ "FORWARDS" | "BACKWARDS" | "TOFRO" ]) <br />
addPERT_DQ(float <DQ>)<br />
<br />
==[[Image:User2.gif|link=]]PURGE== <br />
; PURGE ROT ENABLE [ON|OFF]<sup>1</sup><br />
; PURGE ROT PERCENT <PERC><sup>2</sup><br />
; PURGE ROT NUMBER <NUM><sup>3</sup><br />
: Purging criteria for rotation function (RF), where PERCENT and NUMBER are alternative selection criteria (''OR'' criteria)<br />
::<sup>1</sup> Toggle for whether to purge the solution list from the RF according to the top solution found. If there are a number of RF searches with different partial solution backgrounds, the PURGE is applied to the total list of peaks. If there is one clearly significant RF solution from one of the backgrounds it acts to purge all the less significant solutions. If there is only one RF (a single partial solution background) the PURGE gives no additional selection over and above the PEAKS command. <br />
::<sup>2</sup> [[Molecular_Replacement#How_to_Select_Peaks | Selection by percent]]. PERC is percentage of the top peak, where the value of the top peak is defined as 100% and the value of the mean is defined as 0%. Note that this criterion is applied subsequent to any selection criteria applied through the [[#PEAKS | PEAKS]] command. If the [[#PEAKS | PEAKS]] selection is by percent, then the percent cutoff given in the PURGE command over-rides that for [[#PEAKS | PEAKS]], so as to rationalize results in the case of only a single RF (single partial solution background.)<br />
::<sup>3</sup> NUM is the number of solutions to retain in purging. If NUMBER is given (non-zero) it overrides the PERCENT option. NUMBER given as zero is the flag for not applying this criterion.<br />
; PURGE TRA ENABLE [ON|OFF]<br />
; PURGE TRA PERCENT <PERC><br />
; PURGE TRA NUMBER <NUM><br />
: As above, but for translation function<br />
; PURGE RNP ENABLE [ON|OFF]<br />
; PURGE RNP PERCENT <PERC><br />
; PURGE RNP NUMBER <NUM><br />
: As above but for refinement, but with the important distinction that PERCENT and NUMBER are concurrent selection criteria (''AND'' criteria)<br />
* Default: PURGE ROT ENABLE ON <br />
* Default: PURGE ROT PERC 75<br />
* Default: PURGE ROT NUM 0<br />
* Default: PURGE TRA ENABLE ON<br />
* Default: PURGE TRA PERC 75<br />
* Default: PURGE TRA NUM 0<br />
* Default: PURGE RNP ENABLE ON<br />
* Default: PURGE RNP PERC 75<br />
* Default: PURGE RNP NUM 0<br />
setPURG_ROTA_ENAB(bool <ENABLE>)<br />
setPURG_TRAN_ENAB(bool <ENABLE>) <br />
setPURG_RNP_ENAB(bool <ENABLE>)<br />
setPURG_ROTA_PERC(float <PERC>) <br />
setPURG_TRAN_PERC(float <PERC>) <br />
setPURG_RNP_PERC(float <PERC>)<br />
setPURG_ROTA_NUMB(float <NUM>) <br />
setPURG_TRAN_NUMB(float <NUM>)<br />
setPURG_TRAN_NUMB(float <NUM>)<br />
setPURG_RNP_NUMB(float <NUM>)<br />
<br />
==[[Image:User2.gif|link=]]RESOLUTION== <br />
; RESOLUTION HIGH <HIRES> <br />
: High resolution limit in Ångstroms. <br />
; RESOLUTION LOW <LORES><br />
: Low resolution limit in Ångstroms.<br />
; RESOLUTION AUTO HIGH <HIRES> <br />
: High resolution limit in Ångstroms for final high resolution refinement in MR_AUTO mode.<br />
* Default for molecular replacement: Set by [[#ELLG | ELLG TARGET]] for structure solution, final refinement uses all data<br />
* Default for experimental phasing: All data used<br />
setRESO_HIGH(float <HIRES>) <br />
setRESO_LOW(float <LORES>)<br />
setRESO_AUTO_HIGH(float <HIRES>) <br />
setRESO(float <HIRES>,float <LORES>)<br />
<br />
==[[Image:User2.gif|link=]]ROTATE== <br />
; ROTATE VOLUME FULL<br />
: Sample all unique angles <br />
; ROTATE VOLUME AROUND EULER <A> <nowiki><B></nowiki> <C> RANGE <RANGE> <br />
: Restrict the search to the region of +/- RANGE degrees around orientation given by EULER<br />
setROTA_VOLU(string ["FULL"|"AROUND"|) <br />
setROTA_EULE(dvect3 <A B C>) <br />
setROTA_RANG(float <RANGE>)<br />
<br />
==[[Image:User2.gif|link=]]SCATTERING==<br />
; SCATTERING TYPE <TYPE> FP=<FP> FDP=<FDP> FIX [ON|OFF|EDGE]<br />
: Measured scattering factors for a given atom type, from a fluorescence scan. FIX EDGE (default) fixes the fdp value if it is away from an edge, but refines it if it is close to an edge, while FIX ON or FIX OFF does not depend on proximity of edge.<br />
; SCATTERING RESTRAINT [ON|OFF]<br />
: use Fdp restraints<br />
; SCATTERING SIGMA <SIGMA><br />
: Fdp restraint sigma used is SIGMA multiplied by initial fdp value<br />
* Default: SCATTERING SIGMA 0.2<br />
* Default: SCATTERING RESTRAINT ON<br />
addSCAT(str <TYPE>,float <FP>,float <FDP, string <FIXFDP>) <br />
setSCAT_REST(bool) <br />
setSCAT_SIGM(float <SIGMA>)<br />
<br />
==[[Image:User2.gif|link=]]SCEDS== <br />
; SCEDS NDOM <NDOM><br />
:Number of domains into which to split the protein<br />
; SCEDS WEIGHT SPHERICITY <WS><br />
: Weight factor for the the Density Test in the SCED Score. The Sphericity Test scores boundaries that divide the protein into more spherical domains more highly.<br />
; SCEDS WEIGHT CONTINUITY <WC><br />
: Weight factor for the the Continuity Test in the SCED Score. The Continuity Test scores boundaries that divide the protein into domains contigous in sequence more highly. <br />
; SCEDS WEIGHT EQUALITY <WE><br />
: Weight factor for the the Equality Test in the SCED Score. The Equality Test scores boundaries that divide the protein more equally more highly.<br />
; SCEDS WEIGHT DENSITY <WD><br />
: Weight factor for the the Equality Test in the SCED Score. The Density Test scores boundaries that divide the protein into domains more densely packed with atoms more highly. <br />
* Default: SCEDS NDOM 2<br />
* Default: SCEDS WEIGHT EQUALITY 1<br />
* Default: SCEDS WEIGHT SPHERICITY 4 <br />
* Default: SCEDS WEIGHT DENSITY 1<br />
* Default: SCEDS WEIGHT CONTINUITY 0<br />
setSCED_NDOM(int <NDOM>) <br />
setSCED_WEIG_SPHE(float <WS>) <br />
setSCED_WEIG_CONT(float <WC>)<br />
setSCED_WEIG_EQUA(float <WE>) <br />
setSCED_WEIG_DENS(float <WD>)<br />
<br />
==[[Image:User2.gif|link=]]TARGET==<br />
; TARGET ROT [FAST | BRUTE]<br />
: Target function for fast rotation searches (2). BRUTE searches all angles on a grid with the full rotation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these rotations with the full rotation likelihood target.<br />
; TARGET TRA [FAST | BRUTE | PHASED]<br />
: Target function for fast translation searches (3). BRUTE searches all positions on a grid with the full translation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these positions with the full translation likelihood target. PHASED selects the "phased translation function", for which a LABIN command should also be given, specifying FMAP, PHMAP and (optionally) FOM.<br />
* Default: TARGET ROT FAST<br />
* Default: TARGET TRA FAST<br />
setTARG_ROTA(str ["FAST"|"BRUTE"])<br />
setTARG_TRAN(str ["FAST"|"BRUTE"|"PHASED"])<br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS NMOL <NMOL><br />
: Number of molecules/molecular assemblies related by single TNCS vector (usually only 2). If the TNCS is a pseudo-tripling of the cell then NMOL=3, a pseudo-quadrupling then NMOL=4 etc.<br />
* Default: TNCS NMOL 2<br />
setTNCS_NMOL(int <NMOL>)<br />
<br><br />
<br />
==[[Image:User2.gif|link=]]TRANSLATION== <br />
; TRANSLATION VOLUME [ <sup>1</sup>FULL | <sup>2</sup>REGION | <sup>3</sup>LINE | <sup>4</sup>AROUND ])<br />
: Search volume for brute force translation function.<br />
: <sup>1</sup> Cheshire cell or Primitive cell volume. <br />
: <sup>2</sup> Search region.<br />
: <sup>3</sup> Search along line. <br />
: <sup>4</sup> Search around a point.<br />
; <sup>1 2 3</sup>TRANSLATION START <X Y Z> <br />
; <sup>1 2 3</sup>TRANSLATION END <X Y Z><br />
: Search within region or line bounded by START and END.<br />
; <sup>4</sup>TRANSLATION POINT <X Y Z><br />
; <sup>4</sup>TRANSLATION RANGE <RANGE><br />
: Search within +/- RANGE Ångstroms (not fractional coordinates, even if the search point is given as fractional coordinates) of a point <X Y Z>.<br />
; TRANSLATION [ORTH | FRAC]<br />
: Coordinates are given in orthogonal or fractional values.<br />
; TRANSLATION PACKING USE [ON | OFF]<br />
: Top translation function peak will be testes for packing.<br />
; TRANSLATION PACKING CUTOFF <PERC><br />
: Percent pairwise packing used for packing function test of top TF peak. Equivalent to PACK CUTOFF <PERC> for packing function. <br />
; TRANSLATION PACKING NUM <NUM><br />
: Number of translation function peaks to test for packing before bailing out of packing test. Set to 0 to pack all translation function peaks (slow for large packing volumes). <br />
* Default: TRANSLATION VOLUME FULL<br />
* Default: TRANSLATION PACK CUTOFF 50<br />
* Default: TRANSLATION PACK NUM 0 (helices - all packing checked)<br />
* Default: TRANSLATION PACK NUM 500 (non-helices)<br />
setTRAN_VOLU(string ["FULL"|"REGION"|"LINE"|"AROUND"])<br />
setTRAN_START(dvect <START>)<br />
setTRAN_END(dvect <END>)<br />
setTRAN_POINT(dvect <POINT>)<br />
setTRAN_RANGE(float <RANGE>)<br />
setTRAN_FRAC(bool <True=FRAC False=ORTH>)<br />
setTRAN_PACK_USE(bool)<br />
setTRAN_PACK_CUTO(float)<br />
<br />
==[[Image:User2.gif|link=]]ZSCORE== <br />
; ZSCORE USE [ON|OFF]<br />
: Use the TFZ tests. Only applicable with [[#SEARCH | SEARCH METHOD FAST]]. (Note Phaser-2.4.0 and below use "ZSCORE SOLVED 0" to turn off the TFZ tests)<br />
; ZSCORE SOLVED <ZSCORE_SOLVED><br />
: Set the minimum TFZ that indicates a definite solution for amalgamating solutions in FAST search method. <br />
;ZSCORE STOP [ON|OFF]<br />
: Stop adding components beyond point where TFZ is below cutoff when adding multiple components in FAST mode. However, FAST mode will always add one component even if TFZ is below cutoff, or two components if starting search with no components input (no input solution).<br />
; ZSCORE HALF [ON|OFF]<br />
: Set the TFZ for amalgamating solutions in the FAST search method to the maximum of ZSCORE_SOLVED and half the maximum TFZ, to accommodate cases of partially correct solutions in very high TFZ cases (e.g. TFZ > 16)<br />
* Default: ZSCORE USE ON<br />
* Default: ZSCORE SOLVED 8<br />
* Default: ZSCORE HALF ON<br />
* Default: ZSCORE STOP ON<br />
setZSCO_USE(bool <True=ON False=OFF>)<br />
setZSCO_SOLV(floatType ZSCORE_SOLVED)<br />
setZSCO_HALF(bool <True=ON False=OFF>)<br />
setZSCO_STOP(bool <True=ON False=OFF>)<br />
<br><br />
<br><br />
<br />
=Expert Keywords=<br />
<br />
==[[Image:Expert.gif|link=]]MACANO== <br />
; MACANO PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for the refinement of SigmaN in the anisotropy correction<br />
; MACANO ANISO [ON|OFF] BINS [ON|OFF] SOLK [ON|OFF] SOLB [ON|OFF] ''{NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}''<br />
: Macrocycle for the custom refinement of SigmaN in the anisotropy correction. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACANO PROTOCOL DEFAULT<br />
setMACA_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACA(bool <ANISO>,bool <BINS>,bool <SOLK>,bool <SOLB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACMR== <br />
; MACMR PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACMR ROT [ON|OFF] TRA [ON|OFF] BFAC [ON|OFF] VRMS [ON|OFF] ''CELL [ON|OFF] LAST [ON|OFF] NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of molecular replacement solutions. Macrocycles are performed in the order in which they are entered. For description of VRMS see the [[FAQ]]. CELL is the scale factor for the unit cell for maps (EM maps). LAST is a flag that refines the parameters for the last component of a solution only, fixing all the others.<br />
; MACMR CHAINS [ON|OFF]<br />
: Split the ensembles into chains for refinement<br />
: Not possible as part of an automated mode<br />
* Default: MACMR PROTOCOL DEFAULT<br />
* Default: MACMR CHAINS OFF<br />
setMACM_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACM(bool <ROT>,bool <TRA>,bool <BFAC>,bool <VRMS>,bool <CELL>,bool <LAST>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
setMACM_CHAI(bool])<br />
<br />
==[[Image:Expert.gif|link=]]MACOCC== <br />
; MACOCC PROTOCOL [ DEFAULT | CUSTOM | OFF | ALL ]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACOCC NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of occupancy for solutions. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACOCC PROTOCOL DEFAULT<br />
setMACO_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACO(int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACGYRE== <br />
; MACGYRE PROTOCOL [ DEFAULT | CUSTOM | OFF | ALL ]<br />
: Protocol for refinement of gyre rotations<br />
; MACGYRE ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] ''ANCHOR [ON|OFF] SIGROT <SIGR> SIGTRA <SIGT> NCYCLE <NCYC> MINIMIZER [ BFGS | NEWTON | DESCENT ]''<br />
: Macrocycle for custom refinement of occupancy for solutions. Macrocycles are performed in the order in which they are entered.<br />
; MACGYRE SIGROT <SIGROT> <br />
; MACGYRE SIGTRA <SIGTRA> <br />
; MACGYRE ANCHOR [ON|OFF]<br />
: Override default values for harmonic restraints for rotation and translation refinement, and whether or not to anchor one fragment (no translation) for all macrocycles<br />
* Default: MACGYRE PROTOCOL DEFAULT<br />
setMACG_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACG(bool <REF>,bool <REF>, bool <REF>)<br />
addMACG_FULL(bool <REF>,bool <REF>,bool<REF>,bool <ANCHOR>,float <SIGROT>,float <SIGTRA>,int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
setMACG_SIGR(bool <SIGROT>)<br />
setMACG_SIGT(bool <SIGTRA>)<br />
setMACG_ANCH(bool <ANCHOR>)<br />
<br />
==[[Image:Expert.gif|link=]]MACSAD== <br />
; MACSAD PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for SAD refinement.<br />
:''n.b. PROTOCOL ALL will crash phaser and is only useful for debugging - see code for details''<br />
; MACSAD XYZ [ON|OFF] OCC [ON|OFF] BFAC [ON|OFF] FDP [ON|OFF] SA [ON|OFF] SB [ON|OFF] SP [ON|OFF] SD [ON|OFF] ''{PK [ON|OFF]} {PB [ON|OFF]} {NCYCLE <NCYC>} MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for SAD refinement. Macrocycles are performed in the order in which they are entered.<br />
*Default: MACSAD PROTOCOL DEFAULT<br />
setMACS_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACS(<br />
bool <XYZ>,bool <OCC>,bool <BFAC>,bool <FDP><br />
bool <SA>,bool <SB>,bool <SP>,bool <SD>,<br />
bool <PK>, bool <PB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACTNCS== <br />
; MACTNCS PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for pseudo-translational NCS refinement.<br />
; MACTNCS ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] ''NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for pseudo-translational NCS refinement. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACTNCS PROTOCOL DEFAULT<br />
setMACT_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACT(bool <ROT>,bool <TRA>,bool <VRMS>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]OCCUPANCY== <br />
; OCCUPANCY WINDOW ELLG <ELLG><br />
: Target eLLG for determining number of residues in window for occupancy refinement. The number of residues in a window will be an odd number. Occupancy refinement will be done for each offset of the refinement window.<br />
; OCCUPANCY WINDOW NRES <NRES><br />
: As an alternative to using the eLLG to define the number of residues in window for occupancy refinement, the number may be input directly. NRES must be an odd number.<br />
; OCCUPANCY WINDOW MAX <NRES><br />
: Maximum number of residues in an occupancy window (determined either by ellg or given as NRES) for which occupancy is refined. Prevents the refinement windows from spanning non-local regions of space.<br />
; OCCUPANCY MIN <MINOCC> MAX <MAXOCC><br />
: Minimum and maximum values of occupancy during refinement.<br />
; OCCUPANCY MERGE [ON/OFF]<br />
: Merge refined occupancies from different window offsets to give final occupancies per residue. If OFF, occupancies from a single window offset will be used, selected using OCCUPANCY OFFSET <N><br />
; OCCUPANCY FRAC <FRAC><br />
: Minimum fraction of the protein for which the occupancy may be set to zero.<br />
; OCCUPANCY OFFSET <N><br />
: If OCCUPANCY MERGE OFF, then <N> defines the single window offset from which final occupancies will be taken<br />
* Default: OCCUPANCY WINDOW ELLG 5<br />
* Default: OCCUPANCY WINDOW MAX 111<br />
* Default: OCCUPANCY MIN 0.01 MAX 1<br />
* Default: OCCUPANCY NCYCLES 1<br />
* Default: OCCUPANCY MERGE ON<br />
* Default: OCCUPANCY FRAC 0.5<br />
* Default: OCCUPANCY OFFSET 0<br />
setOCCU_WIND_ELLG(float <ELLG>)<br />
setOCCU_WIND_NRES(int <NRES>)<br />
setOCCU_WIND_MAX(int <NRES>)<br />
setOCCU_MIN(float <MIN>)<br />
setOCCU_MAX(float <MAX>)<br />
setOCCU_MERG(float <FRAC>)<br />
setOCCU_FRAC(bool)<br />
setOCCU_OFFS(int <N>)<br />
<br />
==[[Image:Expert.gif|link=]]RESCORE== <br />
; RESCORE ROT [ON|OFF]<br />
; RESCORE TRA [ON|OFF]<br />
: Toggle for rescoring of fast rotation function (ROT) or fast translation function (TRA) search peaks. <br />
* Default: RESCORE ROT ON<br />
* Default: RESCORE TRA ON|OFF will depend on whether phaser is running in the mode [[#MODE | MODE MR_AUTO]] with [[#SEARCH | SEARCH METHOD FAST]] or with [[#SEARCH | SEARCH METHOD FULL]], or running the translation function separately [[#MODE | MODE MR_FTF]]. For [[#SEARCH | SEARCH METHOD FAST]] the default also depends on whether or not the expected LLG target [[#ELLG | ELLG TARGET <TARGET>]] value is reached.<br />
setRESC_ROTA(bool)<br />
setRESC_TRAN(bool)<br />
<br />
==[[Image:Expert.gif|link=]]RFACTOR== <br />
; RFACTOR USE [ON|OFF]<br />
: For cases of searching for one ensemble when there is one ensemble in the asymmetric unit, the R-factor for the ensemble at the orientation and position in the input is calculated. If this value is low then MR is not performed in the MR_AUTO job in FAST search mode. Instead, rigid body refinement is performed before exiting. Note that the same R-factor test and cutoff is used for judging success in single-atom molecular replacement (MR_ATOM mode).<br />
; RFACTOR CUTOFF <VALUE><br />
: Rfactor in percent used as cutoff for deciding whether or not the R-factor indicates that MR is not necessary.<br />
* Default: RFACTOR USE ON CUTOFF 35<br />
setRFAC_USE(bool)<br />
setRFAC_CUTO(float <PERCENT>)<br />
<br />
==[[Image:Expert.gif|link=]]SAMPLING==<br />
; SAMPLING ROT <SAMP><br />
; SAMPLING TRA <SAMP><br />
: Sampling of search given in degrees for a rotation search and Ångstroms for a translation search. Sampling for rotation search depends on the mean radius of the Ensemble and the high resolution limit (dmin) of the search.<br />
* Default: SAMP = 2*atan(dmin/(4*meanRadius)) (ROTATION FUNCTION)<br />
* Default: SAMP = dmin/5; (BRUTE TRANSLATION FUNCTION)<br />
* Default: SAMP = dmin/4; (FAST TRANSLATION FUNCTION)<br />
setSAMP_ROTA(float <SAMP>)<br />
setSAMP_TRAN(float <SAMP>)<br />
<br><br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS USE [ON|OFF]<br />
: Use TNCS if present: apply TNCS corrections. (Note: was TNCS IGNORE [ON|OFF] in Phaser-2.4.0)<br />
; TNCS RLIST ADD [ON | OFF]<br />
: Supplement the rotation list used in the translation function with rotations already present in the list of known solutions. New molecules in the same orientation as those in the known search (as occurs with translational ncs) may not have peaks associated with them from the rotation function because the known molecules mask the presence of the ones not yet found. <br />
; TNCS PATT HIRES <hires><br />
: High resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT LORES <lores><br />
: Low resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT PERCENT <percent><br />
: Percent of origin Patterson peak that qualifies as a TNCS vector<br />
; TNCS PATT DISTANCE <distance><br />
: Minimum distance of Patterson peak from origin that qualifies as a TNCS vector<br />
; TNCS TRANSLATION PERTURB [ON | OFF]<br />
: If the TNCS translation vector is on a special position, perturb the vector from the special position before refinement<br />
; TNCS ROTATION RANGE <angle><br />
: Maximum deviation from initial rotation from which to look for rotational deviation. Default uses internally determined value based on resolution of data and size of G-function effective molecular radius. Value of 0 turns rotational refinement off.<br />
; TNCS ROTATION SAMPLING <sampling><br />
: Sampling for rotation search. Default uses internally determined value based on resolution of data and size of G-function effective molecular radius. Value of 0 turns rotational refinement off.<br />
* Default: TNCS USE ON<br />
* Default: TNCS RLIST ADD ON<br />
* Default: TNCS PATT HIRES 5<br />
* Default: TNCS PATT LORES 10<br />
* Default: TNCS PATT PERCENT 20<br />
* Default: TNCS PATT DISTANCE 15 <br />
* Default: TNCS TRANSLATION PERTURB ON<br />
setTNCS_USE(bool)<br />
setTNCS_RLIS_ADD(bool)<br />
setTNCS_PATT_HIRE(float <HIRES>)<br />
setTNCS_PATT_LORE(float <LORES>) <br />
setTNCS_PATT_PERC(float <PERCENT>) <br />
setTNCS_PATT_DIST(float <DISTANCE>)<br />
setTNCS_TRAN_PERT(bool)<br />
setTNCS_ROTA_RANG(float <RANGE>) <br />
setTNCS_ROTA_SAMP(float <SAMPLING>) <br />
<br><br />
<br><br />
<br />
=Developer Keywords=<br />
==[[Image:Developer.gif|link=]]BINS== <br />
; BINS DATA [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the data.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections<br />
; BINS ENSE [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the calaculated structure factos for the ensembles.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections<br />
* Default: BINS DATA MIN 6 MAX 50 WIDTH 500 <br />
* Default: BINS ENSE MIN 6 MAX 1000 WIDTH 1000 <br />
setBINS_DATA_MINI(float <L>)<br />
setBINS_DATA_MAXI(float <H>)<br />
setBINS_DATA_WIDT(float <W>)<br />
setBINS_ENSE_MINI(float <L>)<br />
setBINS_ENSE_MAXI(float <H>)<br />
setBINS_ENSE_WIDT(float <W>)<br />
<br />
==[[Image:Developer.gif|link=]]BFACTOR==<br />
; BFACTOR WILSON RESTRAINT [ON|OFF]<br />
: Toggle to use the Wilson restraint on the isotropic component of the atomic B-factors in SAD phasing.<br />
; BFACTOR SPHERICITY RESTRAINT [ON|OFF] <br />
: Toggle to use the sphericity restraint on the anisotropic B-factors in SAD phasing<br />
; BFACTOR REFINE RESTRAINT [ON|OFF] <br />
: Toggle to use the restraint to zero for the molecular B-factor in molecular replacement.<br />
; BFACTOR WILSON SIGMA <SIGMA><br />
: The sigma of the Wilson restraint.<br />
; BFACTOR SPHERICITY SIGMA <SIGMA><br />
: The sigma of the sphericity restraint.<br />
; BFACTOR REFINE SIGMA <SIGMA><br />
: The sigma of the restraint to zero for the molecular B-factor in molecular replacement.<br />
* Default: BFACTOR WILSON RESTRAINT ON <br />
* Default: BFACTOR SPHERICITY RESTRAINT ON <br />
* Default: BFACTOR REFINE RESTRAINT ON <br />
* Default: BFACTOR WILSON SIGMA 5<br />
* Default: BFACTOR SPHERICITY SIGMA 5<br />
* Default: BFACTOR REFINE SIGMA 6<br />
setBFAC_WILS_REST(bool <True|False>)<br />
setBFAC_SPHE_REST(bool <True|False>)<br />
setBFAC_REFI_REST(bool <True|False>) <br />
setBFAC_WILS_SIGM(float <SIGMA>) <br />
setBFAC_SPHE_SIGM(float <SIGMA>) <br />
setBFAC_REFI_SIGM(float <SIGMA>)<br />
<br />
==[[Image:Developer.gif|link=]]BOXSCALE==<br />
; BOXSCALE <BOXSCALE><br />
: Scale for box for calculating structure factors. The ensembles are put in a box equal to (extent of molecule)*BOXSCALE<br />
* Default: BOXSCALE 4<br />
setBOXS<float <BOXSCALE>)<br />
<br />
==[[Image:Developer.gif|link=]]CELL==<br />
; <span style="color:darkorange">Python Only</span> <br />
: Unit cell dimensions<br />
* Default: Cell read from MTZ file<br />
setCELL(float <A>,float <nowiki><B></nowiki>,float <C>,float <ALPHA>,float <BETA>,float <GAMMA>)<br />
setCELL6(float_array <A B C ALPHA BETA GAMMA>)<br />
<br />
==[[Image:Developer.gif|link=]]COMPOSITION== <br />
; COMPOSITION MIN SOLVENT <PERC><br />
: Minimum solvent to give maximum asu packing volume for automated search copy determination (NUM 0)<br />
* Default: COMPOSITION MIN SOLVENT 0.2<br />
setCOMP_MIN_SOLV(float)<br />
<br />
==[[Image:Developer.gif|link=]]DDM== <br />
; DDM SLIDER <VAL> <br />
: The SLIDER window width is used to smooth the Difference Distance Matrix. <br />
; DDM DISTANCE MIN <VAL> MAX <VAL> STEP <VAL><br />
: The range and step interval, as the fraction of the difference between the lowest and highest DDM values used to step.<br />
; DDM SEPARATION MIN <VAL> MAX <VAL><br />
: Through space separation in Angstroms used.<br />
; DDM SEQUENCE MIN <VAL> MAX <VAL><br />
: The range of sequence separations between matrix pairs.<br />
; DDM JOIN MIN <VAL> MAX <VAL><br />
: The range of lengths of the sequences to join if domain segments are discontinuous in percentages of the polypeptide chain.<br />
* Default: DDM SLIDER 0<br />
* Default: DDM DISTANCE MIN 1 MAX 5 STEP 50<br />
* Default: DDM SEPARATION MIN 7 MAX 14<br />
* Default: DDM SEQUENCE MIN 0 MAX 1<br />
* Default: DDM JOIN MIN 2 MAX 12<br />
setDDM_SLID(int <VAL>) <br />
setDDM_DIST_STEP(int <VAL>) <br />
setDDM_DIST_MINI(int <VAL>) <br />
setDDM_DIST_MAXI(int <VAL>) <br />
setDDM_SEPA_MINI(float <VAL>) <br />
setDDM_SEPA_MAXI(float <VAL>)<br />
setDDM_JOIN_MINI(int <VAL>) <br />
setDDM_JOIN_MAXI(int <VAL>) <br />
setDDM_SEQU_MINI(int <VAL>) <br />
setDDM_SEQU_MAXI(int <VAL>)<br />
<br />
==[[Image:Developer.gif|link=]]ENM== <br />
; ENM OSCILLATORS [ <sup>1</sup>RTB | <sup>2</sup>ALL ] <br />
: Define the way the atoms are used for the elastic network model.<br />
: <sup>1</sup>Use the rotation-translation block method.<br />
: <sup>2</sup>Use all atoms to determine the modes (only for use on very small molecules, less than 250 atoms). <br />
; ENM MAXBLOCKS <MAXBLOCKS><br />
: MAXBLOCKS is the number of rotation-translation blocks for the RTB analysis.<br />
; ENM NRES <NRES><br />
: For the RTB analysis, by default NRES=0 and then it is calculated so that it is as small as it can be without reaching MAXBlocks. <br />
; ENM RADIUS <RADIUS><br />
: Elastic Network Model interaction radius (Angstroms)<br />
; ENM FORCE <FORCE><br />
: Elastic Network Model force constant<br />
* Default: ENM OSCILLATORS RTB MAXBLOCKS 250 NRES 0 RADIUS 5 FORCE 1<br />
setENM_OSCI(str ["RTB"|"CA"|"ALL"])<br />
setENM_RTB_MAXB(float <MAXB>)<br />
setENM_RTB_NRES(float <NRES>) <br />
setENM_RADI(float <RADIUS>) <br />
setENM_FORC(float <FORCE>)<br />
<br />
==[[Image:Developer.gif|link=]]NORMALIZATION==<br />
; <span style="color:darkorange">Scripting Only</span><br />
; NORM EPSFAC WRITE <FILENAME><br />
: The normalization factors that correct for anisotropy in the data are written to BINARY file FILENAME<br />
; NORM EPSFAC READ <FILENAME><br />
: The normalization factors that correct for anisotropy in the data are read from BINARY file FILENAME. Further refinement is automatically turned off.<br />
; <span style="color:darkorange">Python Only</span><br />
The normalization factors that correct for anisotropy in the data, extracted from ResultANO object with getSigmaN(). Anisotropy should subsequently be turned off with setMACA_PROT("OFF").<br />
setNORM_DATA(data_norm <SIGMAN>)<br />
<br />
==[[Image:Developer.gif|link=]]OUTLIER==<br />
; OUTLIER REJECT [ON|OFF]<br />
: Reject low probability data outliers<br />
; OUTLIER PROB <PROB><br />
: Cutoff for rejection of low probablity outliers<br />
* Default: OUTLIER REJECT ON PROB 0.000001<br />
setOUTL_REJE(bool) <br />
setOUTL_PROB(float <PROB>)<br />
<br />
==[[Image:Developer.gif|link=]]PTGROUP== <br />
; PTGROUP COVERAGE <COVERAGE><br />
: Percentage coverage for two sequences to be considered in same pointgroup<br />
; PTGROUP IDENTITY <IDENTITY><br />
: Percentage identity for two sequences to be considered in same pointgroup<br />
; PTGROUP RMSD <RMSD><br />
: Percentage rmsd for two models to be considered in same pointgroup<br />
; PTGROUP TOLERANCE ANGULAR <ANG><br />
: Angular tolerance for pointgroup<br />
; PTGROUP TOLERANCE SPATIAL <DIST><br />
: Spatial tolerance for pointgroup<br />
setPTGR_COVE(float <COVERAGE>) <br />
setPTGR_IDEN(float <IDENTITY>) <br />
setPTGR_RMSD(float <RMSD>) <br />
setPTGR_TOLE_ANGU(float <ANG>) <br />
setPTGR_TOLE_SPAT(float <DIST>)<br />
<br />
==[[Image:Developer.gif|link=]]RESHARPEN== <br />
; RESHARPEN PERCENTAGE <PERC><br />
: Perecentage of the B-factor in the direction of lowest fall-off (in anisotropic data) to add back into the structure factors F_ISO and FWT and FDELWT so as to sharpen the electron density maps<br />
* Default: RESHARPEN PERCENT 100<br />
setRESH_PERC(float <PERCENT>)<br />
<br />
==[[Image:Developer.gif|link=]]SOLPARAMETERS==<br />
; SOLPARAMETERS SIGA FSOL <FSOL> BSOL <BSOL> MIN <MINSIGA><br />
: Babinet solvent parameters for Sigma(A) curves. MINSIGA is the minimum SIGA for Babinet solvent term (low resolution only). The solvent term in the Sigma(A) curve is given by <BR>max(1 - FSOL*exp(-BSOL/(4d^2)),MINSIGA).<br />
; SOLPARAMETERS BULK USE [ON|OFF]<br />
: Toggle for use of solvent mask scaling parameters for ensemble structure factors, applied to Fmask.<br />
; SOLPARAMETERS BULK FSOL <FSOL> BSOL <BSOL> <br />
: Solvent mask scaling parameters for ensemble structure factors, applied to Fmask.<br />
* Default: SOLPARAMETERS SIGA FSOL 1.05 BSOL 501 MIN 0.1<br />
* Default: SOLPARAMETERS SIGA RESTRAINT ON<br />
* Default: SOLPARAMETERS BULK USE OFF<br />
* Default: SOLPARAMETERS BULK FSOL 0.35 BSOL 45<br />
setSOLP_SIGA_FSOL(float <FSOL>) <br />
setSOLP_SIGA_BSOL(float <BSOL>)<br />
setSOLP_SIGA_MIN(float <MINSIGA>)<br />
setSOLP_BULK_USE(bool)<br />
setSOLP_BULK_FSOL(float <FSOL>) <br />
setSOLP_BULK_BSOL(float <BSOL>)<br />
<br />
==[[Image:Developer.gif|link=]]TARGET== <br />
; TARGET ROT FAST TYPE [LERF1 | CROWTHER]<br />
: Target function type for fast rotation searches<br />
; TARGET TRA FAST TYPE [LETF1 | LETF2 | CORRELATION]<br />
: Target function type for fast translation searches<br />
setTARG_ROTA_TYPE(string TYPE)<br />
setTARG_TRAN_TYPE(string TYPE)<br />
<br />
==[[Image:Developer.gif|link=]]TNCS==<br />
; TNCS ROTATION ANGLE <A> <nowiki><B></nowiki> <C><br />
: Input rotational difference between molecules related by the pseudo-translational symmetry vector, specified as rotations in degrees about x, y and z axes. Central value for grid search (RANGE > 0).<br />
; TNCS ROTATION RANGE <A><br />
: Range of angular difference in rotation angles to explore around central angle.<br />
; TNCS ROTATION SAMPLING <A><br />
: Sampling step for rotational grid search.<br />
; TNCS TRA VECTOR <x y z> <br />
: Input pseudo-translational symmetry vector (fractional coordinates). By default the translation is determined from the Patterson.<br />
; TNCS VARIANCE RMSD <num><br />
: Input estimated rms deviation between pseudo-translational symmetry vector related molecules.<br />
; TNCS VARIANCE FRAC <num><br />
: Input estimated fraction of cell content that obeys pseudo-translational symmetry.<br />
; TNCS LINK RESTRAINT [ON | OFF]<br />
: Link the occupancy of atoms related by TNCS in SAD phasing<br />
; TNCS LINK SIGMA <sigma><br />
: Sigma of link restraint of the occupancy of atoms related by TNCS in SAD phasing<br />
* Default: TNCS ROTATION ANGLE 0 0 0<br />
* Default: TNCS ROTATION RANGE -999 (determine from structure size and resolution)<br />
* Default: TNCS ROTATION SAMPLING -999 (determine from structure size and resolution)<br />
* Default: TNCS TRANSLATION VECTOR determined from position of Patterson peak<br />
* Default: TNCS VARIANCE RMSD 0.4 <br />
* Default: TNCS VARIANCE FRAC 1 <br />
* Default: TNCS LINK RESTRAINT ON<br />
* Default: TNCS LINK SIGMA 0.1<br />
setTNCS_ROTA_ANGL(dvect3 <A B C>) <br />
setTNCS_TRAN_VECT(dvect3 <X Y Z>) <br />
setTNCS_VARI_RMSD(float <RMSD>) <br />
setTNCS_VARI_FRAC(float <FRAC>)<br />
setTNCS_LINK_REST(bool)<br />
setTNCS_LINK_SIGM(float <SIGMA>)<br />
; <span style="color:darkorange">Scripting Only</span><br />
; TNCS EPSFAC WRITE <FILENAME><br />
: The normalization factors that correct for tNCS in the data are written to BINARY file FILENAME<br />
; TNCS EPSFAC READ <FILENAME><br />
: The normalization factors that correct for tNCS in the data are read from BINARY file FILENAME. Further refinement is automatically turned off.<br />
; <span style="color:darkorange">Python Only</span><br />
The normalization factors that correct for tNCS in the data, extracted from ResultNCS object with getPtNcs(). tNCS refinement should subsequently be turned off with setMACT_PROT("OFF").<br />
setTNCS(data_tncs <PTNCS>)<br />
<br />
==[[Image:Developer.gif|link=]]TRANSLATION== <br />
; TRANSLATION MAPS [ON | OFF]<br />
: Output maps of fast translation function FSS scoring functions<br />
: Maps take the names <ROOT>.<ensemble>.k.e.map where k is the Known backgound number and e is the Euler angle number for that known background<br />
* Default: TRANSLATION MAPS OFF<br />
setTRAN_MAPS(bool)</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Source_Code&diff=2400Source Code2016-12-10T15:48:50Z<p>Airlie: /* Repository */</p>
<hr />
<div>===Repository===<br />
<br />
A public [https://git.csx.cam.ac.uk/x/cimr-phaser/phaser.git/summary Phaser git repository] is available for '''git clone''' and '''git pull''' only. This mirrors commits to the Phaser SVN respository in real time<br />
<br />
The [http://www-structmed.cimr.cam.ac.uk/svn-cgi-bin/viewvc.cgi/ Phaser SVN repository] is located in Cambridge on the CIMR server (password restricted)<br />
<br />
The Berkeley mirror at cci.lbl.gov is updated at midnight Berkeley time<br />
<br />
:/net/cci/auto_build/repositories/phaser<br />
<br />
===Access===<br />
<br />
*You can download nightly builds of Phenix (binaries), which contain the latest version of Phaser that has passed regression tests<br />
*You can compile code with real-time updates from the git repository. This code may not pass regression tests. The git repository is best used for obtaining instant bugfixes, after communication with one of the Phaser developers<br />
*If you are developing a pipeline using Phaser, we are keen to work with you to add features, fix bugs and help you use Phaser optimally<br />
*Note the University of Cambridge's [[ Licences | Licences for Phaser]] with regards to making Phaser part of a pipeline available online<br />
*Source code modifications are allowed under the University of Cambridge's [[ Licences | Licences for Phaser]], provided they are for internal use only. Distribution would require those changes to be incorporated into our SVN repository. <br />
<br />
===Full Access===<br />
<br />
*Requests for permission to commit to the SVN repository via SSH should emailed to [mailto:cimr-phaser@lists.cam.ac.uk phaser-help]</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Source_Code&diff=2399Source Code2016-12-10T15:47:04Z<p>Airlie: </p>
<hr />
<div>===Repository===<br />
<br />
A public [https://git.csx.cam.ac.uk/x/cimr-phaser/phaser.git/shortlog Phaser git repository] is available for '''git clone''' and '''git pull''' only. This mirrors commits to the Phaser SVN respository in real time<br />
<br />
The [http://www-structmed.cimr.cam.ac.uk/svn-cgi-bin/viewvc.cgi/ Phaser SVN repository] is located in Cambridge on the CIMR server (password restricted)<br />
<br />
The Berkeley mirror at cci.lbl.gov is updated at midnight Berkeley time<br />
<br />
:/net/cci/auto_build/repositories/phaser<br />
<br />
===Access===<br />
<br />
*You can download nightly builds of Phenix (binaries), which contain the latest version of Phaser that has passed regression tests<br />
*You can compile code with real-time updates from the git repository. This code may not pass regression tests. The git repository is best used for obtaining instant bugfixes, after communication with one of the Phaser developers<br />
*If you are developing a pipeline using Phaser, we are keen to work with you to add features, fix bugs and help you use Phaser optimally<br />
*Note the University of Cambridge's [[ Licences | Licences for Phaser]] with regards to making Phaser part of a pipeline available online<br />
*Source code modifications are allowed under the University of Cambridge's [[ Licences | Licences for Phaser]], provided they are for internal use only. Distribution would require those changes to be incorporated into our SVN repository. <br />
<br />
===Full Access===<br />
<br />
*Requests for permission to commit to the SVN repository via SSH should emailed to [mailto:cimr-phaser@lists.cam.ac.uk phaser-help]</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Source_Code&diff=2398Source Code2016-12-10T15:46:08Z<p>Airlie: </p>
<hr />
<div>===Repository===<br />
<br />
A public [https://git.csx.cam.ac.uk/x/cimr-phaser//phaser.git/shortlog Phaser git repository] is available for '''git clone''' and '''git pull''' only. This mirrors commits to the Phaser SVN respository in real time<br />
<br />
The [http://www-structmed.cimr.cam.ac.uk/svn-cgi-bin/viewvc.cgi/ Phaser SVN repository] is located in Cambridge on the CIMR server (password restricted)<br />
<br />
The Berkeley mirror at cci.lbl.gov is updated at midnight Berkeley time<br />
<br />
:/net/cci/auto_build/repositories/phaser<br />
<br />
===Access===<br />
<br />
*You can download nightly builds of Phenix (binaries), which contain the latest version of Phaser that has passed regression tests<br />
*You can compile code with real-time updates from the git repository. This code may not pass regression tests. The git repository is best used for obtaining instant bugfixes, after communication with one of the Phaser developers<br />
*If you are developing a pipeline using Phaser, we are keen to work with you to add features, fix bugs and help you use Phaser optimally<br />
*Note the University of Cambridge's [[ Licences | Licences for Phaser]] with regards to making Phaser part of a pipeline available online<br />
*Source code modifications are allowed under the University of Cambridge's [[ Licences | Licences for Phaser]], provided they are for internal use only. Distribution would require those changes to be incorporated into our SVN repository. <br />
<br />
===Full Access===<br />
<br />
*Requests for permission to commit to the SVN repository via SSH should emailed to [mailto:cimr-phaser@lists.cam.ac.uk phaser-help]</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Keywords&diff=2397Keywords2016-12-03T13:52:14Z<p>Airlie: /* link=MACOCC */ Added MACGYRE</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
===Phaser Executable===<br />
<br />
The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the [[#MODE | MODE]] keyword. The different modes and the keywords relevant to each mode are described in [[Modes]].<br />
<br />
Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. However, some keywords are meaningful when entered multiple times. The order may or may not be important. <br />
<br />
*[[Image:User1.gif|link=]] [[#Basic Keywords | Basic Keywords]]<br />
<br />
*[[Image:Output.png|link=]] [[#Output Control Keywords | Output Control Keywords]]<br />
<br />
*[[Image:User2.gif|link=]] [[#Advanced Keywords |Advanced Keywords ]]<br />
<br />
*[[Image:Expert.gif|link=]] [[#Expert Keywords | Expert Keywords]]<br />
<br />
*[[Image:Developer.gif|link=]] [[#Developer Keywords | Developer Keywords]]<br />
<br />
<br />
===Python Interface===<br />
<br />
Phaser can be compiled as a python library. The mode is selected by calling the appropriate run-job. Input to the run-job is via input-objects, which are passed to the run-job. Setter function on the input objects are equivalent to the keywords for input to the phaser executable. The different modes and the keywords relevant to each mode are described in [[Modes]]. See [[Python Interface]] for details. <br />
<br />
The python interface uses standard python and cctbx/scitbx variable types.<br />
<br />
str string<br />
float double precision floating point<br />
Miller cctbx::miller::index<int> <br />
dvect3 scitbx::vec3<float> <br />
dmat33 scitbx::mat3<float> <br />
'''type'''_array scitbx::af::shared<'''type'''> arrays<br />
<br />
=Basic Keywords=<br />
==[[Image:User1.gif|link=]]ATOM== <br />
; ATOM CRYSTAL <XTALID> PDB <FILENAME><br />
: Definition of atom positions using a pdb file.<br />
; ATOM CRYSTAL <XTALID> HA <FILENAME><br />
: Definition of atom positions using a ha file (from RANTAN, MLPHARE etc.).<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> <br />
: Minimal definition of atom position. B-factor defaults to isotropic and Wilson B-factor. Use <TYPE>=TX for Ta6Br12 cluster and <TYPE>=XX for all other clusters. Scattering for cluster is spherically averaged. Coordinates of cluster compounds other than Ta6Br12 must be entered with CLUSTER keyword. Ta6Br12 coordinates are in phaser code and do not need to be given with CLUSTER keyword.<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> [ ISOB <ISOB> | ANOU <HH KK LL HK HL KL> | USTAR <HH KK LL HK HL KL>] FIXX [ON|OFF] FIXO [ON|OFF] FIXB [ON|OFF] BSWAP [ON|OFF] LABEL <SITE_NAME><br />
: Full definition of atom position including B-factor.<br />
;ATOM CHANGE BFACTOR WILSON [ON|OFF]<br />
: Reset all atomic B-factors to the Wilson B-factor.<br />
; ATOM CHANGE SCATTERER <SCATTERER><br />
:Reset all atomic scatterers to element (or cluster) type.<br />
setATOM_PDB(str <XTALID>,str <PDB FILENAME>)<br />
setATOM_IOTBX(str <XTALID>,iotbx::pdb::hierarchy::root <iotbx object>)<br />
setATOM_STR(str <XTALID>,str <pdb format string>)<br />
setATOM_HA(str <XTALID>,str <FILENAME>)<br />
addATOM(str <XTALID>,str <TYPE>,<br />
float <X>,float <Y>,float <Z>,float <OCC>)<br />
addATOM_FULL(str <XTALID>,str <TYPE>,bool <ORTH>,<br />
dvect3 <X Y Z>,float <OCC>,bool <ISO>,float <ISOB>,<br />
bool <ANOU>,dmat6 <HH KK LL HK HL KL>,<br />
bool <FIXX>,bool <FIXO>,bool <FIXB>,bool <SWAPB>,<br />
str <SITE_NAME>)<br />
setATOM_CHAN_BFAC_WILS(bool)<br />
setATOM_CHAN_SCAT(bool)<br />
setATOM_CHAN_SCAT_TYPE(str <TYPE>)<br />
<br />
==[[Image:User1.gif|link=]]CLUSTER== <br />
; CLUSTER PDB <PDBFILE><br />
: Sample coordinates for a cluster compound for experimental phasing. Clusters are specified with type XX. Ta6Br12 clusters do not need to have coordinates specified as the coordinates are in the phaser code. To use Ta6Br12 clusters, specify atomtypes/clusters as TX.<br />
setCLUS_PDB(str <PDBFILE>)<br />
addCLUS_PDB(str <ID>, str <PDBFILE>)<br />
<br />
==[[Image:User1.gif|link=]]COMPOSITION== <br />
; COMPOSITION BY [ <sup>1</sup>AVERAGE| <sup>2</sup>SOLVENT| <sup>3</sup>ASU ]<br />
: Alternative ways of defining composition<br />
: <sup>1</sup> AVERAGE solvent fraction for crystals (50%)<br />
: <sup>2</sup> Composition entered by solvent content.<br />
: <sup>3</sup> Explicit description of composition of ASU by sequence or molecular weight<br />
; <sup>2</sup>COMPOSITION PERCENTAGE <SOLVENT><br />
: Specified SOLVENT content<br />
; <sup>3</sup>COMPOSITION PROTEIN [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of protein in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION NUCLEIC [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of nucleic acid in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION ATOM <TYPE> NUMBER <NUM><br />
: Add NUM copies of an atom (usually a heavy atom) to the composition<br />
* Default: COMPOSITION BY ASU<br />
setCOMP_BY(str ["AVERAGE" | "SOLVENT" | "ASU" ])<br />
setCOMP_PERC(float <SOLVENT>)<br />
addCOMP_PROT_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_PROT_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_PROT_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_PROT_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_NUCL_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_NUCL_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_NUCL_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_NUCL_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_ATOM(str <TYPE>,float <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]CRYSTAL== <br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN Fpos =<F+> SIGFpos=<SIG+> Fneg=<F-> SIGFneg=<SIG-><br />
: Columns of MTZ file to read for this (anomalous) dataset<br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN F =<F> SIGF=<SIGF><br />
: Columns of MTZ file to read for this (non-anomalous) dataset. Used for LLG completion in SAD phasing when there is no anomalous signal (single atom MR protocol). Use LABIN for MR.<br />
setCRYS_ANOM_LABI(str <F+>,str <SIGF+>,str <F->,str <SIGF->) <br />
setCRYS_MEAN_LABI(str <F>,str <SIGF>)<br />
<br />
==[[Image:User1.gif|link=]]ENSEMBLE== <br />
; ENSEMBLE <MODLID> [PDB|CIF] <PDBFILE> [RMS <RMS><sup>1</sup> | ID <ID><sup>2</sup> | CARD ON<sup>3</sup>] ''CHAIN "<CHAIN>"<sup>4</sup> MODEL <NUM><sup>5</sup>''<br />
: The names of the PDB/CIF files used to build the ENSEMBLE, and either<br />
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
:: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file (e.g. "REMARK PHASER ENSEMBLE MODEL 1 ID 31.2") containing the superimposed models concatenated in the one file. This syntax enables simple automation of the use of ensembles. The pdb file can be non-standard because the atom list for the different models need not be the same.<br />
:: <sup>4</sup> CHAIN is selected from the pdb file. <br />
:: <sup>5</sup> MODEL number is selected from the pdb file.<br />
; ENSEMBLE <MODLID> HKLIN <MTZFILE> F=<F> PHI=<PHI> EXTENT <EX> <EY> <EZ> RMS <RMS> CENTRE <CX> <CY> <CZ> PROTEIN MW <PMW> NUCLEIC MW <NMW> ''CELL SCALE <SCALE>''<br />
: An ENSEMBLE defined from a map (via an mtz file). The molecular weight of the object the map represents is required for scaling. The effective RMS coordinate error is needed to judge how the map accuracy falls off with resolution. For density obtained from an EM image reconstruction, a good first guess would be to take the resolution where the FSC curve drops below 0.5 and divide by 3. The extent (difference between maximum and minimum x,y,z coordinates of region containing model density) is needed to determine reasonable rotation steps, and the centre is needed to carry out a proper interpolation of the molecular transform. The extent and the centre are both given in Ångstroms. The cell scale factor defaults to 1 and can be refined (for example, if the map is from electron microscopy when the cell scale may be unknown to within a few percent).<br />
; ENSEMBLE <MODLID> ATOM <TYPE> RMS <RMS><br />
: Define an ensemble as a single atom for single atom MR<br />
; ENSEMBLE <MODLID> HELIX <NUM> <br />
: Define an ensemble as a helix with NUM residues<br />
; ENSEMBLE <MODLID> HETATM [ON|OFF]<br />
: Use scattering from HETATM records in pdb file. See [[Molecular_Replacement#Coordinate_Editing | Coordinate Editing ]]<br />
; ENSEMBLE <MODLID> DISABLE CHECK [ON|OFF]<br />
: Toggle to disable checking of deviation between models in an ensemble. '''Use with extreme caution'''. Results of computations are not guaranteed to be sensible.<br />
; ENSEMBLE <MODLID> ESTIMATOR [OEFFNER | OEFFNERHI | OEFFNERLO | CHOTHIALESK ]<br />
: Define the estimator function for converting ID to RMS<br />
; ENSEMBLE <MODLID> PTGRP [COVERAGE | IDENTITY | RMSD | TOLANG | TOLSPC | EULER | SYMM ]<br />
: Define the pointgroup parameters <br />
; ENSEMBLE <MODLID> BINS [MIN <N>| MAX <M>| WIDTH <W> ]<br />
: Define the Fcalc reflection binning parameters <br />
; ENSEMBLE <MODLID> TRACE [PDB|CIF] <PDBFILE><br />
: Define the coordinates used for packing independent of the coordinates used for structure factor calculation<br />
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
:: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file <br />
; ENSEMBLE <MODLID> TRACE SAMPLING MIN <DIST> <br />
: Set the minimum distance for the sampling of packing grid<br />
; ENSEMBLE <MODLID> TRACE SAMPLING TARGET <NUM> <br />
: Set the target for the number of points to sample the smallest molecule to be packed<br />
; ENSEMBLE <MODLID> TRACE SAMPLING RANGE <NUM> <br />
: Target range (TARGET+/-RANGE) for search for hexgrid points in protein volume<br />
; ENSEMBLE <MODLID> TRACE SAMPLING USE [AUTO | ALL | CALPHA | HEXGRID ]<br />
: Sample trace coordinates using all atoms, C-alpha atoms, a hexagonal grid in the atomic volume or use an automatically determined choice<br />
; ENSEMBLE <MODLID> TRACE SAMPLING DISTANCE <DIST> <br />
: Set the distance for the sampling of the hexagonal grid explicitly and do not use TARGET to find default sampling distance<br />
; ENSEMBLE <MODLID> TRACE SAMPLING WANG <WANG> <br />
: Scale factor for the size of the Wang mask generated from an ensemble map<br />
; ENSEMBLE <MODLID> TRACE PDB <PDBFILE> <br />
: Use the given set of coordinates for packing rather than using the coordinates for structure factor calculation<br />
* Default: ENSEMBLE <MODLID> DISABLE CHECK OFF<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING MIN 1.0<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING TARGET 1000<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING RANGE 100<br />
addENSE_PDB_ID(str <MODLID>,str <FILE>,float <ID>) <br />
addENSE_PDB_RMS(str <MODLID>,str <FILE>,float <RMS>) <br />
setENSE_TRAC_SAMP_MIN(MODLID,float <MIN>)<br />
setENSE_TRAC_SAMP_TARG(MODLID,int <TARGET>)<br />
setENSE_TRAC_SAMP_RANG(MODLID,int <RANGE>)<br />
setENSE_TRAC_SAMP_USE(MODLID,str)<br />
setENSE_TRAC_SAMP_DIST(MODLID,float <DIST>)<br />
setENSE_TRAC_SAMP_WANG(MODLID,float <WANG>)r <FILE>,float <RMS>)<br />
addENSE_CARD(str <MODLID>,str <FILE>,bool)<br />
addENSE_MAP(str <MODLID>,str <MTZFILE>,str <F>,str <PHI>,dvect3 <EX EY EZ>,<br />
float <RMS>,dvect3 <CX CY CZ>,float <PMW>,float <NMW>,float <CELL>)<br />
setENSE_DISA_CHEC(bool)<br />
<br />
==[[Image:User1.gif|link=]]HKLIN==<br />
; HKLIN <FILENAME><br />
: The mtz file containing the data<br />
setHKLI(str <FILENAME>)<br />
<br />
==[[Image:User1.gif|link=]]JOBS== <br />
; JOBS <NUM><br />
: Number of processors to use in parallelized sections of code<br />
* Default: JOBS 2<br />
setJOBS(int <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]LABIN== <br />
; LABIN F = <F> SIGF = <SIGF> <br />
: Columns in mtz file. F must be given. SIGF should be given but is optional<br />
; LABIN I = <nowiki><I></nowiki> SIGI = <SIGI> <br />
: Columns in mtz file. I must be given. SIGI should be given but is optional<br />
; LABIN FMAP = <PH> PHMAP = <PHMAP> <br />
: Columns in mtz file. FMAP/PHMAP are weighted coefficients for use in the Phased Translation Function.<br />
; LABIN FMAP = <PH> PHMAP = <PHMAP> FOM = <FOM><br />
: Columns in mtz file. FMAP/PHMAP are unweighted coefficients for use in the Phased Translation Function and FOM the figure of merit for weighting<br />
setLABI_F_SIGF(str <F>,str <SIGF>)<br />
setLABI_I_SIGI(str <nowiki><I></nowiki>,str <SIGI>)<br />
setLABI_PTF(str <FMAP>,str <PHMAP>,str <FOM>)<br />
<br />
''Data should be input to python run-jobs using one data_refl parameter''<br />
''This is extracted from the ResultMR_DAT object after a call to runMR_DAT''<br />
setREFL_DATA(data_ref)<br />
''Example:''<br />
i = InputMR_DAT()<br />
i.setHKLI("*.mtz")<br />
i.setLABI_F_SIGF("F","SIGF")<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputMR_LLG()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.setREFL_DATA(r.getDATA())<br />
''See also: '' [[Python Example Scripts]]<br />
<br />
''Alternatively, reflection arrays can be set using cctbx::af::shared<double>''<br />
setREFL_F_SIGF(float_array <F>,float_array <SIGF>)<br />
setREFL_I_SIGI(float_array <nowiki><I></nowiki>,float_array <SIGI>)<br />
setREFL_PTF(float_array <FMAP>,float_array <PHMAP>,float_array <FOM>)<br />
<br />
==[[Image:User1.gif|link=]]MODE==<br />
; MODE [ ANO | CCA | SCEDS | NMAXYZ | NCS | MR_ELLG | MR_AUTO | MR_GYRE | MR_ATOM | MR_ROT | MR_TRA | MR_RNP | | MR_OCC | MR_PAK | EP_AUTO | EP_SAD]<br />
: The mode of operation of Phaser. The different modes are described in a separate page on [[Keyword Modes]]<br />
ResultANO r = runANO(InputANO)<br />
ResultCCA r = runCCA(InputCCA)<br />
ResultNMA r = runSCEDS(InputNMA)<br />
ResultNMA r = runNMAXYZ(InputNMA)<br />
ResultNCS r = runNCS(InputNCS)<br />
ResultELLG r = runMR_ELLG(InputMR_ELLG)<br />
ResultMR r = runMR_AUTO(InputMR_AUTO)<br />
ResultEP r = runMR_ATOM(InputMR_ATOM)<br />
ResulrMR_RF r = runMR_FRF(InputMR_FRF)<br />
ResultMR_TF r = runMR_FTF(InputMR_FTF)<br />
ResultMR r = runMR_RNP(InputMR_RNP)<br />
ResultGYRE r = runMR_GYRE(InputMR_RNP)<br />
ResultMR r = runMR_OCC(InputMR_OCC)<br />
ResultMR r = runMR_PAK(InputMR_PAK)<br />
ResultEP r = runEP_AUTO(InputEP_AUTO)<br />
ResultEP_SAD r = runEP_SAD(InputEP_SAD)<br />
<br />
==[[Image:User1.gif|link=]]PARTIAL== <br />
; PARTIAL PDB <PDBFILE> [RMSIDENTITY] <RMS_ID><br />
: The partial structure for MR-SAD substructure completion. Note that this must already be correctly placed, as the experimental phasing module will not carry out molecular replacement.<br />
; PARTIAL HKLIN <MTZFILE> [RMS|IDENTITY] <RMS_ID><br />
: The partial electron density for MR-SAD substructure completion.<br />
; PARTIAL LABIN FC=<FC> PHIC=<PHIC><br />
: Column labels for partial electron density for MR-SAD substructure completion.<br />
setPART_PDB(str <PDBFILE>)<br />
setPART_HKLI(str <MTZFILE>) <br />
setPART_LABI_FC(str <FC>)<br />
setPART_LABI_PHIC(str <PHIC>) <br />
setPART_VARI(str ["ID"|"RMS"])<br />
setPART_DEVI(float <RMS_ID>)<br />
<br />
==[[Image:User1.gif|link=]]SEARCH==<br />
; SEARCH ENSEMBLE <MODLID> ''{OR ENSEMBLE <MODLID>}… NUMBER <NUM><sup>*</sup>''<br />
: The ENSEMBLE to be searched for in a rotation search or an automatic search. When multiple ensembles are given using the OR keyword, the search is performed for each ENSEMBLE in turn. When the keyword is entered multiple times, each SEARCH keyword refers to a new component of the structure. If the component is present multiple times the sub-keyword NUMber can be used (rather than entering the same SEARCH keyword NUMber times).<br />
: <sup>*</sup>For automatic determination of search number use NUMBER 0. If the composition is entered, the maximum number will be that defined by the composition, otherwise the maximum number will fill the asymmetric unit to a minimum solvent content of 20%. Searches for new components will continue until the TFZ score is above 8, and terminate if the TFZ score drops below 8 before the placement of the maximum number of components.<br />
; SEARCH METHOD [FULL|FAST]<br />
: Search using the [[Modes#Modes |full search]] or [[Modes#Modes | fast search]] algorithms.<br />
; SEARCH ORDER AUTO [ON|OFF]<br />
: Search in the "best" order as estimated using estimated rms deviation and completeness of models.<br />
; SEARCH PRUNE [ON|OFF]<br />
: For high TFZ solutions that fail the packing test, carry out a sliding-window occupancy refinement and prune residues that refine to low occupancy, in an effort to resolve packing clashes. If this flag is set to true, the flag for keeping high tfz score solutions (see [[#PACK | PACK]]) that don't pack is also set to true (PACK KEEP HIGH TFZ ON).<br />
; SEARCH AMALGAMATE USE [ON|OFF]<br />
: For multiple high TFZ solutions, enable amalgamation into a single solution<br />
; SEARCH BFACTOR <BFAC><br />
: B-factor applied to search molecule (or atom).<br />
; SEARCH OFACTOR <OFAC><br />
: Occupancy factor applied to search molecule (or atom).<br />
* Default: SEARCH METHOD FAST<br />
* Default: SEARCH ORDER AUTO ON<br />
* Default: SEARCH PRUNE ON<br />
* Default: SEARCH AMALGAMATE USE ON<br />
* Default: SEARCH BFACTOR 0<br />
* Default: SEARCH OFACTOR 1<br />
addSEAR_ENSE_NUM(str <MODLID>,int <NUM>) <br />
addSEAR_ENSE_OR_ENSE_NUM(string_array <MODLIDS>,int <NUM>) <br />
setSEAR_METH(str [ "FULL" | "FAST" ])<br />
setSEAR_ORDE_AUTO(bool)<br />
setSEAR_PRUN(bool <PRUNE>)<br />
setSEAR_AMAL_USE(bool <AMAL>)<br />
setSEAR_BFAC(float <BFAC>)<br />
setSEAR_OFAC(float <OFAC>)<br />
<br />
==[[Image:User1.gif|link=]]SGALTERNATIVE==<br />
; SGALTERNATIVE SELECT [<sup>1</sup>ALL| <sup>2</sup>HAND| <sup>3</sup>LIST| <sup>4</sup>NONE]<br />
: Selection of alternative space groups to test in translation functions i.e. those that are in same laue group as that given in [[#SPACEGROUP | SPACEGROUP]]<br />
: <sup>1</sup> Test all possible space groups, <br />
: <sup>2</sup> Test the given space group and its enantiomorph.<br />
: <sup>3</sup> Test the space groups listed with SGALTERNATIVE TEST <SG>.<br />
: <sup>4</sup> Do not test alternative space groups.<br />
; SGALTERNATIVE TEST <SG><br />
: Alternative space groups to test. Multiple test space groups can be entered.<br />
* Default: SGALTERNATIVE SELECT HAND<br />
setSGAL_SELE(str [ "ALL" | "HAND" | "LIST" | "NONE" ]) <br />
addSGAL_TEST(str <SG>)<br />
<br />
==[[Image:User1.gif|link=]]SOLUTION==<br />
; SOLUTION SET <ANNOTATION><br />
: Start new set of solutions <br />
; SOLUTION TEMPLATE <ANNOTATION><br />
: Specifies a template solution against which other solutions in this run will be compared. Given in place of SOLUTION SET. Template rotation and translations given by subsequent SOLUTION 6DIM cards as per SOLUTION SETS.<br />
; SOLUTION 6DIM ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> [ORTH|FRAC] <X> <Y> <Z> ''FIXR [ON|OFF] FIXT [ON|OFF] FIXB [ON|OFF] BFAC <BFAC> MULT <MULT>''<br />
: This keyword is repeated for each known position and orientation of an ENSEMBLE MODLID. A B G are the Euler angles (z-y-z convention) and X Y Z are the translation elements, expressed either in orthogonal Angstroms (ORTH) or fractions of a cell edge (FRAC). The input ensemble is transformed by a rotation around the origin of the coordinate system, followed by a translation. BFAC default to 0, MULT (for multiplicity) defaults to 1.<br />
; SOLUTION ENSEMBLE <MODLID> VRMS DELTA <DELTA> RMSD <RMSD><br />
: Refined RMS variance terms for pdb files (or map) in ensemble MODLID. RMSD is the input RMSD of the job that produced the sol file, DELTA is the shift with respect to this RMSD. If given as part of a solution, these values overwrite the values used for input in the ENSEMBLE keyword (if refined).<br />
; SOLUTION ENSEMBLE <MODLID> CELL SCALE <SCALE><br />
: Refined cell scale factor. Only applicable to ensembles that are maps<br />
; SOLUTION TRIAL ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> RFZ <RFZ><br />
: Rotation List for translation function<br />
; SOLUTION ORIGIN ENSEMBLE <MODLID><br />
: Create solution for ensemble MODLID at the origin<br />
; SOLUTION SPACEGROUP <SG><br />
: Space Group of the solution (if alternative spacegroups searched)<br />
; SOLUTION RESOLUTION <HIRES><br />
: High resolution limit of data used to find/refine this solution<br />
; SOLUTION PACKS <PACKS><br />
: Flag for whether solution has been retained despite failing packing test, due to having high TFZ<br />
setSOLU(mr_solution <SOL>) <br />
addSOLU_SET(str <ANNOTATION>) <br />
addSOLU_TEMPLATE(str <ANNOTATION>) <br />
addSOLU_6DIM_ENSE(str <MODLID>,dvect3 <A B C>,bool <FRAC>,dvect3 <X Y Z>,<br />
float <BFAC>,bool <FIXR>,bool <FIXT>,bool <FIXB>,int <MULT>, 1.0) <br />
addSOLU_ENSE_DRMS(str <MODLID>, float <DRMS>) <br />
addSOLU_ENSE_CELL(str <MODLID>, float <SCALE>)<br />
addSOLU_TRIAL_ENSE(string <MODLID>,dvect3 <A B C>,float <RFZ>)<br />
addSOLU_ORIG_ENSE(string <MODLID>)<br />
setSOLU_SPAC(str <SG>)<br />
setSOLU_RESO(float <HIRES>)<br />
setSOLU_PACK(bool <PACKS>)<br />
<br />
==[[Image:User1.gif|link=]]SPACEGROUP==<br />
; SPACEGROUP <SG><br />
: Space group may be altered from the one on the MTZ file to a space group in the same point group. The space group can be entered in one of three ways<br />
#The Hermann-Mauguin symbol e.g. P212121 or P 21 21 21 (with or without spaces)<br />
#The international tables number, which gives standard setting e.g. 19 <br />
#The Hall symbols e.g. P 2ac 2ab<br />
: '''The space group can also be a subgroup of the merged space group'''. For example, P1 is always allowed. The reflections will be expanded to the symmetry of the given subgroup. This is only a valid approach when the true symmetry is the symmetry of the subgroup and perfect twinning causes the data to merge "perfectly" in the higher symmetry. <br />
:'''A list of the allowed space groups in the same point group as the given space group (or space group read from MTZ file) and allowed subgroups of these is given in the Cell Content Analysis logfile.'''<br />
* Default: Read from MTZ file<br />
setSPAC_NUM(int <NUM>)<br />
setSPAC_NAME(string <HM>)<br />
setSPAC_HALL(string <HALL>)<br />
<br />
==[[Image:User1.gif|link=]]WAVELENGTH== <br />
; WAVELENGTH <LAMBDA> <br />
: The wavelengh at which the SAD dataset was collected<br />
setWAVE(float <LAMBDA>)<br />
<br><br />
<br><br />
<br />
=Output Control Keywords=<br />
==[[Image:Output.png|link=]]DEBUG== <br />
; DEBUG [ON|OFF]<br />
: Extra verbose output for debugging<br />
* Default: DEBUG OFF<br />
setDEBU(bool) <br />
<br />
==[[Image:Output.png|link=]]EIGEN==<br />
; EIGEN WRITE [ON|OFF]<br />
; EIGEN READ <EIGENFILE><br />
: Read or write a file containing the eigenvectors and eigenvalues. If reading, the eigenvalues and eigenvectors of the Hessian are read from the file generated by a previous run, rather than calculated. This option must be used with the job that generated the eigenfile and the job reading the eigenfile must have identical input for the ENM parameters. Use WRITE to control whether or not the eigenfile is written when not using the READ mode.<br />
* Default: EIGEN WRITE ON<br />
setEIGE_WRIT(bool)<br />
setEIGE_READ(str <EIGENFILE>)<br />
<br />
==[[Image:Output.png|link=]]HKLOUT== <br />
; HKLOUT [ON|OFF]<br />
: Flags for output of an mtz file containing the phasing information<br />
* Default: HKLOUT ON<br />
setHKLO(bool) <br />
<br />
==[[Image:Output.png|link=]]KEYWORDS== <br />
; KEYWORDS [ON|OFF]<br />
: Write output Phaser .sol file (.rlist file for rotation function)<br />
* Default: KEYWORDS ON<br />
setKEYW(bool)<br />
<br />
==[[Image:Output.gif|link=]]LLGMAPS==<br />
; LLGMAPS [ON|OFF]<br />
: Write log-likelihood gradient map coefficients to MTZ file<br />
* Default: LLGMAPS OFF<br />
setLLGM(bool <True|False>)<br />
<br />
==[[Image:Output.png|link=]]MUTE== <br />
; MUTE [ON|OFF]<br />
: Toggle for running in silent/mute mode, where no logfile is written to ''standard output''.<br />
* Default: MUTE OFF<br />
setMUTE(bool) <br />
<br />
==[[Image:Output.png|link=]]KILL== <br />
; KILL TIME [MINS]<br />
: Kill Phaser after MINS minutes of CPU have elapsed, provided parallel section is complete<br />
; KILL FILE [FILENAME]<br />
: Kill Phaser if file FILENAME is present, provided parallel section is complete<br />
* Default: KILL TIME 0 ''Phaser runs to completion''<br />
* Detaulf: KILL FILE "" ''Phaser runs to completion''<br />
setKILL_TIME(float) <br />
setKILL_FILE(string)<br />
<br />
==[[Image:Output.png|link=]]OUTPUT== <br />
; OUTPUT LEVEL [SILENT|CONCISE|SUMMARY|LOGFILE|VERBOSE|DEBUG]<br />
: Output level for logfile<br />
; OUTPUT LEVEL [0|1|2|3|4|5]<br />
: Output level for logfile (equivalent to keyword level setting)<br />
* Default: OUTPUT LEVEL LOGFILE<br />
setOUTP_LEVE(string)<br />
setOUTP(enum)<br />
<br />
==[[Image:Output.png|link=]]TITLE==<br />
; TITLE <TITLE><br />
: Title for job<br />
* Default: TITLE [no title given]<br />
setTITL(str <TITLE>)<br />
<br />
==[[Image:Output.png|link=]]TOPFILES== <br />
; TOPFILES <NUM><br />
: Number of top pdbfiles or mtzfiles to write to output.<br />
* Default: TOPFILES 1<br />
setTOPF(int <NUM>) <br />
<br />
==[[Image:Output.png|link=]]ROOT== <br />
; ROOT <FILEROOT><br />
: Root filename for output files (e.g. FILEROOT.log)<br />
* Default: ROOT PHASER<br />
setROOT(string <FILEROOT>)<br />
<br />
==[[Image:Output.png|link=]]VERBOSE== <br />
; VERBOSE [ON|OFF] <br />
: Toggle to send verbose output to log file.<br />
* Default: VERBOSE OFF<br />
setVERB(bool) <br />
<br />
==[[Image:Output.png|link=]]XYZOUT== <br />
; XYZOUT [ON|OFF] ''ENSEMBLE [ON|OFF]<sup>1</sup> PACKING [ON|OFF]<sup>2</sup>''<br />
: Toggle for output coordinate files. <br />
::<sup>1</sup> If the optional ENSEMBLE keyword is ON, then each placed ensemble is written to its own pdb file. The files are named FILEROOT.#.#.pdb with the first # being the solution number and the second # being the number of the placed ensemble (representing a SOLU 6DIM entry in the .sol file). <br />
::<sup>2</sup> If the optional PACKING keyword is ON, then the hexagonal grid used for the packing analysis is output to its own pdb file FILEROOT.pak.pdb<br />
* Default: XYZOUT OFF (Rotation functions)<br />
* Default: XYZOUT ON ENSEMBLE OFF (all other relevant modes)<br />
* Default: XYZOUT ON PACKING OFF (all other relevant modes)<br />
setXYZO(bool) <br />
setXYZO_ENSE(bool)<br />
setXYZO_PACK(bool)<br />
<br><br />
<br><br />
<br />
=Advanced Keywords=<br />
==[[Image:User2.gif|link=]]ELLG==<br />
([[Molecular_Replacement#Should_Phaser_Solve_It.3F|explained here]])<br />
; ELLG TARGET <TARGET><br />
: Target value for expected LLG for determining resolution limits and search order<br />
<!--; ELLG HIRES <HIRES> Internal control only--><br />
* Default: ELLG TARGET 225<br />
setELLG_TARG(float <TARGET>)<br />
<br />
==[[Image:User2.gif|link=]]FORMFACTORS==<br />
; FORMFACTORS [XRAY | ELECTRON | NEUTRON]<br />
: Use scattering factors from x-ray, electron or neutrons<br />
* Default: FORMFACTORS XRAY<br />
setFORM(string XRAY)<br />
<br />
==[[Image:User2.gif|link=]]HAND==<br />
; HAND [ <sup>1</sup>ON| <sup>2</sup>OFF| <sup>3</sup>BOTH]<br />
: Hand of heavy atoms for experimental phasing<br />
: <sup>1</sup>Phase using the other hand of heavy atoms <br />
: <sup>2</sup>Phase using given hand of heavy atoms <br />
: <sup>3</sup>Phase using both hands of heavy atoms<br />
* Default: HAND BOTH<br />
setHAND(str [ "OFF" | "ON" | "BOTH" ])<br />
<br />
==[[Image:User2.gif|link=]]LLGCOMPLETE==<br />
; LLGCOMPLETE COMPLETE [ON|OFF]<br />
: Toggle for structure completion by log-likelihood gradient maps<br />
; LLGCOMPLETE SCATTERER <TYPE> <br />
: Atom/Cluster type(s) to be used for log-likelihood gradient completion. If more than one element is entered for log-likelihood gradient completion, the atom type that gives the highest Z-score for each peak is selected. Type = "RX" is a purely real scatterer and type="AX" is purely anomalous scatterer<br />
; LLGCOMPLETE REAL ON<br />
: Use a purely real scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER RX)<br />
; LLGCOMPLETE ANOMALOUS ON<br />
: Use a purely anomalous scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER AX)<br />
; LLGCOMPLETE CLASH <CLASH> <br />
: Minimum distance between atoms in log-likelihood gradient maps and also the distance used for determining anisotropy of atoms (default determined by resolution, flagged by CLASH=0)<br />
; LLGCOMPLETE SIGMA <Z><br />
: Z-score (sigma) for accepting peaks as new atoms in log-likelihood gradient maps<br />
; LLGCOMPLETE NCYC <NMAX><br />
: Maximum number of cycles of log-likelihood gradient structure completion. By default, NMAX is 50, but this limit should never be reached, because all features in the log-likelihood gradient maps should be assigned well before 50 cycles are finished. This keyword should be used to reduce the number of cycles to 1 or 2.<br />
; LLGCOMPLETE METHOD [IMAGINARY|ATOMTYPE]<br />
: Pick peaks from the imaginary map only or from all the completion atomtype maps.<br />
* Default: LLGCOMPLETE COMPLETE OFF<br />
* Default: LLGCOMPLETE CLASH 0<br />
* Default: LLGCOMPLETE SIGMA 6<br />
* Default: LLGComplete NCYC 50<br />
* Default: LLGComplete METHOD ATOMTYPE<br />
setLLGC_COMP(bool <True|False>) <br />
setLLGC_CLAS(float <CLASH>) <br />
setLLGC_SIGM(float <Z>) <br />
setLLGC_NCYC(int <NMAX>)<br />
setLLGC_METH(str ["IMAGINARY"|"ATOMTYPE"])<br />
<br />
==[[Image:User2.gif|link=]]NMA== <br />
; NMA MODE <M1> ''{MODE <M2>…}'' <br />
: The MODE keyword gives the mode along which to perturb the structure. If multiple modes are entered, the structure is perturbed along all the modes AND combinations of the modes given. There is no limit on the number of modes that can be entered, but the number of pdb files explodes combinatorially. The first 6 modes are the pure rotation and translation modes and do not lead to perturbation of the structure. If the number M is less than 7 then M is interpreted as the first M modes starting at 7, so for example, MODE 5 would give modes 7 8 9 10 11.<br />
; NMA COMBINATION <NMAX><br />
: Controls how many modes are present in any combination.<br />
* Default: NMA MODE 5<br />
* Default: NMA COMBINATION 2<br />
addNMA_MODE(int <MODE>) <br />
setNMA_COMB(int <NMAX>)<br />
<br />
==[[Image:User2.gif|link=]]PACK==<br />
; PACK SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>ALL ]<br />
: <sup>1</sup>Allow up to the PERCENT of sampling points to clash, considering only pairwise clashes <br />
: <sup>2</sup>Allow all solutions (no packing test)<br />
; PACK CUTOFF <PERCENT> <br />
: Limit on total number (or percent) of clashes <br />
; PACK QUICK [ON|OFF]<br />
: Packing check stops when ALLOWED_CLASHES or MAX_CLASHES is reached. However, all clashes are found when the solution has a high Z-score (see [[#ZSCORE | ZSCORE]]).<br />
; PACK COMPACT [ON|OFF]<br />
: Pack ensembles into a compact association (minimize distances between centres of mass for the addition of each component in a solution).<br />
; PACK KEEP HIGH TFZ [ON|OFF]<br />
: Solutions with high tfz (see [[#ZSCORE | ZSCORE]]) but that fail to pack are retained in the solution list. Set to true if SEARCH PRUNE ON (see [[#SEARCH | SEARCH]])<br />
* Default: PACK SELECT PERCENT<br />
* Default: PACK CUTOFF 5<br />
* Default: PACK COMPACT ON<br />
* Default: PACK QUICK ON<br />
* Default: PACK KEEP HIGH TFZ OFF<br />
* Default: PACK CONSERVATION DISTANCE 1,5<br />
setPACK_SELE(str ["PERCENT"|"ALL"]) <br />
setPACK_CUTO(float <ALLOWED_CLASHES>)<br />
setPACK_QUIC(bool)<br />
setPACK_KEEP_HIGH_TFZ(bool)<br />
setPACK_COMP(bool)<br />
<br />
==[[Image:User2.gif|link=]]PEAKS==<br />
; PEAKS TRA SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL] <br />
; PEAKS ROT SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL]<br />
: Peaks for individual rotation functions (ROT) or individual translation functions (TRA) satisfying selection criteria are saved. To be used for subsequent steps, peaks must also satisfy the overall [[#PURGE | PURGE]] selection criteria, so it will usually be appropriate to set only the PURGE criteria (which over-ride the defaults for the PEAKS criteria if not explicitly set). See [[Molecular_Replacement#How_to_Select_Peaks | How to Select Peaks]]<br />
: <sup>1</sup> Select peaks by taking all peaks over CUTOFF percent of the difference between the top peak and the mean value.<br />
: <sup>2</sup> Select peaks by taking all peaks with a Z-score greater than CUTOFF.<br />
: <sup>3</sup> Select peaks by taking top CUTOFF.<br />
: <sup>4</sup> Select all peaks.<br />
; PEAKS ROT CUTOFF <CUTOFF><br />
; PEAKS TRA CUTOFF <CUTOFF><br />
: Cutoff value for the rotation function (ROT) or translation function (TRA) peak selection criteria.<br />
: If selection is by percent and [[#PURGE | PURGE PERCENT]] is changed from the default, then the PEAKS percent value is set to the lower PURGE percent value.<br />
; PEAKS ROT CLUSTER [ON|OFF] <br />
; PEAKS TRA CLUSTER [ON|OFF]<br />
: Toggle selects clustered or unclustered peaks for rotation function (ROT) or translation function (TRA).<br />
; PEAKS ROT DOWN [PERCENT] <br />
: [[#SEARCH | SEARCH METHOD FAST]] only. Percentage to reduce rotation function cutoff if there is no TFZ over the zscore cutoff that determines a true solution (see [[#ZSCORE | ZSCORE]]) in first search.<br />
* Default: PEAKS ROT SELECT PERCENT<br />
* Default: PEAKS TRA SELECT PERCENT<br />
* Default: PEAKS ROT CUTOFF 75<br />
* Default: PEAKS TRA CUTOFF 75<br />
* Default: PEAKS ROT CLUSTER ON<br />
* Default: PEAKS TRA CLUSTER ON<br />
setPEAK_ROTA_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"]) <br />
setPEAK_TRAN_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"])<br />
setPEAK_ROTA_CUTO(float <CUTOFF>)<br />
setPEAK_TRAN_CUTO(float <CUTOFF>) <br />
setPEAK_ROTA_CLUS(bool <CLUSTER>) <br />
setPEAK_TRAN_CLUS(bool <CLUSTER>)<br />
setPEAK_ROTA_DOWN(float <PERCENT>)<br />
<br />
==[[Image:User2.gif|link=]]PERMUTATIONS== <br />
; PERMUTATIONS [ON|OFF]<br />
: Only relevant to [[#SEARCH | SEARCH METHOD FULL]]. Toggle for whether the order of the search set is to be permuted.<br />
* Default: PERMUTATIONS OFF<br />
setPERM(bool <PERMUTATIONS>)<br />
<br />
==[[Image:User2.gif|link=]]PERTURB== <br />
; PERTURB RMS STEP <RMS><br />
: Increment in rms Ångstroms between pdb files to be written. <br />
; PERTURB RMS MAX <MAXRMS><br />
: The structure will be perturbed along each mode until the MAXRMS deviation has been reached.<br />
; PERTURB RMS DIRECTION [FORWARD|BACKWARD|TOFRO] <br />
: The structure is perturbed either forwards or backwards or to-and-fro (FORWARD|BACKWARD|TOFRO) along the eigenvectors of the modes specified.<br />
; PERTURB INCREMENT [RMS| DQ] <br />
: Perturb the structure by rms devitations along the modes, or by set dq increments<br />
; PERTURB DQ <DQ1> ''{DQ <DQ2>…}''<br />
: Alternatively, the DQ factors (as used by the Elnemo server (K. Suhre & Y-H. Sanejouand, NAR 2004 vol 32) ) by which to perturb the atoms along the eigenvectors can be entered directly.<br />
* Default: PERTURB INCREMENT RMS<br />
* Default: PERTURB RMS STEP 0.2<br />
* Default: PERTURB RMS MAXRMS 0.3<br />
* Default: PERTURB RMS DIRECTION TOFRO<br />
setPERT_INCR(str [ "RMS" | "DQ" ])<br />
setPERT_RMS_MAXI(float <MAX>)<br />
setPERT_RMS_DIRE(str [ "FORWARDS" | "BACKWARDS" | "TOFRO" ]) <br />
addPERT_DQ(float <DQ>)<br />
<br />
==[[Image:User2.gif|link=]]PURGE== <br />
; PURGE ROT ENABLE [ON|OFF]<sup>1</sup><br />
; PURGE ROT PERCENT <PERC><sup>2</sup><br />
; PURGE ROT NUMBER <NUM><sup>3</sup><br />
: Purging criteria for rotation function (RF), where PERCENT and NUMBER are alternative selection criteria (''OR'' criteria)<br />
::<sup>1</sup> Toggle for whether to purge the solution list from the RF according to the top solution found. If there are a number of RF searches with different partial solution backgrounds, the PURGE is applied to the total list of peaks. If there is one clearly significant RF solution from one of the backgrounds it acts to purge all the less significant solutions. If there is only one RF (a single partial solution background) the PURGE gives no additional selection over and above the PEAKS command. <br />
::<sup>2</sup> [[Molecular_Replacement#How_to_Select_Peaks | Selection by percent]]. PERC is percentage of the top peak, where the value of the top peak is defined as 100% and the value of the mean is defined as 0%. Note that this criterion is applied subsequent to any selection criteria applied through the [[#PEAKS | PEAKS]] command. If the [[#PEAKS | PEAKS]] selection is by percent, then the percent cutoff given in the PURGE command over-rides that for [[#PEAKS | PEAKS]], so as to rationalize results in the case of only a single RF (single partial solution background.)<br />
::<sup>3</sup> NUM is the number of solutions to retain in purging. If NUMBER is given (non-zero) it overrides the PERCENT option. NUMBER given as zero is the flag for not applying this criterion.<br />
; PURGE TRA ENABLE [ON|OFF]<br />
; PURGE TRA PERCENT <PERC><br />
; PURGE TRA NUMBER <NUM><br />
: As above, but for translation function<br />
; PURGE RNP ENABLE [ON|OFF]<br />
; PURGE RNP PERCENT <PERC><br />
; PURGE RNP NUMBER <NUM><br />
: As above but for refinement, but with the important distinction that PERCENT and NUMBER are concurrent selection criteria (''AND'' criteria)<br />
* Default: PURGE ROT ENABLE ON <br />
* Default: PURGE ROT PERC 75<br />
* Default: PURGE ROT NUM 0<br />
* Default: PURGE TRA ENABLE ON<br />
* Default: PURGE TRA PERC 75<br />
* Default: PURGE TRA NUM 0<br />
* Default: PURGE RNP ENABLE ON<br />
* Default: PURGE RNP PERC 75<br />
* Default: PURGE RNP NUM 0<br />
setPURG_ROTA_ENAB(bool <ENABLE>)<br />
setPURG_TRAN_ENAB(bool <ENABLE>) <br />
setPURG_RNP_ENAB(bool <ENABLE>)<br />
setPURG_ROTA_PERC(float <PERC>) <br />
setPURG_TRAN_PERC(float <PERC>) <br />
setPURG_RNP_PERC(float <PERC>)<br />
setPURG_ROTA_NUMB(float <NUM>) <br />
setPURG_TRAN_NUMB(float <NUM>)<br />
setPURG_TRAN_NUMB(float <NUM>)<br />
setPURG_RNP_NUMB(float <NUM>)<br />
<br />
==[[Image:User2.gif|link=]]RESOLUTION== <br />
; RESOLUTION HIGH <HIRES> <br />
: High resolution limit in Ångstroms. <br />
; RESOLUTION LOW <LORES><br />
: Low resolution limit in Ångstroms.<br />
; RESOLUTION AUTO HIGH <HIRES> <br />
: High resolution limit in Ångstroms for final high resolution refinement in MR_AUTO mode.<br />
* Default for molecular replacement: Set by [[#ELLG | ELLG TARGET]] for structure solution, final refinement uses all data<br />
* Default for experimental phasing: All data used<br />
setRESO_HIGH(float <HIRES>) <br />
setRESO_LOW(float <LORES>)<br />
setRESO_AUTO_HIGH(float <HIRES>) <br />
setRESO(float <HIRES>,float <LORES>)<br />
<br />
==[[Image:User2.gif|link=]]ROTATE== <br />
; ROTATE VOLUME FULL<br />
: Sample all unique angles <br />
; ROTATE VOLUME AROUND EULER <A> <nowiki><B></nowiki> <C> RANGE <RANGE> <br />
: Restrict the search to the region of +/- RANGE degrees around orientation given by EULER<br />
setROTA_VOLU(string ["FULL"|"AROUND"|) <br />
setROTA_EULE(dvect3 <A B C>) <br />
setROTA_RANG(float <RANGE>)<br />
<br />
==[[Image:User2.gif|link=]]SCATTERING==<br />
; SCATTERING TYPE <TYPE> FP=<FP> FDP=<FDP> FIX [ON|OFF|EDGE]<br />
: Measured scattering factors for a given atom type, from a fluorescence scan. FIX EDGE (default) fixes the fdp value if it is away from an edge, but refines it if it is close to an edge, while FIX ON or FIX OFF does not depend on proximity of edge.<br />
; SCATTERING RESTRAINT [ON|OFF]<br />
: use Fdp restraints<br />
; SCATTERING SIGMA <SIGMA><br />
: Fdp restraint sigma used is SIGMA multiplied by initial fdp value<br />
* Default: SCATTERING SIGMA 0.2<br />
* Default: SCATTERING RESTRAINT ON<br />
addSCAT(str <TYPE>,float <FP>,float <FDP, string <FIXFDP>) <br />
setSCAT_REST(bool) <br />
setSCAT_SIGM(float <SIGMA>)<br />
<br />
==[[Image:User2.gif|link=]]SCEDS== <br />
; SCEDS NDOM <NDOM><br />
:Number of domains into which to split the protein<br />
; SCEDS WEIGHT SPHERICITY <WS><br />
: Weight factor for the the Density Test in the SCED Score. The Sphericity Test scores boundaries that divide the protein into more spherical domains more highly.<br />
; SCEDS WEIGHT CONTINUITY <WC><br />
: Weight factor for the the Continuity Test in the SCED Score. The Continuity Test scores boundaries that divide the protein into domains contigous in sequence more highly. <br />
; SCEDS WEIGHT EQUALITY <WE><br />
: Weight factor for the the Equality Test in the SCED Score. The Equality Test scores boundaries that divide the protein more equally more highly.<br />
; SCEDS WEIGHT DENSITY <WD><br />
: Weight factor for the the Equality Test in the SCED Score. The Density Test scores boundaries that divide the protein into domains more densely packed with atoms more highly. <br />
* Default: SCEDS NDOM 2<br />
* Default: SCEDS WEIGHT EQUALITY 1<br />
* Default: SCEDS WEIGHT SPHERICITY 4 <br />
* Default: SCEDS WEIGHT DENSITY 1<br />
* Default: SCEDS WEIGHT CONTINUITY 0<br />
setSCED_NDOM(int <NDOM>) <br />
setSCED_WEIG_SPHE(float <WS>) <br />
setSCED_WEIG_CONT(float <WC>)<br />
setSCED_WEIG_EQUA(float <WE>) <br />
setSCED_WEIG_DENS(float <WD>)<br />
<br />
==[[Image:User2.gif|link=]]TARGET==<br />
; TARGET ROT [FAST | BRUTE]<br />
: Target function for fast rotation searches (2). BRUTE searches all angles on a grid with the full rotation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these rotations with the full rotation likelihood target.<br />
; TARGET TRA [FAST | BRUTE | PHASED]<br />
: Target function for fast translation searches (3). BRUTE searches all positions on a grid with the full translation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these positions with the full translation likelihood target. PHASED selects the "phased translation function", for which a LABIN command should also be given, specifying FMAP, PHMAP and (optionally) FOM.<br />
* Default: TARGET ROT FAST<br />
* Default: TARGET TRA FAST<br />
setTARG_ROTA(str ["FAST"|"BRUTE"])<br />
setTARG_TRAN(str ["FAST"|"BRUTE"|"PHASED"])<br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS NMOL <NMOL><br />
: Number of molecules/molecular assemblies related by single TNCS vector (usually only 2). If the TNCS is a pseudo-tripling of the cell then NMOL=3, a pseudo-quadrupling then NMOL=4 etc.<br />
* Default: TNCS NMOL 2<br />
setTNCS_NMOL(int <NMOL>)<br />
<br><br />
<br />
==[[Image:User2.gif|link=]]TRANSLATION== <br />
; TRANSLATION VOLUME [ <sup>1</sup>FULL | <sup>2</sup>REGION | <sup>3</sup>LINE | <sup>4</sup>AROUND ])<br />
: Search volume for brute force translation function.<br />
: <sup>1</sup> Cheshire cell or Primitive cell volume. <br />
: <sup>2</sup> Search region.<br />
: <sup>3</sup> Search along line. <br />
: <sup>4</sup> Search around a point.<br />
; <sup>1 2 3</sup>TRANSLATION START <X Y Z> <br />
; <sup>1 2 3</sup>TRANSLATION END <X Y Z><br />
: Search within region or line bounded by START and END.<br />
; <sup>4</sup>TRANSLATION POINT <X Y Z><br />
; <sup>4</sup>TRANSLATION RANGE <RANGE><br />
: Search within +/- RANGE Ångstroms (not fractional coordinates, even if the search point is given as fractional coordinates) of a point <X Y Z>.<br />
; TRANSLATION [ORTH | FRAC]<br />
: Coordinates are given in orthogonal or fractional values.<br />
; TRANSLATION PACKING USE [ON | OFF]<br />
: Top translation function peak will be testes for packing.<br />
; TRANSLATION PACKING CUTOFF <PERC><br />
: Percent pairwise packing used for packing function test of top TF peak. Equivalent to PACK CUTOFF <PERC> for packing function. <br />
; TRANSLATION PACKING NUM <NUM><br />
: Number of translation function peaks to test for packing before bailing out of packing test. Set to 0 to pack all translation function peaks (slow for large packing volumes). <br />
* Default: TRANSLATION VOLUME FULL<br />
* Default: TRANSLATION PACK CUTOFF 50<br />
* Default: TRANSLATION PACK NUM 0 (helices - all packing checked)<br />
* Default: TRANSLATION PACK NUM 500 (non-helices)<br />
setTRAN_VOLU(string ["FULL"|"REGION"|"LINE"|"AROUND"])<br />
setTRAN_START(dvect <START>)<br />
setTRAN_END(dvect <END>)<br />
setTRAN_POINT(dvect <POINT>)<br />
setTRAN_RANGE(float <RANGE>)<br />
setTRAN_FRAC(bool <True=FRAC False=ORTH>)<br />
setTRAN_PACK_USE(bool)<br />
setTRAN_PACK_CUTO(float)<br />
<br />
==[[Image:User2.gif|link=]]ZSCORE== <br />
; ZSCORE USE [ON|OFF]<br />
: Use the TFZ tests. Only applicable with [[#SEARCH | SEARCH METHOD FAST]]. (Note Phaser-2.4.0 and below use "ZSCORE SOLVED 0" to turn off the TFZ tests)<br />
; ZSCORE SOLVED <ZSCORE_SOLVED><br />
: Set the minimum TFZ that indicates a definite solution for amalgamating solutions in FAST search method. <br />
;ZSCORE STOP [ON|OFF]<br />
: Stop adding components beyond point where TFZ is below cutoff when adding multiple components in FAST mode. However, FAST mode will always add one component even if TFZ is below cutoff, or two components if starting search with no components input (no input solution).<br />
; ZSCORE HALF [ON|OFF]<br />
: Set the TFZ for amalgamating solutions in the FAST search method to the maximum of ZSCORE_SOLVED and half the maximum TFZ, to accommodate cases of partially correct solutions in very high TFZ cases (e.g. TFZ > 16)<br />
* Default: ZSCORE USE ON<br />
* Default: ZSCORE SOLVED 8<br />
* Default: ZSCORE HALF ON<br />
* Default: ZSCORE STOP ON<br />
setZSCO_USE(bool <True=ON False=OFF>)<br />
setZSCO_SOLV(floatType ZSCORE_SOLVED)<br />
setZSCO_HALF(bool <True=ON False=OFF>)<br />
setZSCO_STOP(bool <True=ON False=OFF>)<br />
<br><br />
<br><br />
<br />
=Expert Keywords=<br />
<br />
==[[Image:Expert.gif|link=]]MACANO== <br />
; MACANO PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for the refinement of SigmaN in the anisotropy correction<br />
; MACANO ANISO [ON|OFF] BINS [ON|OFF] SOLK [ON|OFF] SOLB [ON|OFF] ''{NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}''<br />
: Macrocycle for the custom refinement of SigmaN in the anisotropy correction. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACANO PROTOCOL DEFAULT<br />
setMACA_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACA(bool <ANISO>,bool <BINS>,bool <SOLK>,bool <SOLB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACMR== <br />
; MACMR PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACMR ROT [ON|OFF] TRA [ON|OFF] BFAC [ON|OFF] VRMS [ON|OFF] ''CELL [ON|OFF] LAST [ON|OFF] NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of molecular replacement solutions. Macrocycles are performed in the order in which they are entered. For description of VRMS see the [[FAQ]]. CELL is the scale factor for the unit cell for maps (EM maps). LAST is a flag that refines the parameters for the last component of a solution only, fixing all the others.<br />
; MACMR CHAINS [ON|OFF]<br />
: Split the ensembles into chains for refinement<br />
: Not possible as part of an automated mode<br />
* Default: MACMR PROTOCOL DEFAULT<br />
* Default: MACMR CHAINS OFF<br />
setMACM_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACM(bool <ROT>,bool <TRA>,bool <BFAC>,bool <VRMS>,bool <CELL>,bool <LAST>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
setMACM_CHAI(bool])<br />
<br />
==[[Image:Expert.gif|link=]]MACOCC== <br />
; MACOCC PROTOCOL [ DEFAULT | CUSTOM | OFF | ALL ]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACOCC NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of occupancy for solutions. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACOCC PROTOCOL DEFAULT<br />
setMACO_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACO(int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACGYRE== <br />
; MACGYRE PROTOCOL [ DEFAULT | CUSTOM | OFF | ALL ]<br />
: Protocol for refinement of gyre rotations<br />
; MACGYRE ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] ''ANCHOR [ON|OFF] SIGROT <SIGR> SIGTRA <SIGT> NCYCLE <NCYC> MINIMIZER [ BFGS | NEWTON | DESCENT ]''<br />
: Macrocycle for custom refinement of occupancy for solutions. Macrocycles are performed in the order in which they are entered.<br />
; MACGYRE SIGROT <SIGROT> <br />
; MACGYRE SIGTRA <SIGTRA> <br />
; MACGYRE ANCHOR [ON|OFF]<br />
: Override default values for harmonic restraints for rotation and translation refinement, and whether or not to anchor one fragment (no translation) for all macrocycles<br />
* Default: MACGYRE PROTOCOL DEFAULT<br />
setMACG_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACG(bool <REF>,bool <REF>, bool <REF>)<br />
addMACG_FULL(bool <REF>,bool <REF>,bool<REF>,bool <ANCHOR>,float <SIGROT>,float <SIGTRA>,int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
setMACG_SIGR(bool <SIGROT>)<br />
setMACG_SIGT(bool <SIGTRA>)<br />
setMACG_ANCH(bool <ANCHOR>)<br />
<br />
==[[Image:Expert.gif|link=]]MACSAD== <br />
; MACSAD PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for SAD refinement.<br />
:''n.b. PROTOCOL ALL will crash phaser and is only useful for debugging - see code for details''<br />
; MACSAD XYZ [ON|OFF] OCC [ON|OFF] BFAC [ON|OFF] FDP [ON|OFF] SA [ON|OFF] SB [ON|OFF] SP [ON|OFF] SD [ON|OFF] ''{PK [ON|OFF]} {PB [ON|OFF]} {NCYCLE <NCYC>} MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for SAD refinement. Macrocycles are performed in the order in which they are entered.<br />
*Default: MACSAD PROTOCOL DEFAULT<br />
setMACS_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACS(<br />
bool <XYZ>,bool <OCC>,bool <BFAC>,bool <FDP><br />
bool <SA>,bool <SB>,bool <SP>,bool <SD>,<br />
bool <PK>, bool <PB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACTNCS== <br />
; MACTNCS PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for pseudo-translational NCS refinement.<br />
; MACTNCS ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] ''NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for pseudo-translational NCS refinement. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACTNCS PROTOCOL DEFAULT<br />
setMACT_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACT(bool <ROT>,bool <TRA>,bool <VRMS>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]OCCUPANCY== <br />
; OCCUPANCY WINDOW ELLG <ELLG><br />
: Target eLLG for determining number of residues in window for occupancy refinement. The number of residues in a window will be an odd number. Occupancy refinement will be done for each offset of the refinement window.<br />
; OCCUPANCY WINDOW NRES <NRES><br />
: As an alternative to using the eLLG to define the number of residues in window for occupancy refinement, the number may be input directly. NRES must be an odd number.<br />
; OCCUPANCY WINDOW MAX <NRES><br />
: Maximum number of residues in an occupancy window (determined either by ellg or given as NRES) for which occupancy is refined. Prevents the refinement windows from spanning non-local regions of space.<br />
; OCCUPANCY MIN <MINOCC> MAX <MAXOCC><br />
: Minimum and maximum values of occupancy during refinement.<br />
; OCCUPANCY MERGE [ON/OFF]<br />
: Merge refined occupancies from different window offsets to give final occupancies per residue. If OFF, occupancies from a single window offset will be used, selected using OCCUPANCY OFFSET <N><br />
; OCCUPANCY FRAC <FRAC><br />
: Minimum fraction of the protein for which the occupancy may be set to zero.<br />
; OCCUPANCY OFFSET <N><br />
: If OCCUPANCY MERGE OFF, then <N> defines the single window offset from which final occupancies will be taken<br />
* Default: OCCUPANCY WINDOW ELLG 5<br />
* Default: OCCUPANCY WINDOW MAX 111<br />
* Default: OCCUPANCY MIN 0.01 MAX 1<br />
* Default: OCCUPANCY NCYCLES 1<br />
* Default: OCCUPANCY MERGE ON<br />
* Default: OCCUPANCY FRAC 0.5<br />
* Default: OCCUPANCY OFFSET 0<br />
setOCCU_WIND_ELLG(float <ELLG>)<br />
setOCCU_WIND_NRES(int <NRES>)<br />
setOCCU_WIND_MAX(int <NRES>)<br />
setOCCU_MIN(float <MIN>)<br />
setOCCU_MAX(float <MAX>)<br />
setOCCU_MERG(float <FRAC>)<br />
setOCCU_FRAC(bool)<br />
setOCCU_OFFS(int <N>)<br />
<br />
==[[Image:Expert.gif|link=]]RESCORE== <br />
; RESCORE ROT [ON|OFF]<br />
; RESCORE TRA [ON|OFF]<br />
: Toggle for rescoring of fast rotation function (ROT) or fast translation function (TRA) search peaks. <br />
* Default: RESCORE ROT ON<br />
* Default: RESCORE TRA ON|OFF will depend on whether phaser is running in the mode [[#MODE | MODE MR_AUTO]] with [[#SEARCH | SEARCH METHOD FAST]] or with [[#SEARCH | SEARCH METHOD FULL]], or running the translation function separately [[#MODE | MODE MR_FTF]]. For [[#SEARCH | SEARCH METHOD FAST]] the default also depends on whether or not the expected LLG target [[#ELLG | ELLG TARGET <TARGET>]] value is reached.<br />
setRESC_ROTA(bool)<br />
setRESC_TRAN(bool)<br />
<br />
==[[Image:Expert.gif|link=]]RFACTOR== <br />
; RFACTOR USE [ON|OFF]<br />
: For cases of searching for one ensemble when there is one ensemble in the asymmetric unit, the R-factor for the ensemble at the orientation and position in the input is calculated. If this value is low then MR is not performed in the MR_AUTO job in FAST search mode. Instead, rigid body refinement is performed before exiting. Note that the same R-factor test and cutoff is used for judging success in single-atom molecular replacement (MR_ATOM mode).<br />
; RFACTOR CUTOFF <VALUE><br />
: Rfactor in percent used as cutoff for deciding whether or not the R-factor indicates that MR is not necessary.<br />
* Default: RFACTOR USE ON CUTOFF 35<br />
setRFAC_USE(bool)<br />
setRFAC_CUTO(float <PERCENT>)<br />
<br />
==[[Image:Expert.gif|link=]]SAMPLING==<br />
; SAMPLING ROT <SAMP><br />
; SAMPLING TRA <SAMP><br />
: Sampling of search given in degrees for a rotation search and Ångstroms for a translation search. Sampling for rotation search depends on the mean radius of the Ensemble and the high resolution limit (dmin) of the search.<br />
* Default: SAMP = 2*atan(dmin/(4*meanRadius)) (ROTATION FUNCTION)<br />
* Default: SAMP = dmin/5; (BRUTE TRANSLATION FUNCTION)<br />
* Default: SAMP = dmin/4; (FAST TRANSLATION FUNCTION)<br />
setSAMP_ROTA(float <SAMP>)<br />
setSAMP_TRAN(float <SAMP>)<br />
<br><br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS USE [ON|OFF]<br />
: Use TNCS if present: apply TNCS corrections. (Note: was TNCS IGNORE [ON|OFF] in Phaser-2.4.0)<br />
; TNCS RLIST ADD [ON | OFF]<br />
: Supplement the rotation list used in the translation function with rotations already present in the list of known solutions. New molecules in the same orientation as those in the known search (as occurs with translational ncs) may not have peaks associated with them from the rotation function because the known molecules mask the presence of the ones not yet found. <br />
; TNCS PATT HIRES <hires><br />
: High resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT LORES <lores><br />
: Low resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT PERCENT <percent><br />
: Percent of origin Patterson peak that qualifies as a TNCS vector<br />
; TNCS PATT DISTANCE <distance><br />
: Minimum distance of Patterson peak from origin that qualifies as a TNCS vector<br />
; TNCS TRANSLATION PERTURB [ON | OFF]<br />
: If the TNCS translation vector is on a special position, perturb the vector from the special position before refinement<br />
; TNCS ROTATION RANGE <angle><br />
: Maximum deviation from initial rotation from which to look for rotational deviation. Default uses internally determined value based on resolution of data and size of G-function effective molecular radius. Value of 0 turns rotational refinement off.<br />
; TNCS ROTATION SAMPLING <sampling><br />
: Sampling for rotation search. Default uses internally determined value based on resolution of data and size of G-function effective molecular radius. Value of 0 turns rotational refinement off.<br />
* Default: TNCS USE ON<br />
* Default: TNCS RLIST ADD ON<br />
* Default: TNCS PATT HIRES 5<br />
* Default: TNCS PATT LORES 10<br />
* Default: TNCS PATT PERCENT 20<br />
* Default: TNCS PATT DISTANCE 15 <br />
* Default: TNCS TRANSLATION PERTURB ON<br />
setTNCS_USE(bool)<br />
setTNCS_RLIS_ADD(bool)<br />
setTNCS_PATT_HIRE(float <HIRES>)<br />
setTNCS_PATT_LORE(float <LORES>) <br />
setTNCS_PATT_PERC(float <PERCENT>) <br />
setTNCS_PATT_DIST(float <DISTANCE>)<br />
setTNCS_TRAN_PERT(bool)<br />
setTNCS_ROTA_RANG(float <RANGE>) <br />
setTNCS_ROTA_SAMP(float <SAMPLING>) <br />
<br><br />
<br><br />
<br />
=Developer Keywords=<br />
==[[Image:Developer.gif|link=]]BINS== <br />
; BINS DATA [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the data.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections<br />
; BINS ENSE [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the calaculated structure factos for the ensembles.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections<br />
* Default: BINS DATA MIN 6 MAX 50 WIDTH 500 <br />
* Default: BINS ENSE MIN 6 MAX 1000 WIDTH 1000 <br />
setBINS_DATA_MINI(float <L>)<br />
setBINS_DATA_MAXI(float <H>)<br />
setBINS_DATA_WIDT(float <W>)<br />
setBINS_ENSE_MINI(float <L>)<br />
setBINS_ENSE_MAXI(float <H>)<br />
setBINS_ENSE_WIDT(float <W>)<br />
<br />
==[[Image:Developer.gif|link=]]BFACTOR==<br />
; BFACTOR WILSON RESTRAINT [ON|OFF]<br />
: Toggle to use the Wilson restraint on the isotropic component of the atomic B-factors in SAD phasing.<br />
; BFACTOR SPHERICITY RESTRAINT [ON|OFF] <br />
: Toggle to use the sphericity restraint on the anisotropic B-factors in SAD phasing<br />
; BFACTOR REFINE RESTRAINT [ON|OFF] <br />
: Toggle to use the restraint to zero for the molecular B-factor in molecular replacement.<br />
; BFACTOR WILSON SIGMA <SIGMA><br />
: The sigma of the Wilson restraint.<br />
; BFACTOR SPHERICITY SIGMA <SIGMA><br />
: The sigma of the sphericity restraint.<br />
; BFACTOR REFINE SIGMA <SIGMA><br />
: The sigma of the restraint to zero for the molecular B-factor in molecular replacement.<br />
* Default: BFACTOR WILSON RESTRAINT ON <br />
* Default: BFACTOR SPHERICITY RESTRAINT ON <br />
* Default: BFACTOR REFINE RESTRAINT ON <br />
* Default: BFACTOR WILSON SIGMA 5<br />
* Default: BFACTOR SPHERICITY SIGMA 5<br />
* Default: BFACTOR REFINE SIGMA 6<br />
setBFAC_WILS_REST(bool <True|False>)<br />
setBFAC_SPHE_REST(bool <True|False>)<br />
setBFAC_REFI_REST(bool <True|False>) <br />
setBFAC_WILS_SIGM(float <SIGMA>) <br />
setBFAC_SPHE_SIGM(float <SIGMA>) <br />
setBFAC_REFI_SIGM(float <SIGMA>)<br />
<br />
==[[Image:Developer.gif|link=]]BOXSCALE==<br />
; BOXSCALE <BOXSCALE><br />
: Scale for box for calculating structure factors. The ensembles are put in a box equal to (extent of molecule)*BOXSCALE<br />
* Default: BOXSCALE 4<br />
setBOXS<float <BOXSCALE>)<br />
<br />
==[[Image:Developer.gif|link=]]CELL==<br />
; <span style="color:darkorange">Python Only</span> <br />
: Unit cell dimensions<br />
* Default: Cell read from MTZ file<br />
setCELL(float <A>,float <nowiki><B></nowiki>,float <C>,float <ALPHA>,float <BETA>,float <GAMMA>)<br />
setCELL6(float_array <A B C ALPHA BETA GAMMA>)<br />
<br />
==[[Image:Developer.gif|link=]]COMPOSITION== <br />
; COMPOSITION MIN SOLVENT <PERC><br />
: Minimum solvent to give maximum asu packing volume for automated search copy determination (NUM 0)<br />
* Default: COMPOSITION MIN SOLVENT 0.2<br />
setCOMP_MIN_SOLV(float)<br />
<br />
==[[Image:Developer.gif|link=]]DDM== <br />
; DDM SLIDER <VAL> <br />
: The SLIDER window width is used to smooth the Difference Distance Matrix. <br />
; DDM DISTANCE MIN <VAL> MAX <VAL> STEP <VAL><br />
: The range and step interval, as the fraction of the difference between the lowest and highest DDM values used to step.<br />
; DDM SEPARATION MIN <VAL> MAX <VAL><br />
: Through space separation in Angstroms used.<br />
; DDM SEQUENCE MIN <VAL> MAX <VAL><br />
: The range of sequence separations between matrix pairs.<br />
; DDM JOIN MIN <VAL> MAX <VAL><br />
: The range of lengths of the sequences to join if domain segments are discontinuous in percentages of the polypeptide chain.<br />
* Default: DDM SLIDER 0<br />
* Default: DDM DISTANCE MIN 1 MAX 5 STEP 50<br />
* Default: DDM SEPARATION MIN 7 MAX 14<br />
* Default: DDM SEQUENCE MIN 0 MAX 1<br />
* Default: DDM JOIN MIN 2 MAX 12<br />
setDDM_SLID(int <VAL>) <br />
setDDM_DIST_STEP(int <VAL>) <br />
setDDM_DIST_MINI(int <VAL>) <br />
setDDM_DIST_MAXI(int <VAL>) <br />
setDDM_SEPA_MINI(float <VAL>) <br />
setDDM_SEPA_MAXI(float <VAL>)<br />
setDDM_JOIN_MINI(int <VAL>) <br />
setDDM_JOIN_MAXI(int <VAL>) <br />
setDDM_SEQU_MINI(int <VAL>) <br />
setDDM_SEQU_MAXI(int <VAL>)<br />
<br />
==[[Image:Developer.gif|link=]]ENM== <br />
; ENM OSCILLATORS [ <sup>1</sup>RTB | <sup>2</sup>ALL ] <br />
: Define the way the atoms are used for the elastic network model.<br />
: <sup>1</sup>Use the rotation-translation block method.<br />
: <sup>2</sup>Use all atoms to determine the modes (only for use on very small molecules, less than 250 atoms). <br />
; ENM MAXBLOCKS <MAXBLOCKS><br />
: MAXBLOCKS is the number of rotation-translation blocks for the RTB analysis.<br />
; ENM NRES <NRES><br />
: For the RTB analysis, by default NRES=0 and then it is calculated so that it is as small as it can be without reaching MAXBlocks. <br />
; ENM RADIUS <RADIUS><br />
: Elastic Network Model interaction radius (Angstroms)<br />
; ENM FORCE <FORCE><br />
: Elastic Network Model force constant<br />
* Default: ENM OSCILLATORS RTB MAXBLOCKS 250 NRES 0 RADIUS 5 FORCE 1<br />
setENM_OSCI(str ["RTB"|"CA"|"ALL"])<br />
setENM_RTB_MAXB(float <MAXB>)<br />
setENM_RTB_NRES(float <NRES>) <br />
setENM_RADI(float <RADIUS>) <br />
setENM_FORC(float <FORCE>)<br />
<br />
==[[Image:Developer.gif|link=]]NORMALIZATION==<br />
; <span style="color:darkorange">Scripting Only</span><br />
; NORM EPSFAC WRITE <FILENAME><br />
: The normalization factors that correct for anisotropy in the data are written to BINARY file FILENAME<br />
; NORM EPSFAC READ <FILENAME><br />
: The normalization factors that correct for anisotropy in the data are read from BINARY file FILENAME. Further refinement is automatically turned off.<br />
; <span style="color:darkorange">Python Only</span><br />
The normalization factors that correct for anisotropy in the data, extracted from ResultANO object with getSigmaN(). Anisotropy should subsequently be turned off with setMACA_PROT("OFF").<br />
setNORM_DATA(data_norm <SIGMAN>)<br />
<br />
==[[Image:Developer.gif|link=]]OUTLIER==<br />
; OUTLIER REJECT [ON|OFF]<br />
: Reject low probability data outliers<br />
; OUTLIER PROB <PROB><br />
: Cutoff for rejection of low probablity outliers<br />
* Default: OUTLIER REJECT ON PROB 0.000001<br />
setOUTL_REJE(bool) <br />
setOUTL_PROB(float <PROB>)<br />
<br />
==[[Image:Developer.gif|link=]]PTGROUP== <br />
; PTGROUP COVERAGE <COVERAGE><br />
: Percentage coverage for two sequences to be considered in same pointgroup<br />
; PTGROUP IDENTITY <IDENTITY><br />
: Percentage identity for two sequences to be considered in same pointgroup<br />
; PTGROUP RMSD <RMSD><br />
: Percentage rmsd for two models to be considered in same pointgroup<br />
; PTGROUP TOLERANCE ANGULAR <ANG><br />
: Angular tolerance for pointgroup<br />
; PTGROUP TOLERANCE SPATIAL <DIST><br />
: Spatial tolerance for pointgroup<br />
setPTGR_COVE(float <COVERAGE>) <br />
setPTGR_IDEN(float <IDENTITY>) <br />
setPTGR_RMSD(float <RMSD>) <br />
setPTGR_TOLE_ANGU(float <ANG>) <br />
setPTGR_TOLE_SPAT(float <DIST>)<br />
<br />
==[[Image:Developer.gif|link=]]RESHARPEN== <br />
; RESHARPEN PERCENTAGE <PERC><br />
: Perecentage of the B-factor in the direction of lowest fall-off (in anisotropic data) to add back into the structure factors F_ISO and FWT and FDELWT so as to sharpen the electron density maps<br />
* Default: RESHARPEN PERCENT 100<br />
setRESH_PERC(float <PERCENT>)<br />
<br />
==[[Image:Developer.gif|link=]]SOLPARAMETERS==<br />
; SOLPARAMETERS SIGA FSOL <FSOL> BSOL <BSOL> MIN <MINSIGA><br />
: Babinet solvent parameters for Sigma(A) curves. MINSIGA is the minimum SIGA for Babinet solvent term (low resolution only). The solvent term in the Sigma(A) curve is given by <BR>max(1 - FSOL*exp(-BSOL/(4d^2)),MINSIGA).<br />
; SOLPARAMETERS BULK USE [ON|OFF]<br />
: Toggle for use of solvent mask scaling parameters for ensemble structure factors, applied to Fmask.<br />
; SOLPARAMETERS BULK FSOL <FSOL> BSOL <BSOL> <br />
: Solvent mask scaling parameters for ensemble structure factors, applied to Fmask.<br />
* Default: SOLPARAMETERS SIGA FSOL 1.05 BSOL 501 MIN 0.1<br />
* Default: SOLPARAMETERS SIGA RESTRAINT ON<br />
* Default: SOLPARAMETERS BULK USE OFF<br />
* Default: SOLPARAMETERS BULK FSOL 0.35 BSOL 45<br />
setSOLP_SIGA_FSOL(float <FSOL>) <br />
setSOLP_SIGA_BSOL(float <BSOL>)<br />
setSOLP_SIGA_MIN(float <MINSIGA>)<br />
setSOLP_BULK_USE(bool)<br />
setSOLP_BULK_FSOL(float <FSOL>) <br />
setSOLP_BULK_BSOL(float <BSOL>)<br />
<br />
==[[Image:Developer.gif|link=]]TARGET== <br />
; TARGET ROT FAST TYPE [LERF1 | CROWTHER]<br />
: Target function type for fast rotation searches<br />
; TARGET TRA FAST TYPE [LETF1 | LETF2 | CORRELATION]<br />
: Target function type for fast translation searches<br />
setTARG_ROTA_TYPE(string TYPE)<br />
setTARG_TRAN_TYPE(string TYPE)<br />
<br />
==[[Image:Developer.gif|link=]]TNCS==<br />
; TNCS ROTATION ANGLE <A> <nowiki><B></nowiki> <C><br />
: Input rotational difference between molecules related by the pseudo-translational symmetry vector, specified as rotations in degrees about x, y and z axes. Central value for grid search (RANGE > 0).<br />
; TNCS ROTATION RANGE <A><br />
: Range of angular difference in rotation angles to explore around central angle.<br />
; TNCS ROTATION SAMPLING <A><br />
: Sampling step for rotational grid search.<br />
; TNCS TRA VECTOR <x y z> <br />
: Input pseudo-translational symmetry vector (fractional coordinates). By default the translation is determined from the Patterson.<br />
; TNCS VARIANCE RMSD <num><br />
: Input estimated rms deviation between pseudo-translational symmetry vector related molecules.<br />
; TNCS VARIANCE FRAC <num><br />
: Input estimated fraction of cell content that obeys pseudo-translational symmetry.<br />
; TNCS LINK RESTRAINT [ON | OFF]<br />
: Link the occupancy of atoms related by TNCS in SAD phasing<br />
; TNCS LINK SIGMA <sigma><br />
: Sigma of link restraint of the occupancy of atoms related by TNCS in SAD phasing<br />
* Default: TNCS ROTATION ANGLE 0 0 0<br />
* Default: TNCS ROTATION RANGE -999 (determine from structure size and resolution)<br />
* Default: TNCS ROTATION SAMPLING -999 (determine from structure size and resolution)<br />
* Default: TNCS TRANSLATION VECTOR determined from position of Patterson peak<br />
* Default: TNCS VARIANCE RMSD 0.4 <br />
* Default: TNCS VARIANCE FRAC 1 <br />
* Default: TNCS LINK RESTRAINT ON<br />
* Default: TNCS LINK SIGMA 0.1<br />
setTNCS_ROTA_ANGL(dvect3 <A B C>) <br />
setTNCS_TRAN_VECT(dvect3 <X Y Z>) <br />
setTNCS_VARI_RMSD(float <RMSD>) <br />
setTNCS_VARI_FRAC(float <FRAC>)<br />
setTNCS_LINK_REST(bool)<br />
setTNCS_LINK_SIGM(float <SIGMA>)<br />
; <span style="color:darkorange">Scripting Only</span><br />
; TNCS EPSFAC WRITE <FILENAME><br />
: The normalization factors that correct for tNCS in the data are written to BINARY file FILENAME<br />
; TNCS EPSFAC READ <FILENAME><br />
: The normalization factors that correct for tNCS in the data are read from BINARY file FILENAME. Further refinement is automatically turned off.<br />
; <span style="color:darkorange">Python Only</span><br />
The normalization factors that correct for tNCS in the data, extracted from ResultNCS object with getPtNcs(). tNCS refinement should subsequently be turned off with setMACT_PROT("OFF").<br />
setTNCS(data_tncs <PTNCS>)<br />
<br />
==[[Image:Developer.gif|link=]]TRANSLATION== <br />
; TRANSLATION MAPS [ON | OFF]<br />
: Output maps of fast translation function FSS scoring functions<br />
: Maps take the names <ROOT>.<ensemble>.k.e.map where k is the Known backgound number and e is the Euler angle number for that known background<br />
* Default: TRANSLATION MAPS OFF<br />
setTRAN_MAPS(bool)</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Keywords&diff=2396Keywords2016-11-29T15:46:48Z<p>Airlie: /* Phaser-2.8 */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
===Phaser Executable===<br />
<br />
The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the [[#MODE | MODE]] keyword. The different modes and the keywords relevant to each mode are described in [[Modes]].<br />
<br />
Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. However, some keywords are meaningful when entered multiple times. The order may or may not be important. <br />
<br />
*[[Image:User1.gif|link=]] [[#Basic Keywords | Basic Keywords]]<br />
<br />
*[[Image:Output.png|link=]] [[#Output Control Keywords | Output Control Keywords]]<br />
<br />
*[[Image:User2.gif|link=]] [[#Advanced Keywords |Advanced Keywords ]]<br />
<br />
*[[Image:Expert.gif|link=]] [[#Expert Keywords | Expert Keywords]]<br />
<br />
*[[Image:Developer.gif|link=]] [[#Developer Keywords | Developer Keywords]]<br />
<br />
<br />
===Python Interface===<br />
<br />
Phaser can be compiled as a python library. The mode is selected by calling the appropriate run-job. Input to the run-job is via input-objects, which are passed to the run-job. Setter function on the input objects are equivalent to the keywords for input to the phaser executable. The different modes and the keywords relevant to each mode are described in [[Modes]]. See [[Python Interface]] for details. <br />
<br />
The python interface uses standard python and cctbx/scitbx variable types.<br />
<br />
str string<br />
float double precision floating point<br />
Miller cctbx::miller::index<int> <br />
dvect3 scitbx::vec3<float> <br />
dmat33 scitbx::mat3<float> <br />
'''type'''_array scitbx::af::shared<'''type'''> arrays<br />
<br />
=Basic Keywords=<br />
==[[Image:User1.gif|link=]]ATOM== <br />
; ATOM CRYSTAL <XTALID> PDB <FILENAME><br />
: Definition of atom positions using a pdb file.<br />
; ATOM CRYSTAL <XTALID> HA <FILENAME><br />
: Definition of atom positions using a ha file (from RANTAN, MLPHARE etc.).<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> <br />
: Minimal definition of atom position. B-factor defaults to isotropic and Wilson B-factor. Use <TYPE>=TX for Ta6Br12 cluster and <TYPE>=XX for all other clusters. Scattering for cluster is spherically averaged. Coordinates of cluster compounds other than Ta6Br12 must be entered with CLUSTER keyword. Ta6Br12 coordinates are in phaser code and do not need to be given with CLUSTER keyword.<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> [ ISOB <ISOB> | ANOU <HH KK LL HK HL KL> | USTAR <HH KK LL HK HL KL>] FIXX [ON|OFF] FIXO [ON|OFF] FIXB [ON|OFF] BSWAP [ON|OFF] LABEL <SITE_NAME><br />
: Full definition of atom position including B-factor.<br />
;ATOM CHANGE BFACTOR WILSON [ON|OFF]<br />
: Reset all atomic B-factors to the Wilson B-factor.<br />
; ATOM CHANGE SCATTERER <SCATTERER><br />
:Reset all atomic scatterers to element (or cluster) type.<br />
setATOM_PDB(str <XTALID>,str <PDB FILENAME>)<br />
setATOM_IOTBX(str <XTALID>,iotbx::pdb::hierarchy::root <iotbx object>)<br />
setATOM_STR(str <XTALID>,str <pdb format string>)<br />
setATOM_HA(str <XTALID>,str <FILENAME>)<br />
addATOM(str <XTALID>,str <TYPE>,<br />
float <X>,float <Y>,float <Z>,float <OCC>)<br />
addATOM_FULL(str <XTALID>,str <TYPE>,bool <ORTH>,<br />
dvect3 <X Y Z>,float <OCC>,bool <ISO>,float <ISOB>,<br />
bool <ANOU>,dmat6 <HH KK LL HK HL KL>,<br />
bool <FIXX>,bool <FIXO>,bool <FIXB>,bool <SWAPB>,<br />
str <SITE_NAME>)<br />
setATOM_CHAN_BFAC_WILS(bool)<br />
setATOM_CHAN_SCAT(bool)<br />
setATOM_CHAN_SCAT_TYPE(str <TYPE>)<br />
<br />
==[[Image:User1.gif|link=]]CLUSTER== <br />
; CLUSTER PDB <PDBFILE><br />
: Sample coordinates for a cluster compound for experimental phasing. Clusters are specified with type XX. Ta6Br12 clusters do not need to have coordinates specified as the coordinates are in the phaser code. To use Ta6Br12 clusters, specify atomtypes/clusters as TX.<br />
setCLUS_PDB(str <PDBFILE>)<br />
addCLUS_PDB(str <ID>, str <PDBFILE>)<br />
<br />
==[[Image:User1.gif|link=]]COMPOSITION== <br />
; COMPOSITION BY [ <sup>1</sup>AVERAGE| <sup>2</sup>SOLVENT| <sup>3</sup>ASU ]<br />
: Alternative ways of defining composition<br />
: <sup>1</sup> AVERAGE solvent fraction for crystals (50%)<br />
: <sup>2</sup> Composition entered by solvent content.<br />
: <sup>3</sup> Explicit description of composition of ASU by sequence or molecular weight<br />
; <sup>2</sup>COMPOSITION PERCENTAGE <SOLVENT><br />
: Specified SOLVENT content<br />
; <sup>3</sup>COMPOSITION PROTEIN [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of protein in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION NUCLEIC [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of nucleic acid in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION ATOM <TYPE> NUMBER <NUM><br />
: Add NUM copies of an atom (usually a heavy atom) to the composition<br />
* Default: COMPOSITION BY ASU<br />
setCOMP_BY(str ["AVERAGE" | "SOLVENT" | "ASU" ])<br />
setCOMP_PERC(float <SOLVENT>)<br />
addCOMP_PROT_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_PROT_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_PROT_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_PROT_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_NUCL_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_NUCL_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_NUCL_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_NUCL_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_ATOM(str <TYPE>,float <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]CRYSTAL== <br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN Fpos =<F+> SIGFpos=<SIG+> Fneg=<F-> SIGFneg=<SIG-><br />
: Columns of MTZ file to read for this (anomalous) dataset<br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN F =<F> SIGF=<SIGF><br />
: Columns of MTZ file to read for this (non-anomalous) dataset. Used for LLG completion in SAD phasing when there is no anomalous signal (single atom MR protocol). Use LABIN for MR.<br />
setCRYS_ANOM_LABI(str <F+>,str <SIGF+>,str <F->,str <SIGF->) <br />
setCRYS_MEAN_LABI(str <F>,str <SIGF>)<br />
<br />
==[[Image:User1.gif|link=]]ENSEMBLE== <br />
; ENSEMBLE <MODLID> [PDB|CIF] <PDBFILE> [RMS <RMS><sup>1</sup> | ID <ID><sup>2</sup> | CARD ON<sup>3</sup>] ''CHAIN "<CHAIN>"<sup>4</sup> MODEL <NUM><sup>5</sup>''<br />
: The names of the PDB/CIF files used to build the ENSEMBLE, and either<br />
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
:: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file (e.g. "REMARK PHASER ENSEMBLE MODEL 1 ID 31.2") containing the superimposed models concatenated in the one file. This syntax enables simple automation of the use of ensembles. The pdb file can be non-standard because the atom list for the different models need not be the same.<br />
:: <sup>4</sup> CHAIN is selected from the pdb file. <br />
:: <sup>5</sup> MODEL number is selected from the pdb file.<br />
; ENSEMBLE <MODLID> HKLIN <MTZFILE> F=<F> PHI=<PHI> EXTENT <EX> <EY> <EZ> RMS <RMS> CENTRE <CX> <CY> <CZ> PROTEIN MW <PMW> NUCLEIC MW <NMW> ''CELL SCALE <SCALE>''<br />
: An ENSEMBLE defined from a map (via an mtz file). The molecular weight of the object the map represents is required for scaling. The effective RMS coordinate error is needed to judge how the map accuracy falls off with resolution. For density obtained from an EM image reconstruction, a good first guess would be to take the resolution where the FSC curve drops below 0.5 and divide by 3. The extent (difference between maximum and minimum x,y,z coordinates of region containing model density) is needed to determine reasonable rotation steps, and the centre is needed to carry out a proper interpolation of the molecular transform. The extent and the centre are both given in Ångstroms. The cell scale factor defaults to 1 and can be refined (for example, if the map is from electron microscopy when the cell scale may be unknown to within a few percent).<br />
; ENSEMBLE <MODLID> ATOM <TYPE> RMS <RMS><br />
: Define an ensemble as a single atom for single atom MR<br />
; ENSEMBLE <MODLID> HELIX <NUM> <br />
: Define an ensemble as a helix with NUM residues<br />
; ENSEMBLE <MODLID> HETATM [ON|OFF]<br />
: Use scattering from HETATM records in pdb file. See [[Molecular_Replacement#Coordinate_Editing | Coordinate Editing ]]<br />
; ENSEMBLE <MODLID> DISABLE CHECK [ON|OFF]<br />
: Toggle to disable checking of deviation between models in an ensemble. '''Use with extreme caution'''. Results of computations are not guaranteed to be sensible.<br />
; ENSEMBLE <MODLID> ESTIMATOR [OEFFNER | OEFFNERHI | OEFFNERLO | CHOTHIALESK ]<br />
: Define the estimator function for converting ID to RMS<br />
; ENSEMBLE <MODLID> PTGRP [COVERAGE | IDENTITY | RMSD | TOLANG | TOLSPC | EULER | SYMM ]<br />
: Define the pointgroup parameters <br />
; ENSEMBLE <MODLID> BINS [MIN <N>| MAX <M>| WIDTH <W> ]<br />
: Define the Fcalc reflection binning parameters <br />
; ENSEMBLE <MODLID> TRACE [PDB|CIF] <PDBFILE><br />
: Define the coordinates used for packing independent of the coordinates used for structure factor calculation<br />
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
:: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file <br />
; ENSEMBLE <MODLID> TRACE SAMPLING MIN <DIST> <br />
: Set the minimum distance for the sampling of packing grid<br />
; ENSEMBLE <MODLID> TRACE SAMPLING TARGET <NUM> <br />
: Set the target for the number of points to sample the smallest molecule to be packed<br />
; ENSEMBLE <MODLID> TRACE SAMPLING RANGE <NUM> <br />
: Target range (TARGET+/-RANGE) for search for hexgrid points in protein volume<br />
; ENSEMBLE <MODLID> TRACE SAMPLING USE [AUTO | ALL | CALPHA | HEXGRID ]<br />
: Sample trace coordinates using all atoms, C-alpha atoms, a hexagonal grid in the atomic volume or use an automatically determined choice<br />
; ENSEMBLE <MODLID> TRACE SAMPLING DISTANCE <DIST> <br />
: Set the distance for the sampling of the hexagonal grid explicitly and do not use TARGET to find default sampling distance<br />
; ENSEMBLE <MODLID> TRACE SAMPLING WANG <WANG> <br />
: Scale factor for the size of the Wang mask generated from an ensemble map<br />
; ENSEMBLE <MODLID> TRACE PDB <PDBFILE> <br />
: Use the given set of coordinates for packing rather than using the coordinates for structure factor calculation<br />
* Default: ENSEMBLE <MODLID> DISABLE CHECK OFF<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING MIN 1.0<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING TARGET 1000<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING RANGE 100<br />
addENSE_PDB_ID(str <MODLID>,str <FILE>,float <ID>) <br />
addENSE_PDB_RMS(str <MODLID>,str <FILE>,float <RMS>) <br />
setENSE_TRAC_SAMP_MIN(MODLID,float <MIN>)<br />
setENSE_TRAC_SAMP_TARG(MODLID,int <TARGET>)<br />
setENSE_TRAC_SAMP_RANG(MODLID,int <RANGE>)<br />
setENSE_TRAC_SAMP_USE(MODLID,str)<br />
setENSE_TRAC_SAMP_DIST(MODLID,float <DIST>)<br />
setENSE_TRAC_SAMP_WANG(MODLID,float <WANG>)r <FILE>,float <RMS>)<br />
addENSE_CARD(str <MODLID>,str <FILE>,bool)<br />
addENSE_MAP(str <MODLID>,str <MTZFILE>,str <F>,str <PHI>,dvect3 <EX EY EZ>,<br />
float <RMS>,dvect3 <CX CY CZ>,float <PMW>,float <NMW>,float <CELL>)<br />
setENSE_DISA_CHEC(bool)<br />
<br />
==[[Image:User1.gif|link=]]HKLIN==<br />
; HKLIN <FILENAME><br />
: The mtz file containing the data<br />
setHKLI(str <FILENAME>)<br />
<br />
==[[Image:User1.gif|link=]]JOBS== <br />
; JOBS <NUM><br />
: Number of processors to use in parallelized sections of code<br />
* Default: JOBS 2<br />
setJOBS(int <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]LABIN== <br />
; LABIN F = <F> SIGF = <SIGF> <br />
: Columns in mtz file. F must be given. SIGF should be given but is optional<br />
; LABIN I = <nowiki><I></nowiki> SIGI = <SIGI> <br />
: Columns in mtz file. I must be given. SIGI should be given but is optional<br />
; LABIN FMAP = <PH> PHMAP = <PHMAP> <br />
: Columns in mtz file. FMAP/PHMAP are weighted coefficients for use in the Phased Translation Function.<br />
; LABIN FMAP = <PH> PHMAP = <PHMAP> FOM = <FOM><br />
: Columns in mtz file. FMAP/PHMAP are unweighted coefficients for use in the Phased Translation Function and FOM the figure of merit for weighting<br />
setLABI_F_SIGF(str <F>,str <SIGF>)<br />
setLABI_I_SIGI(str <nowiki><I></nowiki>,str <SIGI>)<br />
setLABI_PTF(str <FMAP>,str <PHMAP>,str <FOM>)<br />
<br />
''Data should be input to python run-jobs using one data_refl parameter''<br />
''This is extracted from the ResultMR_DAT object after a call to runMR_DAT''<br />
setREFL_DATA(data_ref)<br />
''Example:''<br />
i = InputMR_DAT()<br />
i.setHKLI("*.mtz")<br />
i.setLABI_F_SIGF("F","SIGF")<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputMR_LLG()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.setREFL_DATA(r.getDATA())<br />
''See also: '' [[Python Example Scripts]]<br />
<br />
''Alternatively, reflection arrays can be set using cctbx::af::shared<double>''<br />
setREFL_F_SIGF(float_array <F>,float_array <SIGF>)<br />
setREFL_I_SIGI(float_array <nowiki><I></nowiki>,float_array <SIGI>)<br />
setREFL_PTF(float_array <FMAP>,float_array <PHMAP>,float_array <FOM>)<br />
<br />
==[[Image:User1.gif|link=]]MODE==<br />
; MODE [ ANO | CCA | SCEDS | NMAXYZ | NCS | MR_ELLG | MR_AUTO | MR_GYRE | MR_ATOM | MR_ROT | MR_TRA | MR_RNP | | MR_OCC | MR_PAK | EP_AUTO | EP_SAD]<br />
: The mode of operation of Phaser. The different modes are described in a separate page on [[Keyword Modes]]<br />
ResultANO r = runANO(InputANO)<br />
ResultCCA r = runCCA(InputCCA)<br />
ResultNMA r = runSCEDS(InputNMA)<br />
ResultNMA r = runNMAXYZ(InputNMA)<br />
ResultNCS r = runNCS(InputNCS)<br />
ResultELLG r = runMR_ELLG(InputMR_ELLG)<br />
ResultMR r = runMR_AUTO(InputMR_AUTO)<br />
ResultEP r = runMR_ATOM(InputMR_ATOM)<br />
ResulrMR_RF r = runMR_FRF(InputMR_FRF)<br />
ResultMR_TF r = runMR_FTF(InputMR_FTF)<br />
ResultMR r = runMR_RNP(InputMR_RNP)<br />
ResultGYRE r = runMR_GYRE(InputMR_RNP)<br />
ResultMR r = runMR_OCC(InputMR_OCC)<br />
ResultMR r = runMR_PAK(InputMR_PAK)<br />
ResultEP r = runEP_AUTO(InputEP_AUTO)<br />
ResultEP_SAD r = runEP_SAD(InputEP_SAD)<br />
<br />
==[[Image:User1.gif|link=]]PARTIAL== <br />
; PARTIAL PDB <PDBFILE> [RMSIDENTITY] <RMS_ID><br />
: The partial structure for MR-SAD substructure completion. Note that this must already be correctly placed, as the experimental phasing module will not carry out molecular replacement.<br />
; PARTIAL HKLIN <MTZFILE> [RMS|IDENTITY] <RMS_ID><br />
: The partial electron density for MR-SAD substructure completion.<br />
; PARTIAL LABIN FC=<FC> PHIC=<PHIC><br />
: Column labels for partial electron density for MR-SAD substructure completion.<br />
setPART_PDB(str <PDBFILE>)<br />
setPART_HKLI(str <MTZFILE>) <br />
setPART_LABI_FC(str <FC>)<br />
setPART_LABI_PHIC(str <PHIC>) <br />
setPART_VARI(str ["ID"|"RMS"])<br />
setPART_DEVI(float <RMS_ID>)<br />
<br />
==[[Image:User1.gif|link=]]SEARCH==<br />
; SEARCH ENSEMBLE <MODLID> ''{OR ENSEMBLE <MODLID>}… NUMBER <NUM><sup>*</sup>''<br />
: The ENSEMBLE to be searched for in a rotation search or an automatic search. When multiple ensembles are given using the OR keyword, the search is performed for each ENSEMBLE in turn. When the keyword is entered multiple times, each SEARCH keyword refers to a new component of the structure. If the component is present multiple times the sub-keyword NUMber can be used (rather than entering the same SEARCH keyword NUMber times).<br />
: <sup>*</sup>For automatic determination of search number use NUMBER 0. If the composition is entered, the maximum number will be that defined by the composition, otherwise the maximum number will fill the asymmetric unit to a minimum solvent content of 20%. Searches for new components will continue until the TFZ score is above 8, and terminate if the TFZ score drops below 8 before the placement of the maximum number of components.<br />
; SEARCH METHOD [FULL|FAST]<br />
: Search using the [[Modes#Modes |full search]] or [[Modes#Modes | fast search]] algorithms.<br />
; SEARCH ORDER AUTO [ON|OFF]<br />
: Search in the "best" order as estimated using estimated rms deviation and completeness of models.<br />
; SEARCH PRUNE [ON|OFF]<br />
: For high TFZ solutions that fail the packing test, carry out a sliding-window occupancy refinement and prune residues that refine to low occupancy, in an effort to resolve packing clashes. If this flag is set to true, the flag for keeping high tfz score solutions (see [[#PACK | PACK]]) that don't pack is also set to true (PACK KEEP HIGH TFZ ON).<br />
; SEARCH AMALGAMATE USE [ON|OFF]<br />
: For multiple high TFZ solutions, enable amalgamation into a single solution<br />
; SEARCH BFACTOR <BFAC><br />
: B-factor applied to search molecule (or atom).<br />
; SEARCH OFACTOR <OFAC><br />
: Occupancy factor applied to search molecule (or atom).<br />
* Default: SEARCH METHOD FAST<br />
* Default: SEARCH ORDER AUTO ON<br />
* Default: SEARCH PRUNE ON<br />
* Default: SEARCH AMALGAMATE USE ON<br />
* Default: SEARCH BFACTOR 0<br />
* Default: SEARCH OFACTOR 1<br />
addSEAR_ENSE_NUM(str <MODLID>,int <NUM>) <br />
addSEAR_ENSE_OR_ENSE_NUM(string_array <MODLIDS>,int <NUM>) <br />
setSEAR_METH(str [ "FULL" | "FAST" ])<br />
setSEAR_ORDE_AUTO(bool)<br />
setSEAR_PRUN(bool <PRUNE>)<br />
setSEAR_AMAL_USE(bool <AMAL>)<br />
setSEAR_BFAC(float <BFAC>)<br />
setSEAR_OFAC(float <OFAC>)<br />
<br />
==[[Image:User1.gif|link=]]SGALTERNATIVE==<br />
; SGALTERNATIVE SELECT [<sup>1</sup>ALL| <sup>2</sup>HAND| <sup>3</sup>LIST| <sup>4</sup>NONE]<br />
: Selection of alternative space groups to test in translation functions i.e. those that are in same laue group as that given in [[#SPACEGROUP | SPACEGROUP]]<br />
: <sup>1</sup> Test all possible space groups, <br />
: <sup>2</sup> Test the given space group and its enantiomorph.<br />
: <sup>3</sup> Test the space groups listed with SGALTERNATIVE TEST <SG>.<br />
: <sup>4</sup> Do not test alternative space groups.<br />
; SGALTERNATIVE TEST <SG><br />
: Alternative space groups to test. Multiple test space groups can be entered.<br />
* Default: SGALTERNATIVE SELECT HAND<br />
setSGAL_SELE(str [ "ALL" | "HAND" | "LIST" | "NONE" ]) <br />
addSGAL_TEST(str <SG>)<br />
<br />
==[[Image:User1.gif|link=]]SOLUTION==<br />
; SOLUTION SET <ANNOTATION><br />
: Start new set of solutions <br />
; SOLUTION TEMPLATE <ANNOTATION><br />
: Specifies a template solution against which other solutions in this run will be compared. Given in place of SOLUTION SET. Template rotation and translations given by subsequent SOLUTION 6DIM cards as per SOLUTION SETS.<br />
; SOLUTION 6DIM ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> [ORTH|FRAC] <X> <Y> <Z> ''FIXR [ON|OFF] FIXT [ON|OFF] FIXB [ON|OFF] BFAC <BFAC> MULT <MULT>''<br />
: This keyword is repeated for each known position and orientation of an ENSEMBLE MODLID. A B G are the Euler angles (z-y-z convention) and X Y Z are the translation elements, expressed either in orthogonal Angstroms (ORTH) or fractions of a cell edge (FRAC). The input ensemble is transformed by a rotation around the origin of the coordinate system, followed by a translation. BFAC default to 0, MULT (for multiplicity) defaults to 1.<br />
; SOLUTION ENSEMBLE <MODLID> VRMS DELTA <DELTA> RMSD <RMSD><br />
: Refined RMS variance terms for pdb files (or map) in ensemble MODLID. RMSD is the input RMSD of the job that produced the sol file, DELTA is the shift with respect to this RMSD. If given as part of a solution, these values overwrite the values used for input in the ENSEMBLE keyword (if refined).<br />
; SOLUTION ENSEMBLE <MODLID> CELL SCALE <SCALE><br />
: Refined cell scale factor. Only applicable to ensembles that are maps<br />
; SOLUTION TRIAL ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> RFZ <RFZ><br />
: Rotation List for translation function<br />
; SOLUTION ORIGIN ENSEMBLE <MODLID><br />
: Create solution for ensemble MODLID at the origin<br />
; SOLUTION SPACEGROUP <SG><br />
: Space Group of the solution (if alternative spacegroups searched)<br />
; SOLUTION RESOLUTION <HIRES><br />
: High resolution limit of data used to find/refine this solution<br />
; SOLUTION PACKS <PACKS><br />
: Flag for whether solution has been retained despite failing packing test, due to having high TFZ<br />
setSOLU(mr_solution <SOL>) <br />
addSOLU_SET(str <ANNOTATION>) <br />
addSOLU_TEMPLATE(str <ANNOTATION>) <br />
addSOLU_6DIM_ENSE(str <MODLID>,dvect3 <A B C>,bool <FRAC>,dvect3 <X Y Z>,<br />
float <BFAC>,bool <FIXR>,bool <FIXT>,bool <FIXB>,int <MULT>, 1.0) <br />
addSOLU_ENSE_DRMS(str <MODLID>, float <DRMS>) <br />
addSOLU_ENSE_CELL(str <MODLID>, float <SCALE>)<br />
addSOLU_TRIAL_ENSE(string <MODLID>,dvect3 <A B C>,float <RFZ>)<br />
addSOLU_ORIG_ENSE(string <MODLID>)<br />
setSOLU_SPAC(str <SG>)<br />
setSOLU_RESO(float <HIRES>)<br />
setSOLU_PACK(bool <PACKS>)<br />
<br />
==[[Image:User1.gif|link=]]SPACEGROUP==<br />
; SPACEGROUP <SG><br />
: Space group may be altered from the one on the MTZ file to a space group in the same point group. The space group can be entered in one of three ways<br />
#The Hermann-Mauguin symbol e.g. P212121 or P 21 21 21 (with or without spaces)<br />
#The international tables number, which gives standard setting e.g. 19 <br />
#The Hall symbols e.g. P 2ac 2ab<br />
: '''The space group can also be a subgroup of the merged space group'''. For example, P1 is always allowed. The reflections will be expanded to the symmetry of the given subgroup. This is only a valid approach when the true symmetry is the symmetry of the subgroup and perfect twinning causes the data to merge "perfectly" in the higher symmetry. <br />
:'''A list of the allowed space groups in the same point group as the given space group (or space group read from MTZ file) and allowed subgroups of these is given in the Cell Content Analysis logfile.'''<br />
* Default: Read from MTZ file<br />
setSPAC_NUM(int <NUM>)<br />
setSPAC_NAME(string <HM>)<br />
setSPAC_HALL(string <HALL>)<br />
<br />
==[[Image:User1.gif|link=]]WAVELENGTH== <br />
; WAVELENGTH <LAMBDA> <br />
: The wavelengh at which the SAD dataset was collected<br />
setWAVE(float <LAMBDA>)<br />
<br><br />
<br><br />
<br />
=Output Control Keywords=<br />
==[[Image:Output.png|link=]]DEBUG== <br />
; DEBUG [ON|OFF]<br />
: Extra verbose output for debugging<br />
* Default: DEBUG OFF<br />
setDEBU(bool) <br />
<br />
==[[Image:Output.png|link=]]EIGEN==<br />
; EIGEN WRITE [ON|OFF]<br />
; EIGEN READ <EIGENFILE><br />
: Read or write a file containing the eigenvectors and eigenvalues. If reading, the eigenvalues and eigenvectors of the Hessian are read from the file generated by a previous run, rather than calculated. This option must be used with the job that generated the eigenfile and the job reading the eigenfile must have identical input for the ENM parameters. Use WRITE to control whether or not the eigenfile is written when not using the READ mode.<br />
* Default: EIGEN WRITE ON<br />
setEIGE_WRIT(bool)<br />
setEIGE_READ(str <EIGENFILE>)<br />
<br />
==[[Image:Output.png|link=]]HKLOUT== <br />
; HKLOUT [ON|OFF]<br />
: Flags for output of an mtz file containing the phasing information<br />
* Default: HKLOUT ON<br />
setHKLO(bool) <br />
<br />
==[[Image:Output.png|link=]]KEYWORDS== <br />
; KEYWORDS [ON|OFF]<br />
: Write output Phaser .sol file (.rlist file for rotation function)<br />
* Default: KEYWORDS ON<br />
setKEYW(bool)<br />
<br />
==[[Image:Output.gif|link=]]LLGMAPS==<br />
; LLGMAPS [ON|OFF]<br />
: Write log-likelihood gradient map coefficients to MTZ file<br />
* Default: LLGMAPS OFF<br />
setLLGM(bool <True|False>)<br />
<br />
==[[Image:Output.png|link=]]MUTE== <br />
; MUTE [ON|OFF]<br />
: Toggle for running in silent/mute mode, where no logfile is written to ''standard output''.<br />
* Default: MUTE OFF<br />
setMUTE(bool) <br />
<br />
==[[Image:Output.png|link=]]KILL== <br />
; KILL TIME [MINS]<br />
: Kill Phaser after MINS minutes of CPU have elapsed, provided parallel section is complete<br />
; KILL FILE [FILENAME]<br />
: Kill Phaser if file FILENAME is present, provided parallel section is complete<br />
* Default: KILL TIME 0 ''Phaser runs to completion''<br />
* Detaulf: KILL FILE "" ''Phaser runs to completion''<br />
setKILL_TIME(float) <br />
setKILL_FILE(string)<br />
<br />
==[[Image:Output.png|link=]]OUTPUT== <br />
; OUTPUT LEVEL [SILENT|CONCISE|SUMMARY|LOGFILE|VERBOSE|DEBUG]<br />
: Output level for logfile<br />
; OUTPUT LEVEL [0|1|2|3|4|5]<br />
: Output level for logfile (equivalent to keyword level setting)<br />
* Default: OUTPUT LEVEL LOGFILE<br />
setOUTP_LEVE(string)<br />
setOUTP(enum)<br />
<br />
==[[Image:Output.png|link=]]TITLE==<br />
; TITLE <TITLE><br />
: Title for job<br />
* Default: TITLE [no title given]<br />
setTITL(str <TITLE>)<br />
<br />
==[[Image:Output.png|link=]]TOPFILES== <br />
; TOPFILES <NUM><br />
: Number of top pdbfiles or mtzfiles to write to output.<br />
* Default: TOPFILES 1<br />
setTOPF(int <NUM>) <br />
<br />
==[[Image:Output.png|link=]]ROOT== <br />
; ROOT <FILEROOT><br />
: Root filename for output files (e.g. FILEROOT.log)<br />
* Default: ROOT PHASER<br />
setROOT(string <FILEROOT>)<br />
<br />
==[[Image:Output.png|link=]]VERBOSE== <br />
; VERBOSE [ON|OFF] <br />
: Toggle to send verbose output to log file.<br />
* Default: VERBOSE OFF<br />
setVERB(bool) <br />
<br />
==[[Image:Output.png|link=]]XYZOUT== <br />
; XYZOUT [ON|OFF] ''ENSEMBLE [ON|OFF]<sup>1</sup> PACKING [ON|OFF]<sup>2</sup>''<br />
: Toggle for output coordinate files. <br />
::<sup>1</sup> If the optional ENSEMBLE keyword is ON, then each placed ensemble is written to its own pdb file. The files are named FILEROOT.#.#.pdb with the first # being the solution number and the second # being the number of the placed ensemble (representing a SOLU 6DIM entry in the .sol file). <br />
::<sup>2</sup> If the optional PACKING keyword is ON, then the hexagonal grid used for the packing analysis is output to its own pdb file FILEROOT.pak.pdb<br />
* Default: XYZOUT OFF (Rotation functions)<br />
* Default: XYZOUT ON ENSEMBLE OFF (all other relevant modes)<br />
* Default: XYZOUT ON PACKING OFF (all other relevant modes)<br />
setXYZO(bool) <br />
setXYZO_ENSE(bool)<br />
setXYZO_PACK(bool)<br />
<br><br />
<br><br />
<br />
=Advanced Keywords=<br />
==[[Image:User2.gif|link=]]ELLG==<br />
([[Molecular_Replacement#Should_Phaser_Solve_It.3F|explained here]])<br />
; ELLG TARGET <TARGET><br />
: Target value for expected LLG for determining resolution limits and search order<br />
<!--; ELLG HIRES <HIRES> Internal control only--><br />
* Default: ELLG TARGET 225<br />
setELLG_TARG(float <TARGET>)<br />
<br />
==[[Image:User2.gif|link=]]FORMFACTORS==<br />
; FORMFACTORS [XRAY | ELECTRON | NEUTRON]<br />
: Use scattering factors from x-ray, electron or neutrons<br />
* Default: FORMFACTORS XRAY<br />
setFORM(string XRAY)<br />
<br />
==[[Image:User2.gif|link=]]HAND==<br />
; HAND [ <sup>1</sup>ON| <sup>2</sup>OFF| <sup>3</sup>BOTH]<br />
: Hand of heavy atoms for experimental phasing<br />
: <sup>1</sup>Phase using the other hand of heavy atoms <br />
: <sup>2</sup>Phase using given hand of heavy atoms <br />
: <sup>3</sup>Phase using both hands of heavy atoms<br />
* Default: HAND BOTH<br />
setHAND(str [ "OFF" | "ON" | "BOTH" ])<br />
<br />
==[[Image:User2.gif|link=]]LLGCOMPLETE==<br />
; LLGCOMPLETE COMPLETE [ON|OFF]<br />
: Toggle for structure completion by log-likelihood gradient maps<br />
; LLGCOMPLETE SCATTERER <TYPE> <br />
: Atom/Cluster type(s) to be used for log-likelihood gradient completion. If more than one element is entered for log-likelihood gradient completion, the atom type that gives the highest Z-score for each peak is selected. Type = "RX" is a purely real scatterer and type="AX" is purely anomalous scatterer<br />
; LLGCOMPLETE REAL ON<br />
: Use a purely real scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER RX)<br />
; LLGCOMPLETE ANOMALOUS ON<br />
: Use a purely anomalous scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER AX)<br />
; LLGCOMPLETE CLASH <CLASH> <br />
: Minimum distance between atoms in log-likelihood gradient maps and also the distance used for determining anisotropy of atoms (default determined by resolution, flagged by CLASH=0)<br />
; LLGCOMPLETE SIGMA <Z><br />
: Z-score (sigma) for accepting peaks as new atoms in log-likelihood gradient maps<br />
; LLGCOMPLETE NCYC <NMAX><br />
: Maximum number of cycles of log-likelihood gradient structure completion. By default, NMAX is 50, but this limit should never be reached, because all features in the log-likelihood gradient maps should be assigned well before 50 cycles are finished. This keyword should be used to reduce the number of cycles to 1 or 2.<br />
; LLGCOMPLETE METHOD [IMAGINARY|ATOMTYPE]<br />
: Pick peaks from the imaginary map only or from all the completion atomtype maps.<br />
* Default: LLGCOMPLETE COMPLETE OFF<br />
* Default: LLGCOMPLETE CLASH 0<br />
* Default: LLGCOMPLETE SIGMA 6<br />
* Default: LLGComplete NCYC 50<br />
* Default: LLGComplete METHOD ATOMTYPE<br />
setLLGC_COMP(bool <True|False>) <br />
setLLGC_CLAS(float <CLASH>) <br />
setLLGC_SIGM(float <Z>) <br />
setLLGC_NCYC(int <NMAX>)<br />
setLLGC_METH(str ["IMAGINARY"|"ATOMTYPE"])<br />
<br />
==[[Image:User2.gif|link=]]NMA== <br />
; NMA MODE <M1> ''{MODE <M2>…}'' <br />
: The MODE keyword gives the mode along which to perturb the structure. If multiple modes are entered, the structure is perturbed along all the modes AND combinations of the modes given. There is no limit on the number of modes that can be entered, but the number of pdb files explodes combinatorially. The first 6 modes are the pure rotation and translation modes and do not lead to perturbation of the structure. If the number M is less than 7 then M is interpreted as the first M modes starting at 7, so for example, MODE 5 would give modes 7 8 9 10 11.<br />
; NMA COMBINATION <NMAX><br />
: Controls how many modes are present in any combination.<br />
* Default: NMA MODE 5<br />
* Default: NMA COMBINATION 2<br />
addNMA_MODE(int <MODE>) <br />
setNMA_COMB(int <NMAX>)<br />
<br />
==[[Image:User2.gif|link=]]PACK==<br />
; PACK SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>ALL ]<br />
: <sup>1</sup>Allow up to the PERCENT of sampling points to clash, considering only pairwise clashes <br />
: <sup>2</sup>Allow all solutions (no packing test)<br />
; PACK CUTOFF <PERCENT> <br />
: Limit on total number (or percent) of clashes <br />
; PACK QUICK [ON|OFF]<br />
: Packing check stops when ALLOWED_CLASHES or MAX_CLASHES is reached. However, all clashes are found when the solution has a high Z-score (see [[#ZSCORE | ZSCORE]]).<br />
; PACK COMPACT [ON|OFF]<br />
: Pack ensembles into a compact association (minimize distances between centres of mass for the addition of each component in a solution).<br />
; PACK KEEP HIGH TFZ [ON|OFF]<br />
: Solutions with high tfz (see [[#ZSCORE | ZSCORE]]) but that fail to pack are retained in the solution list. Set to true if SEARCH PRUNE ON (see [[#SEARCH | SEARCH]])<br />
* Default: PACK SELECT PERCENT<br />
* Default: PACK CUTOFF 5<br />
* Default: PACK COMPACT ON<br />
* Default: PACK QUICK ON<br />
* Default: PACK KEEP HIGH TFZ OFF<br />
* Default: PACK CONSERVATION DISTANCE 1,5<br />
setPACK_SELE(str ["PERCENT"|"ALL"]) <br />
setPACK_CUTO(float <ALLOWED_CLASHES>)<br />
setPACK_QUIC(bool)<br />
setPACK_KEEP_HIGH_TFZ(bool)<br />
setPACK_COMP(bool)<br />
<br />
==[[Image:User2.gif|link=]]PEAKS==<br />
; PEAKS TRA SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL] <br />
; PEAKS ROT SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL]<br />
: Peaks for individual rotation functions (ROT) or individual translation functions (TRA) satisfying selection criteria are saved. To be used for subsequent steps, peaks must also satisfy the overall [[#PURGE | PURGE]] selection criteria, so it will usually be appropriate to set only the PURGE criteria (which over-ride the defaults for the PEAKS criteria if not explicitly set). See [[Molecular_Replacement#How_to_Select_Peaks | How to Select Peaks]]<br />
: <sup>1</sup> Select peaks by taking all peaks over CUTOFF percent of the difference between the top peak and the mean value.<br />
: <sup>2</sup> Select peaks by taking all peaks with a Z-score greater than CUTOFF.<br />
: <sup>3</sup> Select peaks by taking top CUTOFF.<br />
: <sup>4</sup> Select all peaks.<br />
; PEAKS ROT CUTOFF <CUTOFF><br />
; PEAKS TRA CUTOFF <CUTOFF><br />
: Cutoff value for the rotation function (ROT) or translation function (TRA) peak selection criteria.<br />
: If selection is by percent and [[#PURGE | PURGE PERCENT]] is changed from the default, then the PEAKS percent value is set to the lower PURGE percent value.<br />
; PEAKS ROT CLUSTER [ON|OFF] <br />
; PEAKS TRA CLUSTER [ON|OFF]<br />
: Toggle selects clustered or unclustered peaks for rotation function (ROT) or translation function (TRA).<br />
; PEAKS ROT DOWN [PERCENT] <br />
: [[#SEARCH | SEARCH METHOD FAST]] only. Percentage to reduce rotation function cutoff if there is no TFZ over the zscore cutoff that determines a true solution (see [[#ZSCORE | ZSCORE]]) in first search.<br />
* Default: PEAKS ROT SELECT PERCENT<br />
* Default: PEAKS TRA SELECT PERCENT<br />
* Default: PEAKS ROT CUTOFF 75<br />
* Default: PEAKS TRA CUTOFF 75<br />
* Default: PEAKS ROT CLUSTER ON<br />
* Default: PEAKS TRA CLUSTER ON<br />
setPEAK_ROTA_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"]) <br />
setPEAK_TRAN_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"])<br />
setPEAK_ROTA_CUTO(float <CUTOFF>)<br />
setPEAK_TRAN_CUTO(float <CUTOFF>) <br />
setPEAK_ROTA_CLUS(bool <CLUSTER>) <br />
setPEAK_TRAN_CLUS(bool <CLUSTER>)<br />
setPEAK_ROTA_DOWN(float <PERCENT>)<br />
<br />
==[[Image:User2.gif|link=]]PERMUTATIONS== <br />
; PERMUTATIONS [ON|OFF]<br />
: Only relevant to [[#SEARCH | SEARCH METHOD FULL]]. Toggle for whether the order of the search set is to be permuted.<br />
* Default: PERMUTATIONS OFF<br />
setPERM(bool <PERMUTATIONS>)<br />
<br />
==[[Image:User2.gif|link=]]PERTURB== <br />
; PERTURB RMS STEP <RMS><br />
: Increment in rms Ångstroms between pdb files to be written. <br />
; PERTURB RMS MAX <MAXRMS><br />
: The structure will be perturbed along each mode until the MAXRMS deviation has been reached.<br />
; PERTURB RMS DIRECTION [FORWARD|BACKWARD|TOFRO] <br />
: The structure is perturbed either forwards or backwards or to-and-fro (FORWARD|BACKWARD|TOFRO) along the eigenvectors of the modes specified.<br />
; PERTURB INCREMENT [RMS| DQ] <br />
: Perturb the structure by rms devitations along the modes, or by set dq increments<br />
; PERTURB DQ <DQ1> ''{DQ <DQ2>…}''<br />
: Alternatively, the DQ factors (as used by the Elnemo server (K. Suhre & Y-H. Sanejouand, NAR 2004 vol 32) ) by which to perturb the atoms along the eigenvectors can be entered directly.<br />
* Default: PERTURB INCREMENT RMS<br />
* Default: PERTURB RMS STEP 0.2<br />
* Default: PERTURB RMS MAXRMS 0.3<br />
* Default: PERTURB RMS DIRECTION TOFRO<br />
setPERT_INCR(str [ "RMS" | "DQ" ])<br />
setPERT_RMS_MAXI(float <MAX>)<br />
setPERT_RMS_DIRE(str [ "FORWARDS" | "BACKWARDS" | "TOFRO" ]) <br />
addPERT_DQ(float <DQ>)<br />
<br />
==[[Image:User2.gif|link=]]PURGE== <br />
; PURGE ROT ENABLE [ON|OFF]<sup>1</sup><br />
; PURGE ROT PERCENT <PERC><sup>2</sup><br />
; PURGE ROT NUMBER <NUM><sup>3</sup><br />
: Purging criteria for rotation function (RF), where PERCENT and NUMBER are alternative selection criteria (''OR'' criteria)<br />
::<sup>1</sup> Toggle for whether to purge the solution list from the RF according to the top solution found. If there are a number of RF searches with different partial solution backgrounds, the PURGE is applied to the total list of peaks. If there is one clearly significant RF solution from one of the backgrounds it acts to purge all the less significant solutions. If there is only one RF (a single partial solution background) the PURGE gives no additional selection over and above the PEAKS command. <br />
::<sup>2</sup> [[Molecular_Replacement#How_to_Select_Peaks | Selection by percent]]. PERC is percentage of the top peak, where the value of the top peak is defined as 100% and the value of the mean is defined as 0%. Note that this criterion is applied subsequent to any selection criteria applied through the [[#PEAKS | PEAKS]] command. If the [[#PEAKS | PEAKS]] selection is by percent, then the percent cutoff given in the PURGE command over-rides that for [[#PEAKS | PEAKS]], so as to rationalize results in the case of only a single RF (single partial solution background.)<br />
::<sup>3</sup> NUM is the number of solutions to retain in purging. If NUMBER is given (non-zero) it overrides the PERCENT option. NUMBER given as zero is the flag for not applying this criterion.<br />
; PURGE TRA ENABLE [ON|OFF]<br />
; PURGE TRA PERCENT <PERC><br />
; PURGE TRA NUMBER <NUM><br />
: As above, but for translation function<br />
; PURGE RNP ENABLE [ON|OFF]<br />
; PURGE RNP PERCENT <PERC><br />
; PURGE RNP NUMBER <NUM><br />
: As above but for refinement, but with the important distinction that PERCENT and NUMBER are concurrent selection criteria (''AND'' criteria)<br />
* Default: PURGE ROT ENABLE ON <br />
* Default: PURGE ROT PERC 75<br />
* Default: PURGE ROT NUM 0<br />
* Default: PURGE TRA ENABLE ON<br />
* Default: PURGE TRA PERC 75<br />
* Default: PURGE TRA NUM 0<br />
* Default: PURGE RNP ENABLE ON<br />
* Default: PURGE RNP PERC 75<br />
* Default: PURGE RNP NUM 0<br />
setPURG_ROTA_ENAB(bool <ENABLE>)<br />
setPURG_TRAN_ENAB(bool <ENABLE>) <br />
setPURG_RNP_ENAB(bool <ENABLE>)<br />
setPURG_ROTA_PERC(float <PERC>) <br />
setPURG_TRAN_PERC(float <PERC>) <br />
setPURG_RNP_PERC(float <PERC>)<br />
setPURG_ROTA_NUMB(float <NUM>) <br />
setPURG_TRAN_NUMB(float <NUM>)<br />
setPURG_TRAN_NUMB(float <NUM>)<br />
setPURG_RNP_NUMB(float <NUM>)<br />
<br />
==[[Image:User2.gif|link=]]RESOLUTION== <br />
; RESOLUTION HIGH <HIRES> <br />
: High resolution limit in Ångstroms. <br />
; RESOLUTION LOW <LORES><br />
: Low resolution limit in Ångstroms.<br />
; RESOLUTION AUTO HIGH <HIRES> <br />
: High resolution limit in Ångstroms for final high resolution refinement in MR_AUTO mode.<br />
* Default for molecular replacement: Set by [[#ELLG | ELLG TARGET]] for structure solution, final refinement uses all data<br />
* Default for experimental phasing: All data used<br />
setRESO_HIGH(float <HIRES>) <br />
setRESO_LOW(float <LORES>)<br />
setRESO_AUTO_HIGH(float <HIRES>) <br />
setRESO(float <HIRES>,float <LORES>)<br />
<br />
==[[Image:User2.gif|link=]]ROTATE== <br />
; ROTATE VOLUME FULL<br />
: Sample all unique angles <br />
; ROTATE VOLUME AROUND EULER <A> <nowiki><B></nowiki> <C> RANGE <RANGE> <br />
: Restrict the search to the region of +/- RANGE degrees around orientation given by EULER<br />
setROTA_VOLU(string ["FULL"|"AROUND"|) <br />
setROTA_EULE(dvect3 <A B C>) <br />
setROTA_RANG(float <RANGE>)<br />
<br />
==[[Image:User2.gif|link=]]SCATTERING==<br />
; SCATTERING TYPE <TYPE> FP=<FP> FDP=<FDP> FIX [ON|OFF|EDGE]<br />
: Measured scattering factors for a given atom type, from a fluorescence scan. FIX EDGE (default) fixes the fdp value if it is away from an edge, but refines it if it is close to an edge, while FIX ON or FIX OFF does not depend on proximity of edge.<br />
; SCATTERING RESTRAINT [ON|OFF]<br />
: use Fdp restraints<br />
; SCATTERING SIGMA <SIGMA><br />
: Fdp restraint sigma used is SIGMA multiplied by initial fdp value<br />
* Default: SCATTERING SIGMA 0.2<br />
* Default: SCATTERING RESTRAINT ON<br />
addSCAT(str <TYPE>,float <FP>,float <FDP, string <FIXFDP>) <br />
setSCAT_REST(bool) <br />
setSCAT_SIGM(float <SIGMA>)<br />
<br />
==[[Image:User2.gif|link=]]SCEDS== <br />
; SCEDS NDOM <NDOM><br />
:Number of domains into which to split the protein<br />
; SCEDS WEIGHT SPHERICITY <WS><br />
: Weight factor for the the Density Test in the SCED Score. The Sphericity Test scores boundaries that divide the protein into more spherical domains more highly.<br />
; SCEDS WEIGHT CONTINUITY <WC><br />
: Weight factor for the the Continuity Test in the SCED Score. The Continuity Test scores boundaries that divide the protein into domains contigous in sequence more highly. <br />
; SCEDS WEIGHT EQUALITY <WE><br />
: Weight factor for the the Equality Test in the SCED Score. The Equality Test scores boundaries that divide the protein more equally more highly.<br />
; SCEDS WEIGHT DENSITY <WD><br />
: Weight factor for the the Equality Test in the SCED Score. The Density Test scores boundaries that divide the protein into domains more densely packed with atoms more highly. <br />
* Default: SCEDS NDOM 2<br />
* Default: SCEDS WEIGHT EQUALITY 1<br />
* Default: SCEDS WEIGHT SPHERICITY 4 <br />
* Default: SCEDS WEIGHT DENSITY 1<br />
* Default: SCEDS WEIGHT CONTINUITY 0<br />
setSCED_NDOM(int <NDOM>) <br />
setSCED_WEIG_SPHE(float <WS>) <br />
setSCED_WEIG_CONT(float <WC>)<br />
setSCED_WEIG_EQUA(float <WE>) <br />
setSCED_WEIG_DENS(float <WD>)<br />
<br />
==[[Image:User2.gif|link=]]TARGET==<br />
; TARGET ROT [FAST | BRUTE]<br />
: Target function for fast rotation searches (2). BRUTE searches all angles on a grid with the full rotation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these rotations with the full rotation likelihood target.<br />
; TARGET TRA [FAST | BRUTE | PHASED]<br />
: Target function for fast translation searches (3). BRUTE searches all positions on a grid with the full translation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these positions with the full translation likelihood target. PHASED selects the "phased translation function", for which a LABIN command should also be given, specifying FMAP, PHMAP and (optionally) FOM.<br />
* Default: TARGET ROT FAST<br />
* Default: TARGET TRA FAST<br />
setTARG_ROTA(str ["FAST"|"BRUTE"])<br />
setTARG_TRAN(str ["FAST"|"BRUTE"|"PHASED"])<br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS NMOL <NMOL><br />
: Number of molecules/molecular assemblies related by single TNCS vector (usually only 2). If the TNCS is a pseudo-tripling of the cell then NMOL=3, a pseudo-quadrupling then NMOL=4 etc.<br />
* Default: TNCS NMOL 2<br />
setTNCS_NMOL(int <NMOL>)<br />
<br><br />
<br />
==[[Image:User2.gif|link=]]TRANSLATION== <br />
; TRANSLATION VOLUME [ <sup>1</sup>FULL | <sup>2</sup>REGION | <sup>3</sup>LINE | <sup>4</sup>AROUND ])<br />
: Search volume for brute force translation function.<br />
: <sup>1</sup> Cheshire cell or Primitive cell volume. <br />
: <sup>2</sup> Search region.<br />
: <sup>3</sup> Search along line. <br />
: <sup>4</sup> Search around a point.<br />
; <sup>1 2 3</sup>TRANSLATION START <X Y Z> <br />
; <sup>1 2 3</sup>TRANSLATION END <X Y Z><br />
: Search within region or line bounded by START and END.<br />
; <sup>4</sup>TRANSLATION POINT <X Y Z><br />
; <sup>4</sup>TRANSLATION RANGE <RANGE><br />
: Search within +/- RANGE Ångstroms (not fractional coordinates, even if the search point is given as fractional coordinates) of a point <X Y Z>.<br />
; TRANSLATION [ORTH | FRAC]<br />
: Coordinates are given in orthogonal or fractional values.<br />
; TRANSLATION PACKING USE [ON | OFF]<br />
: Top translation function peak will be testes for packing.<br />
; TRANSLATION PACKING CUTOFF <PERC><br />
: Percent pairwise packing used for packing function test of top TF peak. Equivalent to PACK CUTOFF <PERC> for packing function. <br />
; TRANSLATION PACKING NUM <NUM><br />
: Number of translation function peaks to test for packing before bailing out of packing test. Set to 0 to pack all translation function peaks (slow for large packing volumes). <br />
* Default: TRANSLATION VOLUME FULL<br />
* Default: TRANSLATION PACK CUTOFF 50<br />
* Default: TRANSLATION PACK NUM 0 (helices - all packing checked)<br />
* Default: TRANSLATION PACK NUM 500 (non-helices)<br />
setTRAN_VOLU(string ["FULL"|"REGION"|"LINE"|"AROUND"])<br />
setTRAN_START(dvect <START>)<br />
setTRAN_END(dvect <END>)<br />
setTRAN_POINT(dvect <POINT>)<br />
setTRAN_RANGE(float <RANGE>)<br />
setTRAN_FRAC(bool <True=FRAC False=ORTH>)<br />
setTRAN_PACK_USE(bool)<br />
setTRAN_PACK_CUTO(float)<br />
<br />
==[[Image:User2.gif|link=]]ZSCORE== <br />
; ZSCORE USE [ON|OFF]<br />
: Use the TFZ tests. Only applicable with [[#SEARCH | SEARCH METHOD FAST]]. (Note Phaser-2.4.0 and below use "ZSCORE SOLVED 0" to turn off the TFZ tests)<br />
; ZSCORE SOLVED <ZSCORE_SOLVED><br />
: Set the minimum TFZ that indicates a definite solution for amalgamating solutions in FAST search method. <br />
;ZSCORE STOP [ON|OFF]<br />
: Stop adding components beyond point where TFZ is below cutoff when adding multiple components in FAST mode. However, FAST mode will always add one component even if TFZ is below cutoff, or two components if starting search with no components input (no input solution).<br />
; ZSCORE HALF [ON|OFF]<br />
: Set the TFZ for amalgamating solutions in the FAST search method to the maximum of ZSCORE_SOLVED and half the maximum TFZ, to accommodate cases of partially correct solutions in very high TFZ cases (e.g. TFZ > 16)<br />
* Default: ZSCORE USE ON<br />
* Default: ZSCORE SOLVED 8<br />
* Default: ZSCORE HALF ON<br />
* Default: ZSCORE STOP ON<br />
setZSCO_USE(bool <True=ON False=OFF>)<br />
setZSCO_SOLV(floatType ZSCORE_SOLVED)<br />
setZSCO_HALF(bool <True=ON False=OFF>)<br />
setZSCO_STOP(bool <True=ON False=OFF>)<br />
<br><br />
<br><br />
<br />
=Expert Keywords=<br />
<br />
==[[Image:Expert.gif|link=]]MACANO== <br />
; MACANO PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for the refinement of SigmaN in the anisotropy correction<br />
; MACANO ANISO [ON|OFF] BINS [ON|OFF] SOLK [ON|OFF] SOLB [ON|OFF] ''{NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}''<br />
: Macrocycle for the custom refinement of SigmaN in the anisotropy correction. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACANO PROTOCOL DEFAULT<br />
setMACA_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACA(bool <ANISO>,bool <BINS>,bool <SOLK>,bool <SOLB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACMR== <br />
; MACMR PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACMR ROT [ON|OFF] TRA [ON|OFF] BFAC [ON|OFF] VRMS [ON|OFF] ''CELL [ON|OFF] LAST [ON|OFF] NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of molecular replacement solutions. Macrocycles are performed in the order in which they are entered. For description of VRMS see the [[FAQ]]. CELL is the scale factor for the unit cell for maps (EM maps). LAST is a flag that refines the parameters for the last component of a solution only, fixing all the others.<br />
; MACMR CHAINS [ON|OFF]<br />
: Split the ensembles into chains for refinement<br />
: Not possible as part of an automated mode<br />
* Default: MACMR PROTOCOL DEFAULT<br />
* Default: MACMR CHAINS OFF<br />
setMACM_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACM(bool <ROT>,bool <TRA>,bool <BFAC>,bool <VRMS>,bool <CELL>,bool <LAST>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
setMACM_CHAI(bool])<br />
<br />
==[[Image:Expert.gif|link=]]MACOCC== <br />
; MACOCC PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACOCC NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of occupancy for solutions. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACOCC PROTOCOL DEFAULT<br />
setMACO_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACO(int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACSAD== <br />
; MACSAD PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for SAD refinement.<br />
:''n.b. PROTOCOL ALL will crash phaser and is only useful for debugging - see code for details''<br />
; MACSAD XYZ [ON|OFF] OCC [ON|OFF] BFAC [ON|OFF] FDP [ON|OFF] SA [ON|OFF] SB [ON|OFF] SP [ON|OFF] SD [ON|OFF] ''{PK [ON|OFF]} {PB [ON|OFF]} {NCYCLE <NCYC>} MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for SAD refinement. Macrocycles are performed in the order in which they are entered.<br />
*Default: MACSAD PROTOCOL DEFAULT<br />
setMACS_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACS(<br />
bool <XYZ>,bool <OCC>,bool <BFAC>,bool <FDP><br />
bool <SA>,bool <SB>,bool <SP>,bool <SD>,<br />
bool <PK>, bool <PB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACTNCS== <br />
; MACTNCS PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for pseudo-translational NCS refinement.<br />
; MACTNCS ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] ''NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for pseudo-translational NCS refinement. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACTNCS PROTOCOL DEFAULT<br />
setMACT_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACT(bool <ROT>,bool <TRA>,bool <VRMS>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]OCCUPANCY== <br />
; OCCUPANCY WINDOW ELLG <ELLG><br />
: Target eLLG for determining number of residues in window for occupancy refinement. The number of residues in a window will be an odd number. Occupancy refinement will be done for each offset of the refinement window.<br />
; OCCUPANCY WINDOW NRES <NRES><br />
: As an alternative to using the eLLG to define the number of residues in window for occupancy refinement, the number may be input directly. NRES must be an odd number.<br />
; OCCUPANCY WINDOW MAX <NRES><br />
: Maximum number of residues in an occupancy window (determined either by ellg or given as NRES) for which occupancy is refined. Prevents the refinement windows from spanning non-local regions of space.<br />
; OCCUPANCY MIN <MINOCC> MAX <MAXOCC><br />
: Minimum and maximum values of occupancy during refinement.<br />
; OCCUPANCY MERGE [ON/OFF]<br />
: Merge refined occupancies from different window offsets to give final occupancies per residue. If OFF, occupancies from a single window offset will be used, selected using OCCUPANCY OFFSET <N><br />
; OCCUPANCY FRAC <FRAC><br />
: Minimum fraction of the protein for which the occupancy may be set to zero.<br />
; OCCUPANCY OFFSET <N><br />
: If OCCUPANCY MERGE OFF, then <N> defines the single window offset from which final occupancies will be taken<br />
* Default: OCCUPANCY WINDOW ELLG 5<br />
* Default: OCCUPANCY WINDOW MAX 111<br />
* Default: OCCUPANCY MIN 0.01 MAX 1<br />
* Default: OCCUPANCY NCYCLES 1<br />
* Default: OCCUPANCY MERGE ON<br />
* Default: OCCUPANCY FRAC 0.5<br />
* Default: OCCUPANCY OFFSET 0<br />
setOCCU_WIND_ELLG(float <ELLG>)<br />
setOCCU_WIND_NRES(int <NRES>)<br />
setOCCU_WIND_MAX(int <NRES>)<br />
setOCCU_MIN(float <MIN>)<br />
setOCCU_MAX(float <MAX>)<br />
setOCCU_MERG(float <FRAC>)<br />
setOCCU_FRAC(bool)<br />
setOCCU_OFFS(int <N>)<br />
<br />
==[[Image:Expert.gif|link=]]RESCORE== <br />
; RESCORE ROT [ON|OFF]<br />
; RESCORE TRA [ON|OFF]<br />
: Toggle for rescoring of fast rotation function (ROT) or fast translation function (TRA) search peaks. <br />
* Default: RESCORE ROT ON<br />
* Default: RESCORE TRA ON|OFF will depend on whether phaser is running in the mode [[#MODE | MODE MR_AUTO]] with [[#SEARCH | SEARCH METHOD FAST]] or with [[#SEARCH | SEARCH METHOD FULL]], or running the translation function separately [[#MODE | MODE MR_FTF]]. For [[#SEARCH | SEARCH METHOD FAST]] the default also depends on whether or not the expected LLG target [[#ELLG | ELLG TARGET <TARGET>]] value is reached.<br />
setRESC_ROTA(bool)<br />
setRESC_TRAN(bool)<br />
<br />
==[[Image:Expert.gif|link=]]RFACTOR== <br />
; RFACTOR USE [ON|OFF]<br />
: For cases of searching for one ensemble when there is one ensemble in the asymmetric unit, the R-factor for the ensemble at the orientation and position in the input is calculated. If this value is low then MR is not performed in the MR_AUTO job in FAST search mode. Instead, rigid body refinement is performed before exiting. Note that the same R-factor test and cutoff is used for judging success in single-atom molecular replacement (MR_ATOM mode).<br />
; RFACTOR CUTOFF <VALUE><br />
: Rfactor in percent used as cutoff for deciding whether or not the R-factor indicates that MR is not necessary.<br />
* Default: RFACTOR USE ON CUTOFF 35<br />
setRFAC_USE(bool)<br />
setRFAC_CUTO(float <PERCENT>)<br />
<br />
==[[Image:Expert.gif|link=]]SAMPLING==<br />
; SAMPLING ROT <SAMP><br />
; SAMPLING TRA <SAMP><br />
: Sampling of search given in degrees for a rotation search and Ångstroms for a translation search. Sampling for rotation search depends on the mean radius of the Ensemble and the high resolution limit (dmin) of the search.<br />
* Default: SAMP = 2*atan(dmin/(4*meanRadius)) (ROTATION FUNCTION)<br />
* Default: SAMP = dmin/5; (BRUTE TRANSLATION FUNCTION)<br />
* Default: SAMP = dmin/4; (FAST TRANSLATION FUNCTION)<br />
setSAMP_ROTA(float <SAMP>)<br />
setSAMP_TRAN(float <SAMP>)<br />
<br><br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS USE [ON|OFF]<br />
: Use TNCS if present: apply TNCS corrections. (Note: was TNCS IGNORE [ON|OFF] in Phaser-2.4.0)<br />
; TNCS RLIST ADD [ON | OFF]<br />
: Supplement the rotation list used in the translation function with rotations already present in the list of known solutions. New molecules in the same orientation as those in the known search (as occurs with translational ncs) may not have peaks associated with them from the rotation function because the known molecules mask the presence of the ones not yet found. <br />
; TNCS PATT HIRES <hires><br />
: High resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT LORES <lores><br />
: Low resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT PERCENT <percent><br />
: Percent of origin Patterson peak that qualifies as a TNCS vector<br />
; TNCS PATT DISTANCE <distance><br />
: Minimum distance of Patterson peak from origin that qualifies as a TNCS vector<br />
; TNCS TRANSLATION PERTURB [ON | OFF]<br />
: If the TNCS translation vector is on a special position, perturb the vector from the special position before refinement<br />
; TNCS ROTATION RANGE <angle><br />
: Maximum deviation from initial rotation from which to look for rotational deviation. Default uses internally determined value based on resolution of data and size of G-function effective molecular radius. Value of 0 turns rotational refinement off.<br />
; TNCS ROTATION SAMPLING <sampling><br />
: Sampling for rotation search. Default uses internally determined value based on resolution of data and size of G-function effective molecular radius. Value of 0 turns rotational refinement off.<br />
* Default: TNCS USE ON<br />
* Default: TNCS RLIST ADD ON<br />
* Default: TNCS PATT HIRES 5<br />
* Default: TNCS PATT LORES 10<br />
* Default: TNCS PATT PERCENT 20<br />
* Default: TNCS PATT DISTANCE 15 <br />
* Default: TNCS TRANSLATION PERTURB ON<br />
setTNCS_USE(bool)<br />
setTNCS_RLIS_ADD(bool)<br />
setTNCS_PATT_HIRE(float <HIRES>)<br />
setTNCS_PATT_LORE(float <LORES>) <br />
setTNCS_PATT_PERC(float <PERCENT>) <br />
setTNCS_PATT_DIST(float <DISTANCE>)<br />
setTNCS_TRAN_PERT(bool)<br />
setTNCS_ROTA_RANG(float <RANGE>) <br />
setTNCS_ROTA_SAMP(float <SAMPLING>) <br />
<br><br />
<br><br />
<br />
=Developer Keywords=<br />
==[[Image:Developer.gif|link=]]BINS== <br />
; BINS DATA [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the data.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections<br />
; BINS ENSE [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the calaculated structure factos for the ensembles.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections<br />
* Default: BINS DATA MIN 6 MAX 50 WIDTH 500 <br />
* Default: BINS ENSE MIN 6 MAX 1000 WIDTH 1000 <br />
setBINS_DATA_MINI(float <L>)<br />
setBINS_DATA_MAXI(float <H>)<br />
setBINS_DATA_WIDT(float <W>)<br />
setBINS_ENSE_MINI(float <L>)<br />
setBINS_ENSE_MAXI(float <H>)<br />
setBINS_ENSE_WIDT(float <W>)<br />
<br />
==[[Image:Developer.gif|link=]]BFACTOR==<br />
; BFACTOR WILSON RESTRAINT [ON|OFF]<br />
: Toggle to use the Wilson restraint on the isotropic component of the atomic B-factors in SAD phasing.<br />
; BFACTOR SPHERICITY RESTRAINT [ON|OFF] <br />
: Toggle to use the sphericity restraint on the anisotropic B-factors in SAD phasing<br />
; BFACTOR REFINE RESTRAINT [ON|OFF] <br />
: Toggle to use the restraint to zero for the molecular B-factor in molecular replacement.<br />
; BFACTOR WILSON SIGMA <SIGMA><br />
: The sigma of the Wilson restraint.<br />
; BFACTOR SPHERICITY SIGMA <SIGMA><br />
: The sigma of the sphericity restraint.<br />
; BFACTOR REFINE SIGMA <SIGMA><br />
: The sigma of the restraint to zero for the molecular B-factor in molecular replacement.<br />
* Default: BFACTOR WILSON RESTRAINT ON <br />
* Default: BFACTOR SPHERICITY RESTRAINT ON <br />
* Default: BFACTOR REFINE RESTRAINT ON <br />
* Default: BFACTOR WILSON SIGMA 5<br />
* Default: BFACTOR SPHERICITY SIGMA 5<br />
* Default: BFACTOR REFINE SIGMA 6<br />
setBFAC_WILS_REST(bool <True|False>)<br />
setBFAC_SPHE_REST(bool <True|False>)<br />
setBFAC_REFI_REST(bool <True|False>) <br />
setBFAC_WILS_SIGM(float <SIGMA>) <br />
setBFAC_SPHE_SIGM(float <SIGMA>) <br />
setBFAC_REFI_SIGM(float <SIGMA>)<br />
<br />
==[[Image:Developer.gif|link=]]BOXSCALE==<br />
; BOXSCALE <BOXSCALE><br />
: Scale for box for calculating structure factors. The ensembles are put in a box equal to (extent of molecule)*BOXSCALE<br />
* Default: BOXSCALE 4<br />
setBOXS<float <BOXSCALE>)<br />
<br />
==[[Image:Developer.gif|link=]]CELL==<br />
; <span style="color:darkorange">Python Only</span> <br />
: Unit cell dimensions<br />
* Default: Cell read from MTZ file<br />
setCELL(float <A>,float <nowiki><B></nowiki>,float <C>,float <ALPHA>,float <BETA>,float <GAMMA>)<br />
setCELL6(float_array <A B C ALPHA BETA GAMMA>)<br />
<br />
==[[Image:Developer.gif|link=]]COMPOSITION== <br />
; COMPOSITION MIN SOLVENT <PERC><br />
: Minimum solvent to give maximum asu packing volume for automated search copy determination (NUM 0)<br />
* Default: COMPOSITION MIN SOLVENT 0.2<br />
setCOMP_MIN_SOLV(float)<br />
<br />
==[[Image:Developer.gif|link=]]DDM== <br />
; DDM SLIDER <VAL> <br />
: The SLIDER window width is used to smooth the Difference Distance Matrix. <br />
; DDM DISTANCE MIN <VAL> MAX <VAL> STEP <VAL><br />
: The range and step interval, as the fraction of the difference between the lowest and highest DDM values used to step.<br />
; DDM SEPARATION MIN <VAL> MAX <VAL><br />
: Through space separation in Angstroms used.<br />
; DDM SEQUENCE MIN <VAL> MAX <VAL><br />
: The range of sequence separations between matrix pairs.<br />
; DDM JOIN MIN <VAL> MAX <VAL><br />
: The range of lengths of the sequences to join if domain segments are discontinuous in percentages of the polypeptide chain.<br />
* Default: DDM SLIDER 0<br />
* Default: DDM DISTANCE MIN 1 MAX 5 STEP 50<br />
* Default: DDM SEPARATION MIN 7 MAX 14<br />
* Default: DDM SEQUENCE MIN 0 MAX 1<br />
* Default: DDM JOIN MIN 2 MAX 12<br />
setDDM_SLID(int <VAL>) <br />
setDDM_DIST_STEP(int <VAL>) <br />
setDDM_DIST_MINI(int <VAL>) <br />
setDDM_DIST_MAXI(int <VAL>) <br />
setDDM_SEPA_MINI(float <VAL>) <br />
setDDM_SEPA_MAXI(float <VAL>)<br />
setDDM_JOIN_MINI(int <VAL>) <br />
setDDM_JOIN_MAXI(int <VAL>) <br />
setDDM_SEQU_MINI(int <VAL>) <br />
setDDM_SEQU_MAXI(int <VAL>)<br />
<br />
==[[Image:Developer.gif|link=]]ENM== <br />
; ENM OSCILLATORS [ <sup>1</sup>RTB | <sup>2</sup>ALL ] <br />
: Define the way the atoms are used for the elastic network model.<br />
: <sup>1</sup>Use the rotation-translation block method.<br />
: <sup>2</sup>Use all atoms to determine the modes (only for use on very small molecules, less than 250 atoms). <br />
; ENM MAXBLOCKS <MAXBLOCKS><br />
: MAXBLOCKS is the number of rotation-translation blocks for the RTB analysis.<br />
; ENM NRES <NRES><br />
: For the RTB analysis, by default NRES=0 and then it is calculated so that it is as small as it can be without reaching MAXBlocks. <br />
; ENM RADIUS <RADIUS><br />
: Elastic Network Model interaction radius (Angstroms)<br />
; ENM FORCE <FORCE><br />
: Elastic Network Model force constant<br />
* Default: ENM OSCILLATORS RTB MAXBLOCKS 250 NRES 0 RADIUS 5 FORCE 1<br />
setENM_OSCI(str ["RTB"|"CA"|"ALL"])<br />
setENM_RTB_MAXB(float <MAXB>)<br />
setENM_RTB_NRES(float <NRES>) <br />
setENM_RADI(float <RADIUS>) <br />
setENM_FORC(float <FORCE>)<br />
<br />
==[[Image:Developer.gif|link=]]NORMALIZATION==<br />
; <span style="color:darkorange">Scripting Only</span><br />
; NORM EPSFAC WRITE <FILENAME><br />
: The normalization factors that correct for anisotropy in the data are written to BINARY file FILENAME<br />
; NORM EPSFAC READ <FILENAME><br />
: The normalization factors that correct for anisotropy in the data are read from BINARY file FILENAME. Further refinement is automatically turned off.<br />
; <span style="color:darkorange">Python Only</span><br />
The normalization factors that correct for anisotropy in the data, extracted from ResultANO object with getSigmaN(). Anisotropy should subsequently be turned off with setMACA_PROT("OFF").<br />
setNORM_DATA(data_norm <SIGMAN>)<br />
<br />
==[[Image:Developer.gif|link=]]OUTLIER==<br />
; OUTLIER REJECT [ON|OFF]<br />
: Reject low probability data outliers<br />
; OUTLIER PROB <PROB><br />
: Cutoff for rejection of low probablity outliers<br />
* Default: OUTLIER REJECT ON PROB 0.000001<br />
setOUTL_REJE(bool) <br />
setOUTL_PROB(float <PROB>)<br />
<br />
==[[Image:Developer.gif|link=]]PTGROUP== <br />
; PTGROUP COVERAGE <COVERAGE><br />
: Percentage coverage for two sequences to be considered in same pointgroup<br />
; PTGROUP IDENTITY <IDENTITY><br />
: Percentage identity for two sequences to be considered in same pointgroup<br />
; PTGROUP RMSD <RMSD><br />
: Percentage rmsd for two models to be considered in same pointgroup<br />
; PTGROUP TOLERANCE ANGULAR <ANG><br />
: Angular tolerance for pointgroup<br />
; PTGROUP TOLERANCE SPATIAL <DIST><br />
: Spatial tolerance for pointgroup<br />
setPTGR_COVE(float <COVERAGE>) <br />
setPTGR_IDEN(float <IDENTITY>) <br />
setPTGR_RMSD(float <RMSD>) <br />
setPTGR_TOLE_ANGU(float <ANG>) <br />
setPTGR_TOLE_SPAT(float <DIST>)<br />
<br />
==[[Image:Developer.gif|link=]]RESHARPEN== <br />
; RESHARPEN PERCENTAGE <PERC><br />
: Perecentage of the B-factor in the direction of lowest fall-off (in anisotropic data) to add back into the structure factors F_ISO and FWT and FDELWT so as to sharpen the electron density maps<br />
* Default: RESHARPEN PERCENT 100<br />
setRESH_PERC(float <PERCENT>)<br />
<br />
==[[Image:Developer.gif|link=]]SOLPARAMETERS==<br />
; SOLPARAMETERS SIGA FSOL <FSOL> BSOL <BSOL> MIN <MINSIGA><br />
: Babinet solvent parameters for Sigma(A) curves. MINSIGA is the minimum SIGA for Babinet solvent term (low resolution only). The solvent term in the Sigma(A) curve is given by <BR>max(1 - FSOL*exp(-BSOL/(4d^2)),MINSIGA).<br />
; SOLPARAMETERS BULK USE [ON|OFF]<br />
: Toggle for use of solvent mask scaling parameters for ensemble structure factors, applied to Fmask.<br />
; SOLPARAMETERS BULK FSOL <FSOL> BSOL <BSOL> <br />
: Solvent mask scaling parameters for ensemble structure factors, applied to Fmask.<br />
* Default: SOLPARAMETERS SIGA FSOL 1.05 BSOL 501 MIN 0.1<br />
* Default: SOLPARAMETERS SIGA RESTRAINT ON<br />
* Default: SOLPARAMETERS BULK USE OFF<br />
* Default: SOLPARAMETERS BULK FSOL 0.35 BSOL 45<br />
setSOLP_SIGA_FSOL(float <FSOL>) <br />
setSOLP_SIGA_BSOL(float <BSOL>)<br />
setSOLP_SIGA_MIN(float <MINSIGA>)<br />
setSOLP_BULK_USE(bool)<br />
setSOLP_BULK_FSOL(float <FSOL>) <br />
setSOLP_BULK_BSOL(float <BSOL>)<br />
<br />
==[[Image:Developer.gif|link=]]TARGET== <br />
; TARGET ROT FAST TYPE [LERF1 | CROWTHER]<br />
: Target function type for fast rotation searches<br />
; TARGET TRA FAST TYPE [LETF1 | LETF2 | CORRELATION]<br />
: Target function type for fast translation searches<br />
setTARG_ROTA_TYPE(string TYPE)<br />
setTARG_TRAN_TYPE(string TYPE)<br />
<br />
==[[Image:Developer.gif|link=]]TNCS==<br />
; TNCS ROTATION ANGLE <A> <nowiki><B></nowiki> <C><br />
: Input rotational difference between molecules related by the pseudo-translational symmetry vector, specified as rotations in degrees about x, y and z axes. Central value for grid search (RANGE > 0).<br />
; TNCS ROTATION RANGE <A><br />
: Range of angular difference in rotation angles to explore around central angle.<br />
; TNCS ROTATION SAMPLING <A><br />
: Sampling step for rotational grid search.<br />
; TNCS TRA VECTOR <x y z> <br />
: Input pseudo-translational symmetry vector (fractional coordinates). By default the translation is determined from the Patterson.<br />
; TNCS VARIANCE RMSD <num><br />
: Input estimated rms deviation between pseudo-translational symmetry vector related molecules.<br />
; TNCS VARIANCE FRAC <num><br />
: Input estimated fraction of cell content that obeys pseudo-translational symmetry.<br />
; TNCS LINK RESTRAINT [ON | OFF]<br />
: Link the occupancy of atoms related by TNCS in SAD phasing<br />
; TNCS LINK SIGMA <sigma><br />
: Sigma of link restraint of the occupancy of atoms related by TNCS in SAD phasing<br />
* Default: TNCS ROTATION ANGLE 0 0 0<br />
* Default: TNCS ROTATION RANGE -999 (determine from structure size and resolution)<br />
* Default: TNCS ROTATION SAMPLING -999 (determine from structure size and resolution)<br />
* Default: TNCS TRANSLATION VECTOR determined from position of Patterson peak<br />
* Default: TNCS VARIANCE RMSD 0.4 <br />
* Default: TNCS VARIANCE FRAC 1 <br />
* Default: TNCS LINK RESTRAINT ON<br />
* Default: TNCS LINK SIGMA 0.1<br />
setTNCS_ROTA_ANGL(dvect3 <A B C>) <br />
setTNCS_TRAN_VECT(dvect3 <X Y Z>) <br />
setTNCS_VARI_RMSD(float <RMSD>) <br />
setTNCS_VARI_FRAC(float <FRAC>)<br />
setTNCS_LINK_REST(bool)<br />
setTNCS_LINK_SIGM(float <SIGMA>)<br />
; <span style="color:darkorange">Scripting Only</span><br />
; TNCS EPSFAC WRITE <FILENAME><br />
: The normalization factors that correct for tNCS in the data are written to BINARY file FILENAME<br />
; TNCS EPSFAC READ <FILENAME><br />
: The normalization factors that correct for tNCS in the data are read from BINARY file FILENAME. Further refinement is automatically turned off.<br />
; <span style="color:darkorange">Python Only</span><br />
The normalization factors that correct for tNCS in the data, extracted from ResultNCS object with getPtNcs(). tNCS refinement should subsequently be turned off with setMACT_PROT("OFF").<br />
setTNCS(data_tncs <PTNCS>)<br />
<br />
==[[Image:Developer.gif|link=]]TRANSLATION== <br />
; TRANSLATION MAPS [ON | OFF]<br />
: Output maps of fast translation function FSS scoring functions<br />
: Maps take the names <ROOT>.<ensemble>.k.e.map where k is the Known backgound number and e is the Euler angle number for that known background<br />
* Default: TRANSLATION MAPS OFF<br />
setTRAN_MAPS(bool)</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Phaser-2.7.17:_Manual&diff=2395Phaser-2.7.17: Manual2016-11-29T15:44:18Z<p>Airlie: fix doc for 2.7.17 as oldid</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__NOTOC__</div><br />
<br />
This is the documentation for Phaser&#8211;2.7.17 There are some changes between this version and previous versions so input scripts may need editing. <br />
<br />
:; [[ Modes | Modes]]<br />
:: The different functions that Phaser can perform <br />
:; {{Oldid|2390|Keywords}}<br />
:: Detailed descriptions of the keywords<br />
<br />
See also:<br />
:; [[Famos | Famos]]<br />
:: A python script for placing MR solutions on the same (common) origin</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Keywords&diff=2394Keywords2016-11-29T15:42:59Z<p>Airlie: </p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
=Phaser-2.8=<br />
<br />
===Phaser Executable===<br />
<br />
The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the [[#MODE | MODE]] keyword. The different modes and the keywords relevant to each mode are described in [[Modes]].<br />
<br />
Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. However, some keywords are meaningful when entered multiple times. The order may or may not be important. <br />
<br />
*[[Image:User1.gif|link=]] [[#Basic Keywords | Basic Keywords]]<br />
<br />
*[[Image:Output.png|link=]] [[#Output Control Keywords | Output Control Keywords]]<br />
<br />
*[[Image:User2.gif|link=]] [[#Advanced Keywords |Advanced Keywords ]]<br />
<br />
*[[Image:Expert.gif|link=]] [[#Expert Keywords | Expert Keywords]]<br />
<br />
*[[Image:Developer.gif|link=]] [[#Developer Keywords | Developer Keywords]]<br />
<br />
<br />
===Python Interface===<br />
<br />
Phaser can be compiled as a python library. The mode is selected by calling the appropriate run-job. Input to the run-job is via input-objects, which are passed to the run-job. Setter function on the input objects are equivalent to the keywords for input to the phaser executable. The different modes and the keywords relevant to each mode are described in [[Modes]]. See [[Python Interface]] for details. <br />
<br />
The python interface uses standard python and cctbx/scitbx variable types.<br />
<br />
str string<br />
float double precision floating point<br />
Miller cctbx::miller::index<int> <br />
dvect3 scitbx::vec3<float> <br />
dmat33 scitbx::mat3<float> <br />
'''type'''_array scitbx::af::shared<'''type'''> arrays<br />
<br />
=Basic Keywords=<br />
==[[Image:User1.gif|link=]]ATOM== <br />
; ATOM CRYSTAL <XTALID> PDB <FILENAME><br />
: Definition of atom positions using a pdb file.<br />
; ATOM CRYSTAL <XTALID> HA <FILENAME><br />
: Definition of atom positions using a ha file (from RANTAN, MLPHARE etc.).<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> <br />
: Minimal definition of atom position. B-factor defaults to isotropic and Wilson B-factor. Use <TYPE>=TX for Ta6Br12 cluster and <TYPE>=XX for all other clusters. Scattering for cluster is spherically averaged. Coordinates of cluster compounds other than Ta6Br12 must be entered with CLUSTER keyword. Ta6Br12 coordinates are in phaser code and do not need to be given with CLUSTER keyword.<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> [ ISOB <ISOB> | ANOU <HH KK LL HK HL KL> | USTAR <HH KK LL HK HL KL>] FIXX [ON|OFF] FIXO [ON|OFF] FIXB [ON|OFF] BSWAP [ON|OFF] LABEL <SITE_NAME><br />
: Full definition of atom position including B-factor.<br />
;ATOM CHANGE BFACTOR WILSON [ON|OFF]<br />
: Reset all atomic B-factors to the Wilson B-factor.<br />
; ATOM CHANGE SCATTERER <SCATTERER><br />
:Reset all atomic scatterers to element (or cluster) type.<br />
setATOM_PDB(str <XTALID>,str <PDB FILENAME>)<br />
setATOM_IOTBX(str <XTALID>,iotbx::pdb::hierarchy::root <iotbx object>)<br />
setATOM_STR(str <XTALID>,str <pdb format string>)<br />
setATOM_HA(str <XTALID>,str <FILENAME>)<br />
addATOM(str <XTALID>,str <TYPE>,<br />
float <X>,float <Y>,float <Z>,float <OCC>)<br />
addATOM_FULL(str <XTALID>,str <TYPE>,bool <ORTH>,<br />
dvect3 <X Y Z>,float <OCC>,bool <ISO>,float <ISOB>,<br />
bool <ANOU>,dmat6 <HH KK LL HK HL KL>,<br />
bool <FIXX>,bool <FIXO>,bool <FIXB>,bool <SWAPB>,<br />
str <SITE_NAME>)<br />
setATOM_CHAN_BFAC_WILS(bool)<br />
setATOM_CHAN_SCAT(bool)<br />
setATOM_CHAN_SCAT_TYPE(str <TYPE>)<br />
<br />
==[[Image:User1.gif|link=]]CLUSTER== <br />
; CLUSTER PDB <PDBFILE><br />
: Sample coordinates for a cluster compound for experimental phasing. Clusters are specified with type XX. Ta6Br12 clusters do not need to have coordinates specified as the coordinates are in the phaser code. To use Ta6Br12 clusters, specify atomtypes/clusters as TX.<br />
setCLUS_PDB(str <PDBFILE>)<br />
addCLUS_PDB(str <ID>, str <PDBFILE>)<br />
<br />
==[[Image:User1.gif|link=]]COMPOSITION== <br />
; COMPOSITION BY [ <sup>1</sup>AVERAGE| <sup>2</sup>SOLVENT| <sup>3</sup>ASU ]<br />
: Alternative ways of defining composition<br />
: <sup>1</sup> AVERAGE solvent fraction for crystals (50%)<br />
: <sup>2</sup> Composition entered by solvent content.<br />
: <sup>3</sup> Explicit description of composition of ASU by sequence or molecular weight<br />
; <sup>2</sup>COMPOSITION PERCENTAGE <SOLVENT><br />
: Specified SOLVENT content<br />
; <sup>3</sup>COMPOSITION PROTEIN [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of protein in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION NUCLEIC [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of nucleic acid in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION ATOM <TYPE> NUMBER <NUM><br />
: Add NUM copies of an atom (usually a heavy atom) to the composition<br />
* Default: COMPOSITION BY ASU<br />
setCOMP_BY(str ["AVERAGE" | "SOLVENT" | "ASU" ])<br />
setCOMP_PERC(float <SOLVENT>)<br />
addCOMP_PROT_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_PROT_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_PROT_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_PROT_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_NUCL_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_NUCL_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_NUCL_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_NUCL_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_ATOM(str <TYPE>,float <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]CRYSTAL== <br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN Fpos =<F+> SIGFpos=<SIG+> Fneg=<F-> SIGFneg=<SIG-><br />
: Columns of MTZ file to read for this (anomalous) dataset<br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN F =<F> SIGF=<SIGF><br />
: Columns of MTZ file to read for this (non-anomalous) dataset. Used for LLG completion in SAD phasing when there is no anomalous signal (single atom MR protocol). Use LABIN for MR.<br />
setCRYS_ANOM_LABI(str <F+>,str <SIGF+>,str <F->,str <SIGF->) <br />
setCRYS_MEAN_LABI(str <F>,str <SIGF>)<br />
<br />
==[[Image:User1.gif|link=]]ENSEMBLE== <br />
; ENSEMBLE <MODLID> [PDB|CIF] <PDBFILE> [RMS <RMS><sup>1</sup> | ID <ID><sup>2</sup> | CARD ON<sup>3</sup>] ''CHAIN "<CHAIN>"<sup>4</sup> MODEL <NUM><sup>5</sup>''<br />
: The names of the PDB/CIF files used to build the ENSEMBLE, and either<br />
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
:: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file (e.g. "REMARK PHASER ENSEMBLE MODEL 1 ID 31.2") containing the superimposed models concatenated in the one file. This syntax enables simple automation of the use of ensembles. The pdb file can be non-standard because the atom list for the different models need not be the same.<br />
:: <sup>4</sup> CHAIN is selected from the pdb file. <br />
:: <sup>5</sup> MODEL number is selected from the pdb file.<br />
; ENSEMBLE <MODLID> HKLIN <MTZFILE> F=<F> PHI=<PHI> EXTENT <EX> <EY> <EZ> RMS <RMS> CENTRE <CX> <CY> <CZ> PROTEIN MW <PMW> NUCLEIC MW <NMW> ''CELL SCALE <SCALE>''<br />
: An ENSEMBLE defined from a map (via an mtz file). The molecular weight of the object the map represents is required for scaling. The effective RMS coordinate error is needed to judge how the map accuracy falls off with resolution. For density obtained from an EM image reconstruction, a good first guess would be to take the resolution where the FSC curve drops below 0.5 and divide by 3. The extent (difference between maximum and minimum x,y,z coordinates of region containing model density) is needed to determine reasonable rotation steps, and the centre is needed to carry out a proper interpolation of the molecular transform. The extent and the centre are both given in Ångstroms. The cell scale factor defaults to 1 and can be refined (for example, if the map is from electron microscopy when the cell scale may be unknown to within a few percent).<br />
; ENSEMBLE <MODLID> ATOM <TYPE> RMS <RMS><br />
: Define an ensemble as a single atom for single atom MR<br />
; ENSEMBLE <MODLID> HELIX <NUM> <br />
: Define an ensemble as a helix with NUM residues<br />
; ENSEMBLE <MODLID> HETATM [ON|OFF]<br />
: Use scattering from HETATM records in pdb file. See [[Molecular_Replacement#Coordinate_Editing | Coordinate Editing ]]<br />
; ENSEMBLE <MODLID> DISABLE CHECK [ON|OFF]<br />
: Toggle to disable checking of deviation between models in an ensemble. '''Use with extreme caution'''. Results of computations are not guaranteed to be sensible.<br />
; ENSEMBLE <MODLID> ESTIMATOR [OEFFNER | OEFFNERHI | OEFFNERLO | CHOTHIALESK ]<br />
: Define the estimator function for converting ID to RMS<br />
; ENSEMBLE <MODLID> PTGRP [COVERAGE | IDENTITY | RMSD | TOLANG | TOLSPC | EULER | SYMM ]<br />
: Define the pointgroup parameters <br />
; ENSEMBLE <MODLID> BINS [MIN <N>| MAX <M>| WIDTH <W> ]<br />
: Define the Fcalc reflection binning parameters <br />
; ENSEMBLE <MODLID> TRACE [PDB|CIF] <PDBFILE><br />
: Define the coordinates used for packing independent of the coordinates used for structure factor calculation<br />
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
:: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file <br />
; ENSEMBLE <MODLID> TRACE SAMPLING MIN <DIST> <br />
: Set the minimum distance for the sampling of packing grid<br />
; ENSEMBLE <MODLID> TRACE SAMPLING TARGET <NUM> <br />
: Set the target for the number of points to sample the smallest molecule to be packed<br />
; ENSEMBLE <MODLID> TRACE SAMPLING RANGE <NUM> <br />
: Target range (TARGET+/-RANGE) for search for hexgrid points in protein volume<br />
; ENSEMBLE <MODLID> TRACE SAMPLING USE [AUTO | ALL | CALPHA | HEXGRID ]<br />
: Sample trace coordinates using all atoms, C-alpha atoms, a hexagonal grid in the atomic volume or use an automatically determined choice<br />
; ENSEMBLE <MODLID> TRACE SAMPLING DISTANCE <DIST> <br />
: Set the distance for the sampling of the hexagonal grid explicitly and do not use TARGET to find default sampling distance<br />
; ENSEMBLE <MODLID> TRACE SAMPLING WANG <WANG> <br />
: Scale factor for the size of the Wang mask generated from an ensemble map<br />
; ENSEMBLE <MODLID> TRACE PDB <PDBFILE> <br />
: Use the given set of coordinates for packing rather than using the coordinates for structure factor calculation<br />
* Default: ENSEMBLE <MODLID> DISABLE CHECK OFF<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING MIN 1.0<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING TARGET 1000<br />
* Default: ENSEMBLE <MODLID> TRACE SAMPLING RANGE 100<br />
addENSE_PDB_ID(str <MODLID>,str <FILE>,float <ID>) <br />
addENSE_PDB_RMS(str <MODLID>,str <FILE>,float <RMS>) <br />
setENSE_TRAC_SAMP_MIN(MODLID,float <MIN>)<br />
setENSE_TRAC_SAMP_TARG(MODLID,int <TARGET>)<br />
setENSE_TRAC_SAMP_RANG(MODLID,int <RANGE>)<br />
setENSE_TRAC_SAMP_USE(MODLID,str)<br />
setENSE_TRAC_SAMP_DIST(MODLID,float <DIST>)<br />
setENSE_TRAC_SAMP_WANG(MODLID,float <WANG>)r <FILE>,float <RMS>)<br />
addENSE_CARD(str <MODLID>,str <FILE>,bool)<br />
addENSE_MAP(str <MODLID>,str <MTZFILE>,str <F>,str <PHI>,dvect3 <EX EY EZ>,<br />
float <RMS>,dvect3 <CX CY CZ>,float <PMW>,float <NMW>,float <CELL>)<br />
setENSE_DISA_CHEC(bool)<br />
<br />
==[[Image:User1.gif|link=]]HKLIN==<br />
; HKLIN <FILENAME><br />
: The mtz file containing the data<br />
setHKLI(str <FILENAME>)<br />
<br />
==[[Image:User1.gif|link=]]JOBS== <br />
; JOBS <NUM><br />
: Number of processors to use in parallelized sections of code<br />
* Default: JOBS 2<br />
setJOBS(int <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]LABIN== <br />
; LABIN F = <F> SIGF = <SIGF> <br />
: Columns in mtz file. F must be given. SIGF should be given but is optional<br />
; LABIN I = <nowiki><I></nowiki> SIGI = <SIGI> <br />
: Columns in mtz file. I must be given. SIGI should be given but is optional<br />
; LABIN FMAP = <PH> PHMAP = <PHMAP> <br />
: Columns in mtz file. FMAP/PHMAP are weighted coefficients for use in the Phased Translation Function.<br />
; LABIN FMAP = <PH> PHMAP = <PHMAP> FOM = <FOM><br />
: Columns in mtz file. FMAP/PHMAP are unweighted coefficients for use in the Phased Translation Function and FOM the figure of merit for weighting<br />
setLABI_F_SIGF(str <F>,str <SIGF>)<br />
setLABI_I_SIGI(str <nowiki><I></nowiki>,str <SIGI>)<br />
setLABI_PTF(str <FMAP>,str <PHMAP>,str <FOM>)<br />
<br />
''Data should be input to python run-jobs using one data_refl parameter''<br />
''This is extracted from the ResultMR_DAT object after a call to runMR_DAT''<br />
setREFL_DATA(data_ref)<br />
''Example:''<br />
i = InputMR_DAT()<br />
i.setHKLI("*.mtz")<br />
i.setLABI_F_SIGF("F","SIGF")<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputMR_LLG()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.setREFL_DATA(r.getDATA())<br />
''See also: '' [[Python Example Scripts]]<br />
<br />
''Alternatively, reflection arrays can be set using cctbx::af::shared<double>''<br />
setREFL_F_SIGF(float_array <F>,float_array <SIGF>)<br />
setREFL_I_SIGI(float_array <nowiki><I></nowiki>,float_array <SIGI>)<br />
setREFL_PTF(float_array <FMAP>,float_array <PHMAP>,float_array <FOM>)<br />
<br />
==[[Image:User1.gif|link=]]MODE==<br />
; MODE [ ANO | CCA | SCEDS | NMAXYZ | NCS | MR_ELLG | MR_AUTO | MR_GYRE | MR_ATOM | MR_ROT | MR_TRA | MR_RNP | | MR_OCC | MR_PAK | EP_AUTO | EP_SAD]<br />
: The mode of operation of Phaser. The different modes are described in a separate page on [[Keyword Modes]]<br />
ResultANO r = runANO(InputANO)<br />
ResultCCA r = runCCA(InputCCA)<br />
ResultNMA r = runSCEDS(InputNMA)<br />
ResultNMA r = runNMAXYZ(InputNMA)<br />
ResultNCS r = runNCS(InputNCS)<br />
ResultELLG r = runMR_ELLG(InputMR_ELLG)<br />
ResultMR r = runMR_AUTO(InputMR_AUTO)<br />
ResultEP r = runMR_ATOM(InputMR_ATOM)<br />
ResulrMR_RF r = runMR_FRF(InputMR_FRF)<br />
ResultMR_TF r = runMR_FTF(InputMR_FTF)<br />
ResultMR r = runMR_RNP(InputMR_RNP)<br />
ResultGYRE r = runMR_GYRE(InputMR_RNP)<br />
ResultMR r = runMR_OCC(InputMR_OCC)<br />
ResultMR r = runMR_PAK(InputMR_PAK)<br />
ResultEP r = runEP_AUTO(InputEP_AUTO)<br />
ResultEP_SAD r = runEP_SAD(InputEP_SAD)<br />
<br />
==[[Image:User1.gif|link=]]PARTIAL== <br />
; PARTIAL PDB <PDBFILE> [RMSIDENTITY] <RMS_ID><br />
: The partial structure for MR-SAD substructure completion. Note that this must already be correctly placed, as the experimental phasing module will not carry out molecular replacement.<br />
; PARTIAL HKLIN <MTZFILE> [RMS|IDENTITY] <RMS_ID><br />
: The partial electron density for MR-SAD substructure completion.<br />
; PARTIAL LABIN FC=<FC> PHIC=<PHIC><br />
: Column labels for partial electron density for MR-SAD substructure completion.<br />
setPART_PDB(str <PDBFILE>)<br />
setPART_HKLI(str <MTZFILE>) <br />
setPART_LABI_FC(str <FC>)<br />
setPART_LABI_PHIC(str <PHIC>) <br />
setPART_VARI(str ["ID"|"RMS"])<br />
setPART_DEVI(float <RMS_ID>)<br />
<br />
==[[Image:User1.gif|link=]]SEARCH==<br />
; SEARCH ENSEMBLE <MODLID> ''{OR ENSEMBLE <MODLID>}… NUMBER <NUM><sup>*</sup>''<br />
: The ENSEMBLE to be searched for in a rotation search or an automatic search. When multiple ensembles are given using the OR keyword, the search is performed for each ENSEMBLE in turn. When the keyword is entered multiple times, each SEARCH keyword refers to a new component of the structure. If the component is present multiple times the sub-keyword NUMber can be used (rather than entering the same SEARCH keyword NUMber times).<br />
: <sup>*</sup>For automatic determination of search number use NUMBER 0. If the composition is entered, the maximum number will be that defined by the composition, otherwise the maximum number will fill the asymmetric unit to a minimum solvent content of 20%. Searches for new components will continue until the TFZ score is above 8, and terminate if the TFZ score drops below 8 before the placement of the maximum number of components.<br />
; SEARCH METHOD [FULL|FAST]<br />
: Search using the [[Modes#Modes |full search]] or [[Modes#Modes | fast search]] algorithms.<br />
; SEARCH ORDER AUTO [ON|OFF]<br />
: Search in the "best" order as estimated using estimated rms deviation and completeness of models.<br />
; SEARCH PRUNE [ON|OFF]<br />
: For high TFZ solutions that fail the packing test, carry out a sliding-window occupancy refinement and prune residues that refine to low occupancy, in an effort to resolve packing clashes. If this flag is set to true, the flag for keeping high tfz score solutions (see [[#PACK | PACK]]) that don't pack is also set to true (PACK KEEP HIGH TFZ ON).<br />
; SEARCH AMALGAMATE USE [ON|OFF]<br />
: For multiple high TFZ solutions, enable amalgamation into a single solution<br />
; SEARCH BFACTOR <BFAC><br />
: B-factor applied to search molecule (or atom).<br />
; SEARCH OFACTOR <OFAC><br />
: Occupancy factor applied to search molecule (or atom).<br />
* Default: SEARCH METHOD FAST<br />
* Default: SEARCH ORDER AUTO ON<br />
* Default: SEARCH PRUNE ON<br />
* Default: SEARCH AMALGAMATE USE ON<br />
* Default: SEARCH BFACTOR 0<br />
* Default: SEARCH OFACTOR 1<br />
addSEAR_ENSE_NUM(str <MODLID>,int <NUM>) <br />
addSEAR_ENSE_OR_ENSE_NUM(string_array <MODLIDS>,int <NUM>) <br />
setSEAR_METH(str [ "FULL" | "FAST" ])<br />
setSEAR_ORDE_AUTO(bool)<br />
setSEAR_PRUN(bool <PRUNE>)<br />
setSEAR_AMAL_USE(bool <AMAL>)<br />
setSEAR_BFAC(float <BFAC>)<br />
setSEAR_OFAC(float <OFAC>)<br />
<br />
==[[Image:User1.gif|link=]]SGALTERNATIVE==<br />
; SGALTERNATIVE SELECT [<sup>1</sup>ALL| <sup>2</sup>HAND| <sup>3</sup>LIST| <sup>4</sup>NONE]<br />
: Selection of alternative space groups to test in translation functions i.e. those that are in same laue group as that given in [[#SPACEGROUP | SPACEGROUP]]<br />
: <sup>1</sup> Test all possible space groups, <br />
: <sup>2</sup> Test the given space group and its enantiomorph.<br />
: <sup>3</sup> Test the space groups listed with SGALTERNATIVE TEST <SG>.<br />
: <sup>4</sup> Do not test alternative space groups.<br />
; SGALTERNATIVE TEST <SG><br />
: Alternative space groups to test. Multiple test space groups can be entered.<br />
* Default: SGALTERNATIVE SELECT HAND<br />
setSGAL_SELE(str [ "ALL" | "HAND" | "LIST" | "NONE" ]) <br />
addSGAL_TEST(str <SG>)<br />
<br />
==[[Image:User1.gif|link=]]SOLUTION==<br />
; SOLUTION SET <ANNOTATION><br />
: Start new set of solutions <br />
; SOLUTION TEMPLATE <ANNOTATION><br />
: Specifies a template solution against which other solutions in this run will be compared. Given in place of SOLUTION SET. Template rotation and translations given by subsequent SOLUTION 6DIM cards as per SOLUTION SETS.<br />
; SOLUTION 6DIM ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> [ORTH|FRAC] <X> <Y> <Z> ''FIXR [ON|OFF] FIXT [ON|OFF] FIXB [ON|OFF] BFAC <BFAC> MULT <MULT>''<br />
: This keyword is repeated for each known position and orientation of an ENSEMBLE MODLID. A B G are the Euler angles (z-y-z convention) and X Y Z are the translation elements, expressed either in orthogonal Angstroms (ORTH) or fractions of a cell edge (FRAC). The input ensemble is transformed by a rotation around the origin of the coordinate system, followed by a translation. BFAC default to 0, MULT (for multiplicity) defaults to 1.<br />
; SOLUTION ENSEMBLE <MODLID> VRMS DELTA <DELTA> RMSD <RMSD><br />
: Refined RMS variance terms for pdb files (or map) in ensemble MODLID. RMSD is the input RMSD of the job that produced the sol file, DELTA is the shift with respect to this RMSD. If given as part of a solution, these values overwrite the values used for input in the ENSEMBLE keyword (if refined).<br />
; SOLUTION ENSEMBLE <MODLID> CELL SCALE <SCALE><br />
: Refined cell scale factor. Only applicable to ensembles that are maps<br />
; SOLUTION TRIAL ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> RFZ <RFZ><br />
: Rotation List for translation function<br />
; SOLUTION ORIGIN ENSEMBLE <MODLID><br />
: Create solution for ensemble MODLID at the origin<br />
; SOLUTION SPACEGROUP <SG><br />
: Space Group of the solution (if alternative spacegroups searched)<br />
; SOLUTION RESOLUTION <HIRES><br />
: High resolution limit of data used to find/refine this solution<br />
; SOLUTION PACKS <PACKS><br />
: Flag for whether solution has been retained despite failing packing test, due to having high TFZ<br />
setSOLU(mr_solution <SOL>) <br />
addSOLU_SET(str <ANNOTATION>) <br />
addSOLU_TEMPLATE(str <ANNOTATION>) <br />
addSOLU_6DIM_ENSE(str <MODLID>,dvect3 <A B C>,bool <FRAC>,dvect3 <X Y Z>,<br />
float <BFAC>,bool <FIXR>,bool <FIXT>,bool <FIXB>,int <MULT>, 1.0) <br />
addSOLU_ENSE_DRMS(str <MODLID>, float <DRMS>) <br />
addSOLU_ENSE_CELL(str <MODLID>, float <SCALE>)<br />
addSOLU_TRIAL_ENSE(string <MODLID>,dvect3 <A B C>,float <RFZ>)<br />
addSOLU_ORIG_ENSE(string <MODLID>)<br />
setSOLU_SPAC(str <SG>)<br />
setSOLU_RESO(float <HIRES>)<br />
setSOLU_PACK(bool <PACKS>)<br />
<br />
==[[Image:User1.gif|link=]]SPACEGROUP==<br />
; SPACEGROUP <SG><br />
: Space group may be altered from the one on the MTZ file to a space group in the same point group. The space group can be entered in one of three ways<br />
#The Hermann-Mauguin symbol e.g. P212121 or P 21 21 21 (with or without spaces)<br />
#The international tables number, which gives standard setting e.g. 19 <br />
#The Hall symbols e.g. P 2ac 2ab<br />
: '''The space group can also be a subgroup of the merged space group'''. For example, P1 is always allowed. The reflections will be expanded to the symmetry of the given subgroup. This is only a valid approach when the true symmetry is the symmetry of the subgroup and perfect twinning causes the data to merge "perfectly" in the higher symmetry. <br />
:'''A list of the allowed space groups in the same point group as the given space group (or space group read from MTZ file) and allowed subgroups of these is given in the Cell Content Analysis logfile.'''<br />
* Default: Read from MTZ file<br />
setSPAC_NUM(int <NUM>)<br />
setSPAC_NAME(string <HM>)<br />
setSPAC_HALL(string <HALL>)<br />
<br />
==[[Image:User1.gif|link=]]WAVELENGTH== <br />
; WAVELENGTH <LAMBDA> <br />
: The wavelengh at which the SAD dataset was collected<br />
setWAVE(float <LAMBDA>)<br />
<br><br />
<br><br />
<br />
=Output Control Keywords=<br />
==[[Image:Output.png|link=]]DEBUG== <br />
; DEBUG [ON|OFF]<br />
: Extra verbose output for debugging<br />
* Default: DEBUG OFF<br />
setDEBU(bool) <br />
<br />
==[[Image:Output.png|link=]]EIGEN==<br />
; EIGEN WRITE [ON|OFF]<br />
; EIGEN READ <EIGENFILE><br />
: Read or write a file containing the eigenvectors and eigenvalues. If reading, the eigenvalues and eigenvectors of the Hessian are read from the file generated by a previous run, rather than calculated. This option must be used with the job that generated the eigenfile and the job reading the eigenfile must have identical input for the ENM parameters. Use WRITE to control whether or not the eigenfile is written when not using the READ mode.<br />
* Default: EIGEN WRITE ON<br />
setEIGE_WRIT(bool)<br />
setEIGE_READ(str <EIGENFILE>)<br />
<br />
==[[Image:Output.png|link=]]HKLOUT== <br />
; HKLOUT [ON|OFF]<br />
: Flags for output of an mtz file containing the phasing information<br />
* Default: HKLOUT ON<br />
setHKLO(bool) <br />
<br />
==[[Image:Output.png|link=]]KEYWORDS== <br />
; KEYWORDS [ON|OFF]<br />
: Write output Phaser .sol file (.rlist file for rotation function)<br />
* Default: KEYWORDS ON<br />
setKEYW(bool)<br />
<br />
==[[Image:Output.gif|link=]]LLGMAPS==<br />
; LLGMAPS [ON|OFF]<br />
: Write log-likelihood gradient map coefficients to MTZ file<br />
* Default: LLGMAPS OFF<br />
setLLGM(bool <True|False>)<br />
<br />
==[[Image:Output.png|link=]]MUTE== <br />
; MUTE [ON|OFF]<br />
: Toggle for running in silent/mute mode, where no logfile is written to ''standard output''.<br />
* Default: MUTE OFF<br />
setMUTE(bool) <br />
<br />
==[[Image:Output.png|link=]]KILL== <br />
; KILL TIME [MINS]<br />
: Kill Phaser after MINS minutes of CPU have elapsed, provided parallel section is complete<br />
; KILL FILE [FILENAME]<br />
: Kill Phaser if file FILENAME is present, provided parallel section is complete<br />
* Default: KILL TIME 0 ''Phaser runs to completion''<br />
* Detaulf: KILL FILE "" ''Phaser runs to completion''<br />
setKILL_TIME(float) <br />
setKILL_FILE(string)<br />
<br />
==[[Image:Output.png|link=]]OUTPUT== <br />
; OUTPUT LEVEL [SILENT|CONCISE|SUMMARY|LOGFILE|VERBOSE|DEBUG]<br />
: Output level for logfile<br />
; OUTPUT LEVEL [0|1|2|3|4|5]<br />
: Output level for logfile (equivalent to keyword level setting)<br />
* Default: OUTPUT LEVEL LOGFILE<br />
setOUTP_LEVE(string)<br />
setOUTP(enum)<br />
<br />
==[[Image:Output.png|link=]]TITLE==<br />
; TITLE <TITLE><br />
: Title for job<br />
* Default: TITLE [no title given]<br />
setTITL(str <TITLE>)<br />
<br />
==[[Image:Output.png|link=]]TOPFILES== <br />
; TOPFILES <NUM><br />
: Number of top pdbfiles or mtzfiles to write to output.<br />
* Default: TOPFILES 1<br />
setTOPF(int <NUM>) <br />
<br />
==[[Image:Output.png|link=]]ROOT== <br />
; ROOT <FILEROOT><br />
: Root filename for output files (e.g. FILEROOT.log)<br />
* Default: ROOT PHASER<br />
setROOT(string <FILEROOT>)<br />
<br />
==[[Image:Output.png|link=]]VERBOSE== <br />
; VERBOSE [ON|OFF] <br />
: Toggle to send verbose output to log file.<br />
* Default: VERBOSE OFF<br />
setVERB(bool) <br />
<br />
==[[Image:Output.png|link=]]XYZOUT== <br />
; XYZOUT [ON|OFF] ''ENSEMBLE [ON|OFF]<sup>1</sup> PACKING [ON|OFF]<sup>2</sup>''<br />
: Toggle for output coordinate files. <br />
::<sup>1</sup> If the optional ENSEMBLE keyword is ON, then each placed ensemble is written to its own pdb file. The files are named FILEROOT.#.#.pdb with the first # being the solution number and the second # being the number of the placed ensemble (representing a SOLU 6DIM entry in the .sol file). <br />
::<sup>2</sup> If the optional PACKING keyword is ON, then the hexagonal grid used for the packing analysis is output to its own pdb file FILEROOT.pak.pdb<br />
* Default: XYZOUT OFF (Rotation functions)<br />
* Default: XYZOUT ON ENSEMBLE OFF (all other relevant modes)<br />
* Default: XYZOUT ON PACKING OFF (all other relevant modes)<br />
setXYZO(bool) <br />
setXYZO_ENSE(bool)<br />
setXYZO_PACK(bool)<br />
<br><br />
<br><br />
<br />
=Advanced Keywords=<br />
==[[Image:User2.gif|link=]]ELLG==<br />
([[Molecular_Replacement#Should_Phaser_Solve_It.3F|explained here]])<br />
; ELLG TARGET <TARGET><br />
: Target value for expected LLG for determining resolution limits and search order<br />
<!--; ELLG HIRES <HIRES> Internal control only--><br />
* Default: ELLG TARGET 225<br />
setELLG_TARG(float <TARGET>)<br />
<br />
==[[Image:User2.gif|link=]]FORMFACTORS==<br />
; FORMFACTORS [XRAY | ELECTRON | NEUTRON]<br />
: Use scattering factors from x-ray, electron or neutrons<br />
* Default: FORMFACTORS XRAY<br />
setFORM(string XRAY)<br />
<br />
==[[Image:User2.gif|link=]]HAND==<br />
; HAND [ <sup>1</sup>ON| <sup>2</sup>OFF| <sup>3</sup>BOTH]<br />
: Hand of heavy atoms for experimental phasing<br />
: <sup>1</sup>Phase using the other hand of heavy atoms <br />
: <sup>2</sup>Phase using given hand of heavy atoms <br />
: <sup>3</sup>Phase using both hands of heavy atoms<br />
* Default: HAND BOTH<br />
setHAND(str [ "OFF" | "ON" | "BOTH" ])<br />
<br />
==[[Image:User2.gif|link=]]LLGCOMPLETE==<br />
; LLGCOMPLETE COMPLETE [ON|OFF]<br />
: Toggle for structure completion by log-likelihood gradient maps<br />
; LLGCOMPLETE SCATTERER <TYPE> <br />
: Atom/Cluster type(s) to be used for log-likelihood gradient completion. If more than one element is entered for log-likelihood gradient completion, the atom type that gives the highest Z-score for each peak is selected. Type = "RX" is a purely real scatterer and type="AX" is purely anomalous scatterer<br />
; LLGCOMPLETE REAL ON<br />
: Use a purely real scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER RX)<br />
; LLGCOMPLETE ANOMALOUS ON<br />
: Use a purely anomalous scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER AX)<br />
; LLGCOMPLETE CLASH <CLASH> <br />
: Minimum distance between atoms in log-likelihood gradient maps and also the distance used for determining anisotropy of atoms (default determined by resolution, flagged by CLASH=0)<br />
; LLGCOMPLETE SIGMA <Z><br />
: Z-score (sigma) for accepting peaks as new atoms in log-likelihood gradient maps<br />
; LLGCOMPLETE NCYC <NMAX><br />
: Maximum number of cycles of log-likelihood gradient structure completion. By default, NMAX is 50, but this limit should never be reached, because all features in the log-likelihood gradient maps should be assigned well before 50 cycles are finished. This keyword should be used to reduce the number of cycles to 1 or 2.<br />
; LLGCOMPLETE METHOD [IMAGINARY|ATOMTYPE]<br />
: Pick peaks from the imaginary map only or from all the completion atomtype maps.<br />
* Default: LLGCOMPLETE COMPLETE OFF<br />
* Default: LLGCOMPLETE CLASH 0<br />
* Default: LLGCOMPLETE SIGMA 6<br />
* Default: LLGComplete NCYC 50<br />
* Default: LLGComplete METHOD ATOMTYPE<br />
setLLGC_COMP(bool <True|False>) <br />
setLLGC_CLAS(float <CLASH>) <br />
setLLGC_SIGM(float <Z>) <br />
setLLGC_NCYC(int <NMAX>)<br />
setLLGC_METH(str ["IMAGINARY"|"ATOMTYPE"])<br />
<br />
==[[Image:User2.gif|link=]]NMA== <br />
; NMA MODE <M1> ''{MODE <M2>…}'' <br />
: The MODE keyword gives the mode along which to perturb the structure. If multiple modes are entered, the structure is perturbed along all the modes AND combinations of the modes given. There is no limit on the number of modes that can be entered, but the number of pdb files explodes combinatorially. The first 6 modes are the pure rotation and translation modes and do not lead to perturbation of the structure. If the number M is less than 7 then M is interpreted as the first M modes starting at 7, so for example, MODE 5 would give modes 7 8 9 10 11.<br />
; NMA COMBINATION <NMAX><br />
: Controls how many modes are present in any combination.<br />
* Default: NMA MODE 5<br />
* Default: NMA COMBINATION 2<br />
addNMA_MODE(int <MODE>) <br />
setNMA_COMB(int <NMAX>)<br />
<br />
==[[Image:User2.gif|link=]]PACK==<br />
; PACK SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>ALL ]<br />
: <sup>1</sup>Allow up to the PERCENT of sampling points to clash, considering only pairwise clashes <br />
: <sup>2</sup>Allow all solutions (no packing test)<br />
; PACK CUTOFF <PERCENT> <br />
: Limit on total number (or percent) of clashes <br />
; PACK QUICK [ON|OFF]<br />
: Packing check stops when ALLOWED_CLASHES or MAX_CLASHES is reached. However, all clashes are found when the solution has a high Z-score (see [[#ZSCORE | ZSCORE]]).<br />
; PACK COMPACT [ON|OFF]<br />
: Pack ensembles into a compact association (minimize distances between centres of mass for the addition of each component in a solution).<br />
; PACK KEEP HIGH TFZ [ON|OFF]<br />
: Solutions with high tfz (see [[#ZSCORE | ZSCORE]]) but that fail to pack are retained in the solution list. Set to true if SEARCH PRUNE ON (see [[#SEARCH | SEARCH]])<br />
* Default: PACK SELECT PERCENT<br />
* Default: PACK CUTOFF 5<br />
* Default: PACK COMPACT ON<br />
* Default: PACK QUICK ON<br />
* Default: PACK KEEP HIGH TFZ OFF<br />
* Default: PACK CONSERVATION DISTANCE 1,5<br />
setPACK_SELE(str ["PERCENT"|"ALL"]) <br />
setPACK_CUTO(float <ALLOWED_CLASHES>)<br />
setPACK_QUIC(bool)<br />
setPACK_KEEP_HIGH_TFZ(bool)<br />
setPACK_COMP(bool)<br />
<br />
==[[Image:User2.gif|link=]]PEAKS==<br />
; PEAKS TRA SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL] <br />
; PEAKS ROT SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL]<br />
: Peaks for individual rotation functions (ROT) or individual translation functions (TRA) satisfying selection criteria are saved. To be used for subsequent steps, peaks must also satisfy the overall [[#PURGE | PURGE]] selection criteria, so it will usually be appropriate to set only the PURGE criteria (which over-ride the defaults for the PEAKS criteria if not explicitly set). See [[Molecular_Replacement#How_to_Select_Peaks | How to Select Peaks]]<br />
: <sup>1</sup> Select peaks by taking all peaks over CUTOFF percent of the difference between the top peak and the mean value.<br />
: <sup>2</sup> Select peaks by taking all peaks with a Z-score greater than CUTOFF.<br />
: <sup>3</sup> Select peaks by taking top CUTOFF.<br />
: <sup>4</sup> Select all peaks.<br />
; PEAKS ROT CUTOFF <CUTOFF><br />
; PEAKS TRA CUTOFF <CUTOFF><br />
: Cutoff value for the rotation function (ROT) or translation function (TRA) peak selection criteria.<br />
: If selection is by percent and [[#PURGE | PURGE PERCENT]] is changed from the default, then the PEAKS percent value is set to the lower PURGE percent value.<br />
; PEAKS ROT CLUSTER [ON|OFF] <br />
; PEAKS TRA CLUSTER [ON|OFF]<br />
: Toggle selects clustered or unclustered peaks for rotation function (ROT) or translation function (TRA).<br />
; PEAKS ROT DOWN [PERCENT] <br />
: [[#SEARCH | SEARCH METHOD FAST]] only. Percentage to reduce rotation function cutoff if there is no TFZ over the zscore cutoff that determines a true solution (see [[#ZSCORE | ZSCORE]]) in first search.<br />
* Default: PEAKS ROT SELECT PERCENT<br />
* Default: PEAKS TRA SELECT PERCENT<br />
* Default: PEAKS ROT CUTOFF 75<br />
* Default: PEAKS TRA CUTOFF 75<br />
* Default: PEAKS ROT CLUSTER ON<br />
* Default: PEAKS TRA CLUSTER ON<br />
setPEAK_ROTA_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"]) <br />
setPEAK_TRAN_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"])<br />
setPEAK_ROTA_CUTO(float <CUTOFF>)<br />
setPEAK_TRAN_CUTO(float <CUTOFF>) <br />
setPEAK_ROTA_CLUS(bool <CLUSTER>) <br />
setPEAK_TRAN_CLUS(bool <CLUSTER>)<br />
setPEAK_ROTA_DOWN(float <PERCENT>)<br />
<br />
==[[Image:User2.gif|link=]]PERMUTATIONS== <br />
; PERMUTATIONS [ON|OFF]<br />
: Only relevant to [[#SEARCH | SEARCH METHOD FULL]]. Toggle for whether the order of the search set is to be permuted.<br />
* Default: PERMUTATIONS OFF<br />
setPERM(bool <PERMUTATIONS>)<br />
<br />
==[[Image:User2.gif|link=]]PERTURB== <br />
; PERTURB RMS STEP <RMS><br />
: Increment in rms Ångstroms between pdb files to be written. <br />
; PERTURB RMS MAX <MAXRMS><br />
: The structure will be perturbed along each mode until the MAXRMS deviation has been reached.<br />
; PERTURB RMS DIRECTION [FORWARD|BACKWARD|TOFRO] <br />
: The structure is perturbed either forwards or backwards or to-and-fro (FORWARD|BACKWARD|TOFRO) along the eigenvectors of the modes specified.<br />
; PERTURB INCREMENT [RMS| DQ] <br />
: Perturb the structure by rms devitations along the modes, or by set dq increments<br />
; PERTURB DQ <DQ1> ''{DQ <DQ2>…}''<br />
: Alternatively, the DQ factors (as used by the Elnemo server (K. Suhre & Y-H. Sanejouand, NAR 2004 vol 32) ) by which to perturb the atoms along the eigenvectors can be entered directly.<br />
* Default: PERTURB INCREMENT RMS<br />
* Default: PERTURB RMS STEP 0.2<br />
* Default: PERTURB RMS MAXRMS 0.3<br />
* Default: PERTURB RMS DIRECTION TOFRO<br />
setPERT_INCR(str [ "RMS" | "DQ" ])<br />
setPERT_RMS_MAXI(float <MAX>)<br />
setPERT_RMS_DIRE(str [ "FORWARDS" | "BACKWARDS" | "TOFRO" ]) <br />
addPERT_DQ(float <DQ>)<br />
<br />
==[[Image:User2.gif|link=]]PURGE== <br />
; PURGE ROT ENABLE [ON|OFF]<sup>1</sup><br />
; PURGE ROT PERCENT <PERC><sup>2</sup><br />
; PURGE ROT NUMBER <NUM><sup>3</sup><br />
: Purging criteria for rotation function (RF), where PERCENT and NUMBER are alternative selection criteria (''OR'' criteria)<br />
::<sup>1</sup> Toggle for whether to purge the solution list from the RF according to the top solution found. If there are a number of RF searches with different partial solution backgrounds, the PURGE is applied to the total list of peaks. If there is one clearly significant RF solution from one of the backgrounds it acts to purge all the less significant solutions. If there is only one RF (a single partial solution background) the PURGE gives no additional selection over and above the PEAKS command. <br />
::<sup>2</sup> [[Molecular_Replacement#How_to_Select_Peaks | Selection by percent]]. PERC is percentage of the top peak, where the value of the top peak is defined as 100% and the value of the mean is defined as 0%. Note that this criterion is applied subsequent to any selection criteria applied through the [[#PEAKS | PEAKS]] command. If the [[#PEAKS | PEAKS]] selection is by percent, then the percent cutoff given in the PURGE command over-rides that for [[#PEAKS | PEAKS]], so as to rationalize results in the case of only a single RF (single partial solution background.)<br />
::<sup>3</sup> NUM is the number of solutions to retain in purging. If NUMBER is given (non-zero) it overrides the PERCENT option. NUMBER given as zero is the flag for not applying this criterion.<br />
; PURGE TRA ENABLE [ON|OFF]<br />
; PURGE TRA PERCENT <PERC><br />
; PURGE TRA NUMBER <NUM><br />
: As above, but for translation function<br />
; PURGE RNP ENABLE [ON|OFF]<br />
; PURGE RNP PERCENT <PERC><br />
; PURGE RNP NUMBER <NUM><br />
: As above but for refinement, but with the important distinction that PERCENT and NUMBER are concurrent selection criteria (''AND'' criteria)<br />
* Default: PURGE ROT ENABLE ON <br />
* Default: PURGE ROT PERC 75<br />
* Default: PURGE ROT NUM 0<br />
* Default: PURGE TRA ENABLE ON<br />
* Default: PURGE TRA PERC 75<br />
* Default: PURGE TRA NUM 0<br />
* Default: PURGE RNP ENABLE ON<br />
* Default: PURGE RNP PERC 75<br />
* Default: PURGE RNP NUM 0<br />
setPURG_ROTA_ENAB(bool <ENABLE>)<br />
setPURG_TRAN_ENAB(bool <ENABLE>) <br />
setPURG_RNP_ENAB(bool <ENABLE>)<br />
setPURG_ROTA_PERC(float <PERC>) <br />
setPURG_TRAN_PERC(float <PERC>) <br />
setPURG_RNP_PERC(float <PERC>)<br />
setPURG_ROTA_NUMB(float <NUM>) <br />
setPURG_TRAN_NUMB(float <NUM>)<br />
setPURG_TRAN_NUMB(float <NUM>)<br />
setPURG_RNP_NUMB(float <NUM>)<br />
<br />
==[[Image:User2.gif|link=]]RESOLUTION== <br />
; RESOLUTION HIGH <HIRES> <br />
: High resolution limit in Ångstroms. <br />
; RESOLUTION LOW <LORES><br />
: Low resolution limit in Ångstroms.<br />
; RESOLUTION AUTO HIGH <HIRES> <br />
: High resolution limit in Ångstroms for final high resolution refinement in MR_AUTO mode.<br />
* Default for molecular replacement: Set by [[#ELLG | ELLG TARGET]] for structure solution, final refinement uses all data<br />
* Default for experimental phasing: All data used<br />
setRESO_HIGH(float <HIRES>) <br />
setRESO_LOW(float <LORES>)<br />
setRESO_AUTO_HIGH(float <HIRES>) <br />
setRESO(float <HIRES>,float <LORES>)<br />
<br />
==[[Image:User2.gif|link=]]ROTATE== <br />
; ROTATE VOLUME FULL<br />
: Sample all unique angles <br />
; ROTATE VOLUME AROUND EULER <A> <nowiki><B></nowiki> <C> RANGE <RANGE> <br />
: Restrict the search to the region of +/- RANGE degrees around orientation given by EULER<br />
setROTA_VOLU(string ["FULL"|"AROUND"|) <br />
setROTA_EULE(dvect3 <A B C>) <br />
setROTA_RANG(float <RANGE>)<br />
<br />
==[[Image:User2.gif|link=]]SCATTERING==<br />
; SCATTERING TYPE <TYPE> FP=<FP> FDP=<FDP> FIX [ON|OFF|EDGE]<br />
: Measured scattering factors for a given atom type, from a fluorescence scan. FIX EDGE (default) fixes the fdp value if it is away from an edge, but refines it if it is close to an edge, while FIX ON or FIX OFF does not depend on proximity of edge.<br />
; SCATTERING RESTRAINT [ON|OFF]<br />
: use Fdp restraints<br />
; SCATTERING SIGMA <SIGMA><br />
: Fdp restraint sigma used is SIGMA multiplied by initial fdp value<br />
* Default: SCATTERING SIGMA 0.2<br />
* Default: SCATTERING RESTRAINT ON<br />
addSCAT(str <TYPE>,float <FP>,float <FDP, string <FIXFDP>) <br />
setSCAT_REST(bool) <br />
setSCAT_SIGM(float <SIGMA>)<br />
<br />
==[[Image:User2.gif|link=]]SCEDS== <br />
; SCEDS NDOM <NDOM><br />
:Number of domains into which to split the protein<br />
; SCEDS WEIGHT SPHERICITY <WS><br />
: Weight factor for the the Density Test in the SCED Score. The Sphericity Test scores boundaries that divide the protein into more spherical domains more highly.<br />
; SCEDS WEIGHT CONTINUITY <WC><br />
: Weight factor for the the Continuity Test in the SCED Score. The Continuity Test scores boundaries that divide the protein into domains contigous in sequence more highly. <br />
; SCEDS WEIGHT EQUALITY <WE><br />
: Weight factor for the the Equality Test in the SCED Score. The Equality Test scores boundaries that divide the protein more equally more highly.<br />
; SCEDS WEIGHT DENSITY <WD><br />
: Weight factor for the the Equality Test in the SCED Score. The Density Test scores boundaries that divide the protein into domains more densely packed with atoms more highly. <br />
* Default: SCEDS NDOM 2<br />
* Default: SCEDS WEIGHT EQUALITY 1<br />
* Default: SCEDS WEIGHT SPHERICITY 4 <br />
* Default: SCEDS WEIGHT DENSITY 1<br />
* Default: SCEDS WEIGHT CONTINUITY 0<br />
setSCED_NDOM(int <NDOM>) <br />
setSCED_WEIG_SPHE(float <WS>) <br />
setSCED_WEIG_CONT(float <WC>)<br />
setSCED_WEIG_EQUA(float <WE>) <br />
setSCED_WEIG_DENS(float <WD>)<br />
<br />
==[[Image:User2.gif|link=]]TARGET==<br />
; TARGET ROT [FAST | BRUTE]<br />
: Target function for fast rotation searches (2). BRUTE searches all angles on a grid with the full rotation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these rotations with the full rotation likelihood target.<br />
; TARGET TRA [FAST | BRUTE | PHASED]<br />
: Target function for fast translation searches (3). BRUTE searches all positions on a grid with the full translation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these positions with the full translation likelihood target. PHASED selects the "phased translation function", for which a LABIN command should also be given, specifying FMAP, PHMAP and (optionally) FOM.<br />
* Default: TARGET ROT FAST<br />
* Default: TARGET TRA FAST<br />
setTARG_ROTA(str ["FAST"|"BRUTE"])<br />
setTARG_TRAN(str ["FAST"|"BRUTE"|"PHASED"])<br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS NMOL <NMOL><br />
: Number of molecules/molecular assemblies related by single TNCS vector (usually only 2). If the TNCS is a pseudo-tripling of the cell then NMOL=3, a pseudo-quadrupling then NMOL=4 etc.<br />
* Default: TNCS NMOL 2<br />
setTNCS_NMOL(int <NMOL>)<br />
<br><br />
<br />
==[[Image:User2.gif|link=]]TRANSLATION== <br />
; TRANSLATION VOLUME [ <sup>1</sup>FULL | <sup>2</sup>REGION | <sup>3</sup>LINE | <sup>4</sup>AROUND ])<br />
: Search volume for brute force translation function.<br />
: <sup>1</sup> Cheshire cell or Primitive cell volume. <br />
: <sup>2</sup> Search region.<br />
: <sup>3</sup> Search along line. <br />
: <sup>4</sup> Search around a point.<br />
; <sup>1 2 3</sup>TRANSLATION START <X Y Z> <br />
; <sup>1 2 3</sup>TRANSLATION END <X Y Z><br />
: Search within region or line bounded by START and END.<br />
; <sup>4</sup>TRANSLATION POINT <X Y Z><br />
; <sup>4</sup>TRANSLATION RANGE <RANGE><br />
: Search within +/- RANGE Ångstroms (not fractional coordinates, even if the search point is given as fractional coordinates) of a point <X Y Z>.<br />
; TRANSLATION [ORTH | FRAC]<br />
: Coordinates are given in orthogonal or fractional values.<br />
; TRANSLATION PACKING USE [ON | OFF]<br />
: Top translation function peak will be testes for packing.<br />
; TRANSLATION PACKING CUTOFF <PERC><br />
: Percent pairwise packing used for packing function test of top TF peak. Equivalent to PACK CUTOFF <PERC> for packing function. <br />
; TRANSLATION PACKING NUM <NUM><br />
: Number of translation function peaks to test for packing before bailing out of packing test. Set to 0 to pack all translation function peaks (slow for large packing volumes). <br />
* Default: TRANSLATION VOLUME FULL<br />
* Default: TRANSLATION PACK CUTOFF 50<br />
* Default: TRANSLATION PACK NUM 0 (helices - all packing checked)<br />
* Default: TRANSLATION PACK NUM 500 (non-helices)<br />
setTRAN_VOLU(string ["FULL"|"REGION"|"LINE"|"AROUND"])<br />
setTRAN_START(dvect <START>)<br />
setTRAN_END(dvect <END>)<br />
setTRAN_POINT(dvect <POINT>)<br />
setTRAN_RANGE(float <RANGE>)<br />
setTRAN_FRAC(bool <True=FRAC False=ORTH>)<br />
setTRAN_PACK_USE(bool)<br />
setTRAN_PACK_CUTO(float)<br />
<br />
==[[Image:User2.gif|link=]]ZSCORE== <br />
; ZSCORE USE [ON|OFF]<br />
: Use the TFZ tests. Only applicable with [[#SEARCH | SEARCH METHOD FAST]]. (Note Phaser-2.4.0 and below use "ZSCORE SOLVED 0" to turn off the TFZ tests)<br />
; ZSCORE SOLVED <ZSCORE_SOLVED><br />
: Set the minimum TFZ that indicates a definite solution for amalgamating solutions in FAST search method. <br />
;ZSCORE STOP [ON|OFF]<br />
: Stop adding components beyond point where TFZ is below cutoff when adding multiple components in FAST mode. However, FAST mode will always add one component even if TFZ is below cutoff, or two components if starting search with no components input (no input solution).<br />
; ZSCORE HALF [ON|OFF]<br />
: Set the TFZ for amalgamating solutions in the FAST search method to the maximum of ZSCORE_SOLVED and half the maximum TFZ, to accommodate cases of partially correct solutions in very high TFZ cases (e.g. TFZ > 16)<br />
* Default: ZSCORE USE ON<br />
* Default: ZSCORE SOLVED 8<br />
* Default: ZSCORE HALF ON<br />
* Default: ZSCORE STOP ON<br />
setZSCO_USE(bool <True=ON False=OFF>)<br />
setZSCO_SOLV(floatType ZSCORE_SOLVED)<br />
setZSCO_HALF(bool <True=ON False=OFF>)<br />
setZSCO_STOP(bool <True=ON False=OFF>)<br />
<br><br />
<br><br />
<br />
=Expert Keywords=<br />
<br />
==[[Image:Expert.gif|link=]]MACANO== <br />
; MACANO PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for the refinement of SigmaN in the anisotropy correction<br />
; MACANO ANISO [ON|OFF] BINS [ON|OFF] SOLK [ON|OFF] SOLB [ON|OFF] ''{NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}''<br />
: Macrocycle for the custom refinement of SigmaN in the anisotropy correction. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACANO PROTOCOL DEFAULT<br />
setMACA_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACA(bool <ANISO>,bool <BINS>,bool <SOLK>,bool <SOLB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACMR== <br />
; MACMR PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACMR ROT [ON|OFF] TRA [ON|OFF] BFAC [ON|OFF] VRMS [ON|OFF] ''CELL [ON|OFF] LAST [ON|OFF] NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of molecular replacement solutions. Macrocycles are performed in the order in which they are entered. For description of VRMS see the [[FAQ]]. CELL is the scale factor for the unit cell for maps (EM maps). LAST is a flag that refines the parameters for the last component of a solution only, fixing all the others.<br />
; MACMR CHAINS [ON|OFF]<br />
: Split the ensembles into chains for refinement<br />
: Not possible as part of an automated mode<br />
* Default: MACMR PROTOCOL DEFAULT<br />
* Default: MACMR CHAINS OFF<br />
setMACM_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACM(bool <ROT>,bool <TRA>,bool <BFAC>,bool <VRMS>,bool <CELL>,bool <LAST>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
setMACM_CHAI(bool])<br />
<br />
==[[Image:Expert.gif|link=]]MACOCC== <br />
; MACOCC PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACOCC NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of occupancy for solutions. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACOCC PROTOCOL DEFAULT<br />
setMACO_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACO(int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACSAD== <br />
; MACSAD PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for SAD refinement.<br />
:''n.b. PROTOCOL ALL will crash phaser and is only useful for debugging - see code for details''<br />
; MACSAD XYZ [ON|OFF] OCC [ON|OFF] BFAC [ON|OFF] FDP [ON|OFF] SA [ON|OFF] SB [ON|OFF] SP [ON|OFF] SD [ON|OFF] ''{PK [ON|OFF]} {PB [ON|OFF]} {NCYCLE <NCYC>} MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for SAD refinement. Macrocycles are performed in the order in which they are entered.<br />
*Default: MACSAD PROTOCOL DEFAULT<br />
setMACS_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACS(<br />
bool <XYZ>,bool <OCC>,bool <BFAC>,bool <FDP><br />
bool <SA>,bool <SB>,bool <SP>,bool <SD>,<br />
bool <PK>, bool <PB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACTNCS== <br />
; MACTNCS PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for pseudo-translational NCS refinement.<br />
; MACTNCS ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] ''NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for pseudo-translational NCS refinement. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACTNCS PROTOCOL DEFAULT<br />
setMACT_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACT(bool <ROT>,bool <TRA>,bool <VRMS>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]OCCUPANCY== <br />
; OCCUPANCY WINDOW ELLG <ELLG><br />
: Target eLLG for determining number of residues in window for occupancy refinement. The number of residues in a window will be an odd number. Occupancy refinement will be done for each offset of the refinement window.<br />
; OCCUPANCY WINDOW NRES <NRES><br />
: As an alternative to using the eLLG to define the number of residues in window for occupancy refinement, the number may be input directly. NRES must be an odd number.<br />
; OCCUPANCY WINDOW MAX <NRES><br />
: Maximum number of residues in an occupancy window (determined either by ellg or given as NRES) for which occupancy is refined. Prevents the refinement windows from spanning non-local regions of space.<br />
; OCCUPANCY MIN <MINOCC> MAX <MAXOCC><br />
: Minimum and maximum values of occupancy during refinement.<br />
; OCCUPANCY MERGE [ON/OFF]<br />
: Merge refined occupancies from different window offsets to give final occupancies per residue. If OFF, occupancies from a single window offset will be used, selected using OCCUPANCY OFFSET <N><br />
; OCCUPANCY FRAC <FRAC><br />
: Minimum fraction of the protein for which the occupancy may be set to zero.<br />
; OCCUPANCY OFFSET <N><br />
: If OCCUPANCY MERGE OFF, then <N> defines the single window offset from which final occupancies will be taken<br />
* Default: OCCUPANCY WINDOW ELLG 5<br />
* Default: OCCUPANCY WINDOW MAX 111<br />
* Default: OCCUPANCY MIN 0.01 MAX 1<br />
* Default: OCCUPANCY NCYCLES 1<br />
* Default: OCCUPANCY MERGE ON<br />
* Default: OCCUPANCY FRAC 0.5<br />
* Default: OCCUPANCY OFFSET 0<br />
setOCCU_WIND_ELLG(float <ELLG>)<br />
setOCCU_WIND_NRES(int <NRES>)<br />
setOCCU_WIND_MAX(int <NRES>)<br />
setOCCU_MIN(float <MIN>)<br />
setOCCU_MAX(float <MAX>)<br />
setOCCU_MERG(float <FRAC>)<br />
setOCCU_FRAC(bool)<br />
setOCCU_OFFS(int <N>)<br />
<br />
==[[Image:Expert.gif|link=]]RESCORE== <br />
; RESCORE ROT [ON|OFF]<br />
; RESCORE TRA [ON|OFF]<br />
: Toggle for rescoring of fast rotation function (ROT) or fast translation function (TRA) search peaks. <br />
* Default: RESCORE ROT ON<br />
* Default: RESCORE TRA ON|OFF will depend on whether phaser is running in the mode [[#MODE | MODE MR_AUTO]] with [[#SEARCH | SEARCH METHOD FAST]] or with [[#SEARCH | SEARCH METHOD FULL]], or running the translation function separately [[#MODE | MODE MR_FTF]]. For [[#SEARCH | SEARCH METHOD FAST]] the default also depends on whether or not the expected LLG target [[#ELLG | ELLG TARGET <TARGET>]] value is reached.<br />
setRESC_ROTA(bool)<br />
setRESC_TRAN(bool)<br />
<br />
==[[Image:Expert.gif|link=]]RFACTOR== <br />
; RFACTOR USE [ON|OFF]<br />
: For cases of searching for one ensemble when there is one ensemble in the asymmetric unit, the R-factor for the ensemble at the orientation and position in the input is calculated. If this value is low then MR is not performed in the MR_AUTO job in FAST search mode. Instead, rigid body refinement is performed before exiting. Note that the same R-factor test and cutoff is used for judging success in single-atom molecular replacement (MR_ATOM mode).<br />
; RFACTOR CUTOFF <VALUE><br />
: Rfactor in percent used as cutoff for deciding whether or not the R-factor indicates that MR is not necessary.<br />
* Default: RFACTOR USE ON CUTOFF 35<br />
setRFAC_USE(bool)<br />
setRFAC_CUTO(float <PERCENT>)<br />
<br />
==[[Image:Expert.gif|link=]]SAMPLING==<br />
; SAMPLING ROT <SAMP><br />
; SAMPLING TRA <SAMP><br />
: Sampling of search given in degrees for a rotation search and Ångstroms for a translation search. Sampling for rotation search depends on the mean radius of the Ensemble and the high resolution limit (dmin) of the search.<br />
* Default: SAMP = 2*atan(dmin/(4*meanRadius)) (ROTATION FUNCTION)<br />
* Default: SAMP = dmin/5; (BRUTE TRANSLATION FUNCTION)<br />
* Default: SAMP = dmin/4; (FAST TRANSLATION FUNCTION)<br />
setSAMP_ROTA(float <SAMP>)<br />
setSAMP_TRAN(float <SAMP>)<br />
<br><br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS USE [ON|OFF]<br />
: Use TNCS if present: apply TNCS corrections. (Note: was TNCS IGNORE [ON|OFF] in Phaser-2.4.0)<br />
; TNCS RLIST ADD [ON | OFF]<br />
: Supplement the rotation list used in the translation function with rotations already present in the list of known solutions. New molecules in the same orientation as those in the known search (as occurs with translational ncs) may not have peaks associated with them from the rotation function because the known molecules mask the presence of the ones not yet found. <br />
; TNCS PATT HIRES <hires><br />
: High resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT LORES <lores><br />
: Low resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT PERCENT <percent><br />
: Percent of origin Patterson peak that qualifies as a TNCS vector<br />
; TNCS PATT DISTANCE <distance><br />
: Minimum distance of Patterson peak from origin that qualifies as a TNCS vector<br />
; TNCS TRANSLATION PERTURB [ON | OFF]<br />
: If the TNCS translation vector is on a special position, perturb the vector from the special position before refinement<br />
; TNCS ROTATION RANGE <angle><br />
: Maximum deviation from initial rotation from which to look for rotational deviation. Default uses internally determined value based on resolution of data and size of G-function effective molecular radius. Value of 0 turns rotational refinement off.<br />
; TNCS ROTATION SAMPLING <sampling><br />
: Sampling for rotation search. Default uses internally determined value based on resolution of data and size of G-function effective molecular radius. Value of 0 turns rotational refinement off.<br />
* Default: TNCS USE ON<br />
* Default: TNCS RLIST ADD ON<br />
* Default: TNCS PATT HIRES 5<br />
* Default: TNCS PATT LORES 10<br />
* Default: TNCS PATT PERCENT 20<br />
* Default: TNCS PATT DISTANCE 15 <br />
* Default: TNCS TRANSLATION PERTURB ON<br />
setTNCS_USE(bool)<br />
setTNCS_RLIS_ADD(bool)<br />
setTNCS_PATT_HIRE(float <HIRES>)<br />
setTNCS_PATT_LORE(float <LORES>) <br />
setTNCS_PATT_PERC(float <PERCENT>) <br />
setTNCS_PATT_DIST(float <DISTANCE>)<br />
setTNCS_TRAN_PERT(bool)<br />
setTNCS_ROTA_RANG(float <RANGE>) <br />
setTNCS_ROTA_SAMP(float <SAMPLING>) <br />
<br><br />
<br><br />
<br />
=Developer Keywords=<br />
==[[Image:Developer.gif|link=]]BINS== <br />
; BINS DATA [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the data.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections<br />
; BINS ENSE [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]<br />
: The binning of the calaculated structure factos for the ensembles.<br />
: <sup>1</sup> L = minimum number of bins<br />
: <sup>2</sup> H = maximum number of bins.<br />
: <sup>3</sup> W = width of the bins in number of reflections<br />
* Default: BINS DATA MIN 6 MAX 50 WIDTH 500 <br />
* Default: BINS ENSE MIN 6 MAX 1000 WIDTH 1000 <br />
setBINS_DATA_MINI(float <L>)<br />
setBINS_DATA_MAXI(float <H>)<br />
setBINS_DATA_WIDT(float <W>)<br />
setBINS_ENSE_MINI(float <L>)<br />
setBINS_ENSE_MAXI(float <H>)<br />
setBINS_ENSE_WIDT(float <W>)<br />
<br />
==[[Image:Developer.gif|link=]]BFACTOR==<br />
; BFACTOR WILSON RESTRAINT [ON|OFF]<br />
: Toggle to use the Wilson restraint on the isotropic component of the atomic B-factors in SAD phasing.<br />
; BFACTOR SPHERICITY RESTRAINT [ON|OFF] <br />
: Toggle to use the sphericity restraint on the anisotropic B-factors in SAD phasing<br />
; BFACTOR REFINE RESTRAINT [ON|OFF] <br />
: Toggle to use the restraint to zero for the molecular B-factor in molecular replacement.<br />
; BFACTOR WILSON SIGMA <SIGMA><br />
: The sigma of the Wilson restraint.<br />
; BFACTOR SPHERICITY SIGMA <SIGMA><br />
: The sigma of the sphericity restraint.<br />
; BFACTOR REFINE SIGMA <SIGMA><br />
: The sigma of the restraint to zero for the molecular B-factor in molecular replacement.<br />
* Default: BFACTOR WILSON RESTRAINT ON <br />
* Default: BFACTOR SPHERICITY RESTRAINT ON <br />
* Default: BFACTOR REFINE RESTRAINT ON <br />
* Default: BFACTOR WILSON SIGMA 5<br />
* Default: BFACTOR SPHERICITY SIGMA 5<br />
* Default: BFACTOR REFINE SIGMA 6<br />
setBFAC_WILS_REST(bool <True|False>)<br />
setBFAC_SPHE_REST(bool <True|False>)<br />
setBFAC_REFI_REST(bool <True|False>) <br />
setBFAC_WILS_SIGM(float <SIGMA>) <br />
setBFAC_SPHE_SIGM(float <SIGMA>) <br />
setBFAC_REFI_SIGM(float <SIGMA>)<br />
<br />
==[[Image:Developer.gif|link=]]BOXSCALE==<br />
; BOXSCALE <BOXSCALE><br />
: Scale for box for calculating structure factors. The ensembles are put in a box equal to (extent of molecule)*BOXSCALE<br />
* Default: BOXSCALE 4<br />
setBOXS<float <BOXSCALE>)<br />
<br />
==[[Image:Developer.gif|link=]]CELL==<br />
; <span style="color:darkorange">Python Only</span> <br />
: Unit cell dimensions<br />
* Default: Cell read from MTZ file<br />
setCELL(float <A>,float <nowiki><B></nowiki>,float <C>,float <ALPHA>,float <BETA>,float <GAMMA>)<br />
setCELL6(float_array <A B C ALPHA BETA GAMMA>)<br />
<br />
==[[Image:Developer.gif|link=]]COMPOSITION== <br />
; COMPOSITION MIN SOLVENT <PERC><br />
: Minimum solvent to give maximum asu packing volume for automated search copy determination (NUM 0)<br />
* Default: COMPOSITION MIN SOLVENT 0.2<br />
setCOMP_MIN_SOLV(float)<br />
<br />
==[[Image:Developer.gif|link=]]DDM== <br />
; DDM SLIDER <VAL> <br />
: The SLIDER window width is used to smooth the Difference Distance Matrix. <br />
; DDM DISTANCE MIN <VAL> MAX <VAL> STEP <VAL><br />
: The range and step interval, as the fraction of the difference between the lowest and highest DDM values used to step.<br />
; DDM SEPARATION MIN <VAL> MAX <VAL><br />
: Through space separation in Angstroms used.<br />
; DDM SEQUENCE MIN <VAL> MAX <VAL><br />
: The range of sequence separations between matrix pairs.<br />
; DDM JOIN MIN <VAL> MAX <VAL><br />
: The range of lengths of the sequences to join if domain segments are discontinuous in percentages of the polypeptide chain.<br />
* Default: DDM SLIDER 0<br />
* Default: DDM DISTANCE MIN 1 MAX 5 STEP 50<br />
* Default: DDM SEPARATION MIN 7 MAX 14<br />
* Default: DDM SEQUENCE MIN 0 MAX 1<br />
* Default: DDM JOIN MIN 2 MAX 12<br />
setDDM_SLID(int <VAL>) <br />
setDDM_DIST_STEP(int <VAL>) <br />
setDDM_DIST_MINI(int <VAL>) <br />
setDDM_DIST_MAXI(int <VAL>) <br />
setDDM_SEPA_MINI(float <VAL>) <br />
setDDM_SEPA_MAXI(float <VAL>)<br />
setDDM_JOIN_MINI(int <VAL>) <br />
setDDM_JOIN_MAXI(int <VAL>) <br />
setDDM_SEQU_MINI(int <VAL>) <br />
setDDM_SEQU_MAXI(int <VAL>)<br />
<br />
==[[Image:Developer.gif|link=]]ENM== <br />
; ENM OSCILLATORS [ <sup>1</sup>RTB | <sup>2</sup>ALL ] <br />
: Define the way the atoms are used for the elastic network model.<br />
: <sup>1</sup>Use the rotation-translation block method.<br />
: <sup>2</sup>Use all atoms to determine the modes (only for use on very small molecules, less than 250 atoms). <br />
; ENM MAXBLOCKS <MAXBLOCKS><br />
: MAXBLOCKS is the number of rotation-translation blocks for the RTB analysis.<br />
; ENM NRES <NRES><br />
: For the RTB analysis, by default NRES=0 and then it is calculated so that it is as small as it can be without reaching MAXBlocks. <br />
; ENM RADIUS <RADIUS><br />
: Elastic Network Model interaction radius (Angstroms)<br />
; ENM FORCE <FORCE><br />
: Elastic Network Model force constant<br />
* Default: ENM OSCILLATORS RTB MAXBLOCKS 250 NRES 0 RADIUS 5 FORCE 1<br />
setENM_OSCI(str ["RTB"|"CA"|"ALL"])<br />
setENM_RTB_MAXB(float <MAXB>)<br />
setENM_RTB_NRES(float <NRES>) <br />
setENM_RADI(float <RADIUS>) <br />
setENM_FORC(float <FORCE>)<br />
<br />
==[[Image:Developer.gif|link=]]NORMALIZATION==<br />
; <span style="color:darkorange">Scripting Only</span><br />
; NORM EPSFAC WRITE <FILENAME><br />
: The normalization factors that correct for anisotropy in the data are written to BINARY file FILENAME<br />
; NORM EPSFAC READ <FILENAME><br />
: The normalization factors that correct for anisotropy in the data are read from BINARY file FILENAME. Further refinement is automatically turned off.<br />
; <span style="color:darkorange">Python Only</span><br />
The normalization factors that correct for anisotropy in the data, extracted from ResultANO object with getSigmaN(). Anisotropy should subsequently be turned off with setMACA_PROT("OFF").<br />
setNORM_DATA(data_norm <SIGMAN>)<br />
<br />
==[[Image:Developer.gif|link=]]OUTLIER==<br />
; OUTLIER REJECT [ON|OFF]<br />
: Reject low probability data outliers<br />
; OUTLIER PROB <PROB><br />
: Cutoff for rejection of low probablity outliers<br />
* Default: OUTLIER REJECT ON PROB 0.000001<br />
setOUTL_REJE(bool) <br />
setOUTL_PROB(float <PROB>)<br />
<br />
==[[Image:Developer.gif|link=]]PTGROUP== <br />
; PTGROUP COVERAGE <COVERAGE><br />
: Percentage coverage for two sequences to be considered in same pointgroup<br />
; PTGROUP IDENTITY <IDENTITY><br />
: Percentage identity for two sequences to be considered in same pointgroup<br />
; PTGROUP RMSD <RMSD><br />
: Percentage rmsd for two models to be considered in same pointgroup<br />
; PTGROUP TOLERANCE ANGULAR <ANG><br />
: Angular tolerance for pointgroup<br />
; PTGROUP TOLERANCE SPATIAL <DIST><br />
: Spatial tolerance for pointgroup<br />
setPTGR_COVE(float <COVERAGE>) <br />
setPTGR_IDEN(float <IDENTITY>) <br />
setPTGR_RMSD(float <RMSD>) <br />
setPTGR_TOLE_ANGU(float <ANG>) <br />
setPTGR_TOLE_SPAT(float <DIST>)<br />
<br />
==[[Image:Developer.gif|link=]]RESHARPEN== <br />
; RESHARPEN PERCENTAGE <PERC><br />
: Perecentage of the B-factor in the direction of lowest fall-off (in anisotropic data) to add back into the structure factors F_ISO and FWT and FDELWT so as to sharpen the electron density maps<br />
* Default: RESHARPEN PERCENT 100<br />
setRESH_PERC(float <PERCENT>)<br />
<br />
==[[Image:Developer.gif|link=]]SOLPARAMETERS==<br />
; SOLPARAMETERS SIGA FSOL <FSOL> BSOL <BSOL> MIN <MINSIGA><br />
: Babinet solvent parameters for Sigma(A) curves. MINSIGA is the minimum SIGA for Babinet solvent term (low resolution only). The solvent term in the Sigma(A) curve is given by <BR>max(1 - FSOL*exp(-BSOL/(4d^2)),MINSIGA).<br />
; SOLPARAMETERS BULK USE [ON|OFF]<br />
: Toggle for use of solvent mask scaling parameters for ensemble structure factors, applied to Fmask.<br />
; SOLPARAMETERS BULK FSOL <FSOL> BSOL <BSOL> <br />
: Solvent mask scaling parameters for ensemble structure factors, applied to Fmask.<br />
* Default: SOLPARAMETERS SIGA FSOL 1.05 BSOL 501 MIN 0.1<br />
* Default: SOLPARAMETERS SIGA RESTRAINT ON<br />
* Default: SOLPARAMETERS BULK USE OFF<br />
* Default: SOLPARAMETERS BULK FSOL 0.35 BSOL 45<br />
setSOLP_SIGA_FSOL(float <FSOL>) <br />
setSOLP_SIGA_BSOL(float <BSOL>)<br />
setSOLP_SIGA_MIN(float <MINSIGA>)<br />
setSOLP_BULK_USE(bool)<br />
setSOLP_BULK_FSOL(float <FSOL>) <br />
setSOLP_BULK_BSOL(float <BSOL>)<br />
<br />
==[[Image:Developer.gif|link=]]TARGET== <br />
; TARGET ROT FAST TYPE [LERF1 | CROWTHER]<br />
: Target function type for fast rotation searches<br />
; TARGET TRA FAST TYPE [LETF1 | LETF2 | CORRELATION]<br />
: Target function type for fast translation searches<br />
setTARG_ROTA_TYPE(string TYPE)<br />
setTARG_TRAN_TYPE(string TYPE)<br />
<br />
==[[Image:Developer.gif|link=]]TNCS==<br />
; TNCS ROTATION ANGLE <A> <nowiki><B></nowiki> <C><br />
: Input rotational difference between molecules related by the pseudo-translational symmetry vector, specified as rotations in degrees about x, y and z axes. Central value for grid search (RANGE > 0).<br />
; TNCS ROTATION RANGE <A><br />
: Range of angular difference in rotation angles to explore around central angle.<br />
; TNCS ROTATION SAMPLING <A><br />
: Sampling step for rotational grid search.<br />
; TNCS TRA VECTOR <x y z> <br />
: Input pseudo-translational symmetry vector (fractional coordinates). By default the translation is determined from the Patterson.<br />
; TNCS VARIANCE RMSD <num><br />
: Input estimated rms deviation between pseudo-translational symmetry vector related molecules.<br />
; TNCS VARIANCE FRAC <num><br />
: Input estimated fraction of cell content that obeys pseudo-translational symmetry.<br />
; TNCS LINK RESTRAINT [ON | OFF]<br />
: Link the occupancy of atoms related by TNCS in SAD phasing<br />
; TNCS LINK SIGMA <sigma><br />
: Sigma of link restraint of the occupancy of atoms related by TNCS in SAD phasing<br />
* Default: TNCS ROTATION ANGLE 0 0 0<br />
* Default: TNCS ROTATION RANGE -999 (determine from structure size and resolution)<br />
* Default: TNCS ROTATION SAMPLING -999 (determine from structure size and resolution)<br />
* Default: TNCS TRANSLATION VECTOR determined from position of Patterson peak<br />
* Default: TNCS VARIANCE RMSD 0.4 <br />
* Default: TNCS VARIANCE FRAC 1 <br />
* Default: TNCS LINK RESTRAINT ON<br />
* Default: TNCS LINK SIGMA 0.1<br />
setTNCS_ROTA_ANGL(dvect3 <A B C>) <br />
setTNCS_TRAN_VECT(dvect3 <X Y Z>) <br />
setTNCS_VARI_RMSD(float <RMSD>) <br />
setTNCS_VARI_FRAC(float <FRAC>)<br />
setTNCS_LINK_REST(bool)<br />
setTNCS_LINK_SIGM(float <SIGMA>)<br />
; <span style="color:darkorange">Scripting Only</span><br />
; TNCS EPSFAC WRITE <FILENAME><br />
: The normalization factors that correct for tNCS in the data are written to BINARY file FILENAME<br />
; TNCS EPSFAC READ <FILENAME><br />
: The normalization factors that correct for tNCS in the data are read from BINARY file FILENAME. Further refinement is automatically turned off.<br />
; <span style="color:darkorange">Python Only</span><br />
The normalization factors that correct for tNCS in the data, extracted from ResultNCS object with getPtNcs(). tNCS refinement should subsequently be turned off with setMACT_PROT("OFF").<br />
setTNCS(data_tncs <PTNCS>)<br />
<br />
==[[Image:Developer.gif|link=]]TRANSLATION== <br />
; TRANSLATION MAPS [ON | OFF]<br />
: Output maps of fast translation function FSS scoring functions<br />
: Maps take the names <ROOT>.<ensemble>.k.e.map where k is the Known backgound number and e is the Euler angle number for that known background<br />
* Default: TRANSLATION MAPS OFF<br />
setTRAN_MAPS(bool)</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Phaser-2.7.17:_Manual&diff=2393Phaser-2.7.17: Manual2016-11-29T15:40:39Z<p>Airlie: </p>
<hr />
<div><div style="margin-left: 25px; float: right;">__NOTOC__</div><br />
<br />
This is the documentation for Phaser&#8211;2.7.17 There are some changes between this version and previous versions so input scripts may need editing. <br />
<br />
:; [[ Modes | Modes]]<br />
:: The different functions that Phaser can perform <br />
:; [[ Keywords | Keywords]]<!--{{Oldid|1917|Keywords}}--><br />
:: Detailed descriptions of the keywords<br />
<br />
See also:<br />
:; [[Famos | Famos]]<br />
:: A python script for placing MR solutions on the same (common) origin</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Phaser-2.8:_Manual&diff=2392Phaser-2.8: Manual2016-11-29T15:40:27Z<p>Airlie: Created page with "<div style="margin-left: 25px; float: right;">__NOTOC__</div> This is the documentation for Phaser&#8211;2.8 There are some changes between this version and previous versions..."</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__NOTOC__</div><br />
<br />
This is the documentation for Phaser&#8211;2.8 There are some changes between this version and previous versions so input scripts may need editing. <br />
<br />
:; [[ Modes | Modes]]<br />
:: The different functions that Phaser can perform <br />
:; [[ Keywords | Keywords]]<!--{{Oldid|1917|Keywords}}--><br />
:: Detailed descriptions of the keywords<br />
<br />
See also:<br />
:; [[Famos | Famos]]<br />
:: A python script for placing MR solutions on the same (common) origin</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Manuals&diff=2391Manuals2016-11-29T15:35:25Z<p>Airlie: Add phaser 2.8 manual page</p>
<hr />
<div>The manuals for Phaser are in two sections<br />
;Modes<br />
: The different functions that Phaser can perform (e.g. automated MR, automated SAD). The number of modes increases as major new functionality is added.<br />
;Keywords<br />
: Detailed descriptions of the keywords. The keywords change significantly between versions. We attempt to keep backwards compatibility in the use and meaning of keywords between versions but this is not always possible. The ccp4i interface must be compatible with the keywords of the phaser version run. The ccp4-style keyword and phenix-style python input functions are described on the same page (''n.b.'' the manual pages for versions prior to Phaser-2.5 describe these on separate pages).<br />
<br />
The manual pages for versions prior to Phaser-2.5 also have information on XML output, which has been deprecated<br />
<br />
[[Image:Bug.png|link=]] See also: [[Bugs | Bugs]]<br />
<br />
<div style="margin-left: 25px; float: right;">__NOTOC__</div><br />
==Prerelease==<br />
*'''Phaser-2.8''' → [[Phaser-2.8: Manual | Manual]]<br />
<br />
==Currently Supported Releases==<br />
*'''Phaser-2.7.17''' → [[Phaser-2.7.17: Manual | Manual]]<br />
<br />
==Obsolete==<br />
*'''Phaser-2.6.0''' → [[Phaser-2.6.0: Manual | Manual]]<br />
*'''Phaser-2.5.6''' → [[Phaser-2.5.6: Manual | Manual]]<br />
*'''Phaser-2.5.5''' → [[Phaser-2.5.5: Manual | Manual]]<br />
*'''Phaser-2.5.4''' → [[Phaser-2.5.4: Manual | Manual]]<br />
*'''Phaser-2.5.3''' → [[Phaser-2.5.3: Manual | Manual]]<br />
*'''Phaser-2.5.2''' → [[Phaser-2.5.2: Manual | Manual]]<br />
<!-- *<span style="color:darkorange">''Under Construction'': </span>'''Phaser-2.5.3''' → [[Phaser: Manual | Manual]] --><br />
*'''Phaser-2.5.1''' → [[Phaser-2.5.1: Manual | Manual]]<br />
*'''Phaser-2.5''' → [[Phaser-2.5: Manual | Manual]]<br />
*'''Phaser-2.4''' → [[Phaser-2.4: Manual | Manual]]<br />
*'''Phaser-2.3''' → [[Phaser-2.3: Manual | Manual]]<br />
*'''Phaser-2.2''' → [[Phaser-2.2: Manual | Manual]]<br />
<br />
==Ancient==<br />
Versions older than Phaser-2.1 are located at the [http://www-structmed.cimr.cam.ac.uk/phaser/ '''obsolete Phaser website'''] <br />
* '''Phaser-2.1''' → [http://www-structmed.cimr.cam.ac.uk/phaser_obsolete/documentation/phaser-2.1.html Manual]<br />
* '''Phaser-2.0''' → [http://www-structmed.cimr.cam.ac.uk/phaser_obsolete/documentation/phaser-2.0.html Manual]<br />
* '''Phaser-1.3''' → [http://www-structmed.cimr.cam.ac.uk/phaser_obsolete/documentation/phaser-1.3.html Manual]<br />
* '''Phaser-1.4''' → [http://www-structmed.cimr.cam.ac.uk/phaser_obsolete/documentation/phaser-1.2.html Manual]</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Source_Code&diff=2388Source Code2016-11-28T16:56:02Z<p>Airlie: /* Repository */</p>
<hr />
<div>===Repository===<br />
<br />
A public [https://git.csx.cam.ac.uk/x/cimr-phaser//phaser.git Phaser git repository] is available for '''git clone''' and '''git pull''' only. This mirrors commits to the Phaser SVN respository in real time<br />
<br />
The [http://www-structmed.cimr.cam.ac.uk/svn-cgi-bin/viewvc.cgi/ Phaser SVN repository] is located in Cambridge on the CIMR server (password restricted)<br />
<br />
The Berkeley mirror at cci.lbl.gov is updated at midnight Berkeley time<br />
<br />
:/net/cci/auto_build/repositories/phaser<br />
<br />
===Access===<br />
<br />
*You can download nightly builds of Phenix (binaries), which contain the latest version of Phaser that has passed regression tests<br />
*You can compile code with real-time updates from the git repository. This code may not pass regression tests. The git repository is best used for obtaining instant bugfixes, after communication with one of the Phaser developers<br />
*If you are developing a pipeline using Phaser, we are keen to work with you to add features, fix bugs and help you use Phaser optimally<br />
*Note the University of Cambridge's [[ Licences | Licences for Phaser]] with regards to making Phaser part of a pipeline available online<br />
*Source code modifications are allowed under the University of Cambridge's [[ Licences | Licences for Phaser]], provided they are for internal use only. Distribution would require those changes to be incorporated into our SVN repository. <br />
<br />
===Full Access===<br />
<br />
*Requests for permission to commit to the SVN repository via SSH should emailed to [mailto:cimr-phaser@lists.cam.ac.uk phaser-help]</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Source_Code&diff=2384Source Code2016-11-28T11:40:09Z<p>Airlie: </p>
<hr />
<div>===Repository===<br />
<br />
A public [https://git.csx.cam.ac.uk/x/cimr-phaser//phaser.git Phaser git repository] is available for checkout only. This mirrors commits to the Phaser SVN respository in real time<br />
<br />
The [http://www-structmed.cimr.cam.ac.uk/svn-cgi-bin/viewvc.cgi/ Phaser SVN repository] is located in Cambridge on the CIMR server (password restricted)<br />
<br />
The Berkeley mirror at cci.lbl.gov is updated at midnight Berkeley time<br />
<br />
:/net/cci/auto_build/repositories/phaser<br />
<br />
===Access===<br />
<br />
*You can download nightly builds of Phenix (binaries), which contain the latest version of Phaser that has passed regression tests<br />
*You can compile code with real-time updates from the git repository. This code may not pass regression tests. The git repository is best used for obtaining instant bugfixes, after communication with one of the Phaser developers<br />
*If you are developing a pipeline using Phaser, we are keen to work with you to add features, fix bugs and help you use Phaser optimally<br />
*Note the University of Cambridge's [[ Licences | Licences for Phaser]] with regards to making Phaser part of a pipeline available online<br />
*Source code modifications are allowed under the University of Cambridge's [[ Licences | Licences for Phaser]], provided they are for internal use only. Distribution would require those changes to be incorporated into our SVN repository. <br />
<br />
===Full Access===<br />
<br />
*Requests for permission to commit to the SVN repository via SSH should emailed to [mailto:cimr-phaser@lists.cam.ac.uk phaser-help]</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=MediaWiki:Sidebar&diff=2383MediaWiki:Sidebar2016-11-28T11:08:04Z<p>Airlie: </p>
<hr />
<div>** Phaser Crystallographic Software | PhaserWiki Home<br />
** Releases | Releases<br />
** Downloads | Downloads<br />
** Manuals | Manuals<br />
** Tutorials | Tutorials<br />
** FAQ | FAQ<br />
** Top Ten Tips | Top Ten Tips<br />
** Publications | Publications<br />
** External Links | External Links<br />
*users<br />
** Molecular Replacement | MR Phasing<br />
** Experimental Phasing | SAD Phasing<br />
*developers<br />
** Python Interface | Python Interface<br />
** Contact | Contact Developers<br />
** Developers | Developer Pages<br />
** Licences | Licences<br />
** Source Code | Source Code</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Source_Code&diff=2381Source Code2016-11-28T11:07:05Z<p>Airlie: Airlie moved page SVN Repository to Source Code: SVN now also has git access</p>
<hr />
<div>===Code Development===<br />
<br />
Phaser code is open source. Code development is managed by [http://subversion.apache.org subversion] (SVN)<br />
<br />
; Pipeline Developers<br />
:If you are developing a pipeline using Phaser, please contact us for svn access so that we can work with you to add features and fix bugs.<br />
:Note the University of Cambridge's [[ Licences | Licences for Phaser]] <br />
<br />
; Advanced Users<br />
:If you want the latest version of Phaser, then you don't need svn access. You can download recent nightly builds of Phenix, which always contain the latest version of Phaser that has passed regression tests.<br />
:If you would like to be kept informed in real-time of changes to the Phaser source code we can give you permission to view the svn repository online (see below).<br />
<br />
; Source Code Developers<br />
:Source code modifications are allowed under the University of Cambridge's [[ Licences | Licences for Phaser]], provided they are for internal use only. Distribution would require those changes to be incorporated into our svn repository. Please email to [mailto:cimr-phaser@lists.cam.ac.uk phaser-help] for further advice if you would like to modify the Phaser source code.<br />
<br />
===Repository===<br />
The SVN repository for Phaser is located in Cambridge on the CIMR server<br />
;View the [http://www-structmed.cimr.cam.ac.uk/svn-cgi-bin/viewvc.cgi/ Phaser SVN repository] online<br />
<br />
:''Viewing the Phaser SVN respository online is password restricted in order to manage IT security. Please email requests for the password to [mailto:cimr-phaser@lists.cam.ac.uk phaser-help].''<br />
<br />
;SSH Access<br />
:Requests for permission to access to SVN repository at phaser-svn.cimr.cam.ac.uk through ssh should emailed to [mailto:cimr-phaser@lists.cam.ac.uk phaser-help].''<br />
<br />
===Mirrors===<br />
<br />
The Berkeley mirror at cci.lbl.gov is updated at midnight Berkeley time<br />
<br />
:/net/cci/auto_build/repositories/phaser</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=SVN_Repository&diff=2382SVN Repository2016-11-28T11:07:05Z<p>Airlie: Airlie moved page SVN Repository to Source Code: SVN now also has git access</p>
<hr />
<div>#REDIRECT [[Source Code]]</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Molecular_Replacement&diff=2380Molecular Replacement2016-11-28T11:03:05Z<p>Airlie: /* Translational Non-crystallographic Symmetry */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
'''Quicklink to example scripts''' → [[MR using keyword input]]<br />
<br />
'''Quicklink to phaser.famos (find_alt_orig_sym_mate) documentation''' → [[Famos]]<br />
<br />
Phaser should be able to solve most structures with the Automated Molecular Replacement mode, and this is the first mode that you should try. Give Phaser your data ([[#How to Define Data|How to Define Data]]) and your models ([[#How to Define Models|How to Define Models]]), tell Phaser what to search for, and a list of possible spacegroups (in the same point group).<br />
<br />
If this doesn't work (see [[#Has Phaser Solved It?| Has Phaser Solved It?]]), you can try selecting peaks of lower significance in the rotation function in case the real orientation was not within the selection criteria. By default peaks above 75% of the top peak are selected (see [[#How to Select Peaks| How to Select Peaks]]). See [[#What to do in Difficult Cases| What to do in Difficult Cases]] for more hints and tips. If the automated molecular replacement mode doesn't work even with non-default input you need to run the modes of Phaser separately. The possibilities are endless - you can even try exhaustive searches (translations of all orientations) if you want - but experience has shown that most structures that can be solved by Phaser can be solved by relatively simple strategies.<br />
<br />
==Automated Molecular Replacement==<br />
Automated Molecular Replacement combines the anisotropy correction, likelihood enhanced fast rotation function, likelihood enhanced fast translation function, packing and refinement modes for multiple search models and a set of possible spacegroups to automatically solve a structure by molecular replacement. Top solutions are output to the files FILEROOT.sol, FILEROOT.#.mtz and FILEROOT.#.pdb (where "#" refers to the sorted solution number, 1 being the best, and only 1 is output by default). Many structures can be solved by running an automated molecular replacement search with defaults, giving the ensembles that you expect to be easiest to find first.<br />
<br />
At the completion of Molecular Replacement you may wish to place your solutions on a common origin with a previous solution, for which [[Famos | Famos ]] can be used.<br />
<br />
[[Image:Phaser_MR_auto.gif|Flow Diagram for Automated MR]]<br />
<br />
==Should Phaser Solve It?==<br />
The difficulty of a molecular replacement problem depends primarily on two major factors: how well the model will be able to explain the diffraction data (which depends both on the accuracy of the model and on its completeness), and how many reflections can be explained, at least in part. Each reflection provides a piece of information that helps to identify correct MR solutions.<br />
<br />
It is possible to make a reasonable prediction of whether or not a solution will be found. If the quality of the model (its accuracy and completeness) can be estimated, then the expected contribution of each reflection to the total LLG can also be estimated. From a large battery of tests, we know that an LLG of 40 or greater usually indicates a correct solution (at least in the absence of complicating factors such as translational non-crystallographic symmetry, tNCS). Building on this understanding, if it is estimated that the LLG will be 60 or less, then Phaser will assume that the problem is a difficult one, and will implement search procedures optimised for difficult problems.<br />
<br />
==What Resolution of Data Should be Used?==<br />
The signal for a molecular replacement solution should be very clear if the expected value of the LLG is much higher than the minimum required to be fairly certain of a solution. Currently Phaser aims for a minimum LLG of 120 and, if it is possible to achieve an even higher value, given the quality of the model and the quantity of diffraction data, then the resolution for the initial search is limited to the value required to achieve an expected LLG of 120. Data to the full resolution are still used for a final rigid-body refinement, or in a second pass if a clear solution is not found in the first attempt.<br />
<br />
However, if the model is expected to have a large RMS error (based usually on the correlation between sequence identity and RMS error), then data to high resolution will not contribute any significant signal. Regardless of the expected LLG at the highest resolution limit, the resolution used is limited to 1.8 times the estimated RMS error of the model, because this resolution limit gives about 99% of the LLG that could be achieved.<br />
<br />
Because Phaser implements strategies designed to solve structures with as much confidence as possible, as efficiently as possible, it is best to leave the choice of resolution to Phaser, at least in the first instance.<br />
<br />
==Has Phaser Solved It?==<br />
{| class="wikitable" style="text-align:center" align="right" style="margin-left: 30px" <br />
|-<br />
! TF Z-score !! Have I solved it?<br />
|-<br />
| less than 5 || no<br />
|-<br />
| 5 - 6 || unlikely<br />
|-<br />
| 6 - 7 || possibly<br />
|-<br />
| 7 - 8 || probably<br />
|-<br />
| more than 8* ||definitely<br />
|-<br />
|colspan="2" style="text-align: center;" | *''6 for 1st model in monoclinic space groups''<br />
|} <br />
<br />
Ideally, a unique solution with a strong signal will be found at the end of the search. If you are searching for multiple components, then ideally the search for each component will also give a strong signal. However if the signal-to-noise of your search is low, there will be noise peaks and multiple ambiguous solutions. Signal-to-noise is judged using the '''Z-score''', which is computed by comparing the LLG values from the rotation or translation search with LLG values for a set of random rotations or translations. The mean and the RMS deviation from the mean are computed from the random set, then the Z-score for a search peak is defined as its LLG minus the mean, all divided by the RMS deviation, ''i.e. '' '''the number of standard deviations above (or below) the mean. '''<br />
<br />
For a rotation function, the correct orientation may be well down the list with a Z-score (number of standard deviations above the mean value, or RFZ) under 4, and it is often not possible to identify the correct orientation until a translation function is performed and yields a clear solution. Note that the signal-to-noise of the rotation function drops with increasing number of primitive symmetry operations (the number of different orientations for symmetry-related molecules), because there is more uncertainty about how the structure factor contributions from symmetry-related copies will add up.<br />
<br />
For a translation function the correct solution will generally have a Z-score (TFZ) over 5 and be well separated from the rest of the solutions. Of course, there will always be exceptions! The table gives a very rough guide to interpreting TFZ scores. This table will be updated, as we learn more from systematic molecular replacement trials.<br />
<br />
When you are searching for multiple components, the signal may be low for the first few components but, as the model becomes more complete, the signal should become stronger. Finding a clear solution for a new component is a good sign that the partial solution to which that component was added was indeed correct.<br />
<br />
You should always at least glance through the summary of the logfile. One thing to look for, in particular, is whether any translation solutions with a high Z-score have been rejected by the packing step. By default up to 5 percent of marker atoms (C-alpha atoms for protein) are allowed to be involved in clashes. A solution with more clashes may still be correct, and the clashes may arise only because of differences in small surface loops. If this happens, repeat the run allowing a suitable number of clashes. Note that, unless there is specific evidence in the logfile that a high TFZ-score solution is being rejected with a few clashes, it is much better to edit the model to remove the loops than to increase the number of allowed clashes. Packing criteria are a very powerful constraint on the translation function, and increasing the number of allowed clashes beyond the default will increase the search time enormously without the possibility of generating any correct solutions that would not have otherwise been found.<br />
<br />
Note that, by default, Phaser will produce a single PDB file corresponding to the top solution found (if any), so finding a single PDB file in your output directory is not an indication that the search succeeded! You have to look, at least, at the summary of the logfile, or at the list of possible solutions in the .sol file that is produced if you run Phaser from ccp4i or command-line scripts.<br />
<br />
==Annotation==<br />
<br />
A highly compact summary of the history of the statistics of a solution is given in the SOLUTION SET in the .sol file. This is a good place to start your analysis of the output. The annotation gives the Z-score of the solution at each rotation and translation function, the number of clashes in the packing, and the refined LLG.<br />
<br />
{| class="wikitable" style="text-align:center" style="margin-left: 30px" <br />
|-<br />
! Annotation !! Meaning<br />
|-<br />
| RFZ= || Rotation Function Z-score<br />
|-<br />
| TFZ= || Translation Function Z-score<br />
|-<br />
| PAK= || Number of packing clashes<br />
|-<br />
| LLG= || LLG after refinement. Will be repeated when a low resolution refinement is followed by a high resolution refinement.<br />
|-<br />
| TFZ== || Translation Function Z-score equivalent, only calculated for the top solution after refinement (or for the number of top files specified by TOPFILES)<br />
|-<br />
| RF++ || Rotation angle from previous strong solution has been used in the addition of next solution<br />
|-<br />
| RF*0 || Rotation angle 000 identified by low R-factor of input model<br />
|-<br />
| TFZ=* || First molecule in P1 (arbitrary origin, no Translation Function required)<br />
|-<br />
| TF*0 || Translation vector 000 identified by low R-factor of input model<br />
|-<br />
| (&&nbsp;... & ...) || Set of TFZ PAK and LLG values for placements that were amalgamated (more than one placement from a single Translation Function)<br />
|-<br />
| LLG+=(...&nbsp;&&nbsp;...)&nbsp;|| Set of LLG values calculated during amalgamation, which will always be increasing in value<br />
|-<br />
| +TNCS || Components added by Translational NCS relation<br />
|-<br />
| *T=<i>n</i> || Solution matches template solution <i>n</i><br />
|} <br />
<br />
Two versions of TFZ (the translation function Z-score) now appear for each component. The first ("TFZ=") is the Z-score from the actual translation search, which depends on the accuracy of the orientation used for that search. The second ("TFZ==") is the TFZ-equivalent, which indicates what the TFZ score would have been with the correct (refined) orientation. You should see the TFZ-equivalent is high at least for the final components of the solution, and that the LLG (log-likelihood gain) increases as each component of the solution is added. For example, in the case of beta-blip the annotation for the single solution output in the .sol file shows these features<br />
<br />
SOLU SET RFZ=10.7 TFZ=24.3 PAK=0 LLG=472 TFZ==24.7 RFZ=6.4 TFZ=24.4 PAK=0 LLG=1006 TFZ==29.7 LLG=1006 TFZ==29.7<br />
SOLU 6DIM ENSE beta EULER 200.849 41.269 183.909 FRAC -0.49604 -0.15830 -0.28092 BFAC 0.00000<br />
SOLU 6DIM ENSE blip EULER 43.749 80.793 117.292 FRAC -0.12289 0.29435 -0.09266 BFAC 0.00000<br />
<br />
Note that the Euler angles in Phaser follow the same convention as those defined for the Crowther fast rotation function, i.e. z-y-z (rotate around the z-axis, followed by the new y-axis, followed by the new z-axis).<br />
<br />
==History==<br />
<br />
A highly compact summary of the history of the peak positions of a solution is given in the SOLUTION HISTORY in the .sol file. Together with the SOLUTION SET annotation, this is useful in your analysis of the output. <br />
<br />
{| class="wikitable" style="text-align:center" style="margin-left: 30px" <br />
|-<br />
! History !! Meaning<br />
|-<br />
| RF/TF(r/t:n) || (r) Rotation Function peak number/(t) Translation Function peak number for the rotation function : (n) number of peak in final merged and sorted list<br />
|-<br />
| PAK(n:m) || (n) input solution number : (m) output solution number after packing condition applied<br />
|-<br />
| RNP(m,a,b,c,... : p) || All input peaks amalgamated after refinement to give output solution number (m and others): (p) output solution number<br />
|-<br />
| FUSE(A,B,C) || Solution numbers merged in amalgamation<br />
|} <br />
<br />
For example, in the case of beta-blip the annotation for the single solution output in the .sol file shows these features<br />
<br />
SOLU HISTORY RF/TF(1/1:1)PAK(1:1)RNP(1:1)RNP(1:1)<br />
SOLU 6DIM ENSE beta EULER 200.849 41.269 183.909 FRAC -0.49604 -0.15830 -0.28092 BFAC 0.00000<br />
SOLU 6DIM ENSE blip EULER 43.749 80.793 117.292 FRAC -0.12289 0.29435 -0.09266 BFAC 0.00000<br />
<br />
A more complicated structure solution may have<br />
<br />
SOLU HISTORY RF/TF(7/1:10)PAK(10:10)RNP(10,12,13,11,17,16,18,25,3,8,22,21,20,7,969,6,5,201,9,4,390,2,1,19:1)RNP(1:1)<br />
<br />
==What to do in Difficult Cases==<br />
<br />
Not every structure can be solved by molecular replacement, but the right strategy can push the limits. What to do when the default jobs fail depends on why your structure is difficult.<br />
*'''Flexible Structure'''<br />
*:The relative orientations of the domains may be different in your crystal than in the model. If that may be the case, break the model into separate PDB files containing rigid-body units, enter these as separate ensembles, and search for them separately. If you find a convincing solution for one domain, but fail to find a solution for the next domain, you can take advantage of the knowledge that its orientation is likely to be similar to that of the first domain. The ROTAte&nbsp;AROUnd option of the brute rotation search can be used to restrict the search to orientations within, say, 30 degrees of that of the known domain. Allow for close approach of the domains by increasing the allowed clashes with the PACK keyword by, say, 1 for each domain break that you introduce. Note that it is possible to use the brute rotation search as part of the automated molecular replacement pipeline, by changing the choice of the type of rotation search. Alternatively, you could try generating a series of models perturbed by normal modes, with the NMAPdb keyword. One of these may duplicate the hinge motion and provide a good single model.<br />
*'''Poor or Incomplete Model'''<br />
*:Signal-to-noise is reduced by coordinate errors or incompleteness of the model. Since the rotation search has lower signal to begin with than the translation search, it is usually more severely affected. For this reason, it can be very useful to use the subsequent translation search as a way to choose among many (say 1000) orientations. THe MR_AUTO FAST search mode automatically reduces the cutoff for accepting peaks from the fast rotation function if the decault pass does not find a solution with a high z-score, but you can manually reduce this further with the PEAKS and PURGE keywords. You can also try turning off the clustering of fast rotation function peaks because the correct orientation may sit on the shoulder of a peak in the rotation function. <br />
*:As shown convincingly by Schwarzenbacher ''et al.'' (Schwarzenbacher, Godzik, Grzechnik &amp; Jaroszewski, ''Acta Cryst.'' D'''60''', 1229-1236, 2004), judicious editing can make a significant difference in the quality of a distant model. In a number of tests with their data on models below 30% sequence identity, we have found that Phaser works best with a "mixed model" (non-identical sidechains longer than Ser replaced by Ser). In agreement with their results, the best models are generally derived using more sophisticated alignment protocols, such as their FFAS protocol. Use [http://www.phenix-online.org/documentation/sculptor.htm phenix.sculptor] to edit your model.<br />
*'''High Degree of Non-crystallographic Symmetry'''<br />
*:If there are clear peaks in the self-rotation function, you can expect orientations to be related by this known NCS. Methods to automatically use such information will be implemented in a future version of Phaser. In the meantime, you can work out for yourself the orientations that would be consistent with NCS and use the ROTAte&nbsp;AROUnd option to sample similar orientations. Alternatively, you may have an oligomeric model and expect similar NCS in the crystal. First search with the oligomeric model; if this fails, search with a monomer. If that succeeds, you can again use the ROTAte&nbsp;AROUnd option to force a subsequent monomer to adopt an orientation similar to the one you expect.<br />
*'''What <u>not</u> to do'''<br />
*:The automated mode of Phaser is fast when Phaser finds a high Z-score solution to your problem. When Phaser cannot find a solution with a significant Z-score, it "thrashes", meaning it maintains a list of 100-1000's of low Z-score potential solutions and tries to improve them. This can lead to exceptionally long Phaser runs (over a week of CPU time). Such runs are possible because the highly automated script allows many consecutive MR jobs to be run without you having to manually set 100-1000's of jobs running and keep track of the results. "Thrashing" generally does not produce a solution: solutions generally appear relatively quickly or not at all. It is more useful to go back and analyse your models and your data to see where improvements can be made. Your system manager will appreciate you terminating these jobs.<br />
*:It is also not a good idea to effectively remove the packing test. Unless there is specific evidence in the logfile that a high TF-function Z-score solution is being rejected with a few clashes, it is much better to edit the model to remove the loops than to increase the number of allowed clashes. Packing criteria are a very powerful constraint on the translation function, and increasing the number of allowed clashes beyond a few (e.g. 1-5) will increase the search time enormously without the possibility of generating any correct solutions that would not have otherwise been found.<br />
*'''Other suggestions'''<br />
*:Phaser has powerful input, output and scripting facilities that allow a large number of possibilities for altering default behaviour and forcing Phaser to do what you think it should. However, you will need to read the information in the manual below to take advantage of these facilities!<br />
<br />
==How to Define Data==<br />
You need to tell Phaser the name of the mtz file containing your data and the columns in the mtz file to be used using the HKLIn and LABIn keywords. Additional keywords (BINS CELL OUTLier RESOlution SPACegroup) define how the data are used.<br />
<br />
==How to Define Models==<br />
Phaser must be given the models that it will use for molecular replacement. A model in Phaser is referred to as an "ensemble", even when it is described by a single file. This is because it is possible to provide a set of aligned structures as an ensemble, from which a statistically-weighted averaged model is calculated. A molecular replacement model is provided either as one or more aligned pdb files, or as an electron density map, entered as structure factors in an mtz file. Each ensemble is treated as a separate type of rigid body to be placed in the molecular replacement solution. An ensemble should only be defined once, even if there are several copies of the molecule in the asymmetric unit.<br />
<br />
Fundamental to the way in which Phaser uses MR models (either from coordinates or maps) is to estimate how the accuracy of the model falls off as a function of resolution, represented by the Sigma(A) curve. To generate the Sigma(A) curve, Phaser needs to know the RMS coordinate error expected for the model and the fraction of the scattering power in the asymmetric unit that this model contributes.<br />
<br />
A Babinet-style correction is used to account for the effects of disordered solvent on the completeness of the model at low resolution.<br />
<br />
Molecular replacement models are defined with the ENSEmble keyword and the COMPosition keyword. The ENSEmble keyword gives (amongst other things) the RMS deviation for the Sigma(A) curve. The COMPosition keyword is used to deduce the fraction of the scattering power in the asymmetric unit that each ensemble contributes. The composition of the asymmetric unit is defined either by entering the molecular weights or sequences of the components in the asymmetric unit, and giving the number of copies of each. Expert users can also enter the fraction of the scattering of each component directly, although the composition must still be entered for the absolute scale calculation. Please note that the composition supplied to Phaser has to include everything in the asymmetric unit, not just what is being looked for in the current search!<br />
<br />
===Building an Ensemble from Coordinates===<br />
The RMS deviation is determined directly from RMS or indirectly from IDENtity in the ENSEmble<br />
keyword using a formula that depends on the sequence identity and the number of residues in the model.<br />
<br />
{| class="wikitable" style="text-align:center" align=right style="margin-left: 30px" <br />
|colspan="11" style="text-align: center;" | Initial estimate of RMS deviation<br />
|-<br />
|colspan="11" style="text-align: center;" | Number of residues in model versus sequence identity<br />
|-<br />
! !! #50 !! #100 !! #200 !! #300 !! #400 !! #600 !! #850 !! #1000 !! #1500 !! #2000<br />
|-<br />
|'''ID=0%''' || 1.579 || 1.689 || 1.875 || 2.030 || 2.164 || 2.391 || 2.625 || 2.748 || 3.093 || 3.375<br />
|-<br />
|'''ID=10%''' || 1.356 || 1.451 || 1.610 || 1.743 || 1.858 || 2.053 || 2.255 || 2.360 || 2.657 || 2.899<br />
|-<br />
|'''ID=20%''' || 1.165 || 1.246 || 1.383 || 1.497 || 1.596 || 1.764 || 1.936 || 2.027 || 2.281 || 2.489<br />
|-<br />
|'''ID=30%''' || 1.000 || 1.070 || 1.188 || 1.286 || 1.371 || 1.515 || 1.663 || 1.741 || 1.959 || 2.138<br />
|-<br />
|'''ID=40%''' || 0.859 || 0.919 || 1.020 || 1.104 || 1.177 || 1.301 || 1.428 || 1.495 || 1.683 || 1.836<br />
|-<br />
|'''ID=50%''' || 0.738 || 0.789 || 0.876 || 0.948 || 1.011 || 1.117 || 1.227 || 1.284 || 1.445 || 1.577<br />
|-<br />
|'''ID=60%''' || 0.634 || 0.678 || 0.752 || 0.814 || 0.868 || 0.959 || 1.053 || 1.103 || 1.241 || 1.354<br />
|-<br />
|'''ID=70%''' || 0.544 || 0.582 || 0.646 || 0.699 || 0.746 || 0.824 || 0.905 || 0.947 || 1.066 || 1.163<br />
|-<br />
|'''ID=80%''' || 0.467 || 0.500 || 0.555 || 0.601 || 0.640 || 0.708 || 0.777 || 0.813 || 0.915 || 0.999<br />
|-<br />
|'''ID=90%''' || 0.401 || 0.429 || 0.477 || 0.516 || 0.550 || 0.608 || 0.667 || 0.698 || 0.786 || 0.858<br />
|-<br />
|'''ID=100%''' || 0.345 || 0.369 || 0.409 || 0.443 || 0.472 || 0.522 || 0.573 || 0.600 || 0.675 || 0.737<br />
|-<br />
|}<br />
<br />
The RMS deviation estimated from ID may be an underestimate of the true value if there is a slight conformational change between the model and target structures. To find a solution in these cases it may be necessary to increase the RMS from the default value generated from the ID, by say 0.5 Ångstroms. On the other hand, when Phaser succeeds in solving a structure from a model with sequence identity much below 30%, it is often found that the fold is preserved better than the average for that level of sequence identity. So it may be worth submitting a run in which the RMS error is set at, say, 1.5, even if the sequence identity is low. The table below can be used as a guide as to the default RMS value corresponding to ID.<br />
<br />
If you construct a model by homology modelling, remember that the RMS error you expect is essentially the error you expect from the template structure (if not worse!). So specify the sequence identity of the template, not of the homology model.<br />
<br />
Only the model with the highest sequence identity is reported in the output pdb file. Also, HETATM cards in the input pdb file are ignored in the calculation of the structure factors for the ensemble, but are carried through to the output pdb file. Thus, the phases on the output mtz file (which come from the structure factors of the ensemble) do not correspond to those that would be calculated from the output pdb file, when there is more than one pdb file in an ensemble and/or the pdbfile(s) have HETATM records.<br />
<br />
====Coordinate Editing====<br />
=====HETATM/LIGANDS=====<br />
Phaser ignores the scattering from HETATM records. The HETATM records are carried though to output with occupancy set to zero. Ligands will therefore not contribute to the scattering used for molecular replacement. The exceptions to this rule are the HETATM records for MSE (seleno-methionine) MSO (seleno-methionine selenoxide) CSE (seleno-cysteine) CSO (seleno-cysteine selenoxide) ALY (acetyllysine) MLY (n-dimethyl-lysine) and MLZ (n-methyl-lysine) which are used in the scattering and carried through to output with their original occupancy. If you wish to include any HETATM records in the scattering the record name use the keyword ENSE modlid HETATOM ON<br />
<br />
=====WATER=====<br />
Water molecules (identified by the residue name OW WAT HOH H2O OH2 MOH WTR or TIP) are deleted from the pdb file on input, are not used in the scattering and are not carried through to file output. If you want to retain water molecules you will need to change the residue name to something other than this (e.g. WWW) so that the atoms are not identified as water. To include the water molecules in the scattering, the HETATM records will also have to be changed to ATOM records as described above.<br />
<br />
===Building an Ensemble from Electron Density===<br />
When using density as a model, it is necessary to specify both the extent (x,y,z limits) of the cut-out region of density, and the centre of this region. With coordinates, Phaser can work this out by itself. This information is needed, for instance, to decide how large rotational steps can be in the rotation search and to carry out the molecular transform interpolation correctly. In the case of electron density, the RMS value does not have the same physical meaning that it has when the model is specified by atomic coordinates, but it is used to judge how the accuracy of the calculated structure factors drops off with resolution. A suitable value for RMS can be obtained, in the case of density from an experimentally-phased map, by choosing a value that makes the SigmaA curve fall off with resolution similarly to the mean figures-of-merit. In the case of density from an EM image reconstruction, the RMS value should make the SigmaA curve fall off similarly to a Fourier correlation curve used to judge the resolution of the EM image.<br />
<br />
For detailed information, including a tutorial with example scripts, see<br />
[[Using Electron Density as a Model| Using density as a model]]<br />
<br />
==How to Define Composition==<br />
The composition defines the total amount of protein and nucleic acid that you have in the asymmetric unit not the fraction of the asymmetric unit that you are searching for.<br />
<br />
===Default Composition===<br />
For convenience, the composition defaults to 50% protein scattering by volume (the average for protein crystals). It is better to enter it explicitly, even if only to check that you have correctly deduced the probable content of your crystal. If your crystal has higher or lower solvent content than this, or contains nucleic acid, then the composition should be entered explicitly.<br />
===Composition by Solvent Content===<br />
Scattering is determined from the solvent content of the crystal, assuming that the crystal contains protein only, and the average distribution of amino acids in protein. If your crystal contains nucleic acid or your protein has an unusual amino acid distribution then the composition should be entered explicitly using the MW or sequence options.<br />
===Composition by Number of Residues in ASU===<br />
Scattering is determined from the number of residues in the asymmetric unit, assuming that the crystal contains protein only or nucleic acid only, and assuming an average distribution of residues for either. If your crystal contains a mixture then the composition should be entered explicitly using the MW or sequence options. If your crystal has an unusual residue distribution then the composition should be entered explicitly using the sequence options.<br />
===Composition by Molecular Weight===<br />
The composition is calculated from the molecular weight of the protein and nucleic acid assuming the protein and nucleic acid have the average distribution of amino acids and bases. If your protein or nucleic acid has an unusual amino acid or base distribution the composition should be entered by sequence. You can mix compositions entered by molecular weight with those entered by sequence.<br />
===Composition by Sequence===<br />
The composition is calculated from the amino acid sequence of the protein and the base sequence of the nucleic acid in fasta format. You can mix compositions entered by molecular weight with those entered by sequence. Individual atoms can be added to the composition with the COMPOSITION ATOM keyword. This allows the explicit addition of heavy atoms in the structure e.g. Fe atoms.<br />
===Composition by Percentage Scattering===<br />
The fraction scattering of each ensemble can be entered directly. The fraction scattering of each ensemble is normally automatically worked out from the average scattering from each ensemble (calculated from the pdb files if entered as coordinates, or from the protein and nucleic acid molecular weights if entered as a map) divided by the total scattering given by the composition, but entering the fraction scattering directly overrides this calculation. This option is for use when the pdb files of the models in the ensemble are unusual e.g. consist only of C-alpha atoms, or only of hydrogen atoms (as in the CLOUDS method for NMR).<br />
<br />
==How to Define Solutions==<br />
Phaser writes out files ending in ".sol" and ".rlist" that contain the solution information from the job. The root of the files is given by the ROOT keyword. By default, the root filename is PHASER. These files can be read back into subsequent runs of Phaser to build up solutions containing more than one molecule in the asymmetric unit.<br />
<br />
"PHASER.sol" files are generated by all modes (rotation function modes with VERBOSE output), and contain the current idea of potential molecular replacement solutions.<br />
<br />
"PHASER.rlist" files are generated by the rotation function modes, and are used as input for performing translation functions.<br />
<br />
For simple MR cases you don't really need to know how to define molecular replacement solutions. However, for difficult cases you might need to edit the files "PHASER.sol" and "PHASER.rlist" files manually<br />
<br />
=== "sol" Files===<br />
SOLUtion 6DIM keywords describe Ensembles that have been oriented by a rotation search and positioned by a translation search. Each Ensemble in the asymmetric unit has its own SOLUtion keyword. When more than one (potential) molecular replacement solution is present, the solutions are separated with the SOLUTION SET keywords.<br />
<br />
==="rlist" Files===<br />
These files define a rotation function list. The peak list is given with a series of SOLUtion TRIAl keywords.<br />
<br />
If a partial solution is already known, then the information for the currently "known" parts of the asymmetric unit is given in the form used for the PHASER.sol file, followed by the list of trial orientations for which a translation function is to be performed.<br />
<br />
===Fixed partial structure===<br />
If you have the coordinates of a partial solution with the pdb coordinates of the known structure in the correct orientation and position, then you can force Phaser to use these coordinates. Use the SOLUTION keyword to fix a rotation of 0 0 0 and a position of 0 0 0 for these coordinates.<br />
<br />
==How to Select Peaks==<br />
<br />
<br />
<br />
The selection of peaks saved for output in the rotation and translation functions can be done in four different ways.<br />
*'''Select by Percentage'''<br />
*: Percentage of the top peak, where the value of the top peak is defined as 100% and the value of the mean is defined as 0%.<br />
*: Default, cutoff=75%. This criteria has the advantange that at least one peak (the top peak) always survives the selection. If the top solution is clear, then only the one solution will be output, but if the distribution of peaks is rather flat, then many peaks will be output for testing in the next part of the MR procedure (e.g. many peaks selected from the rotation function for testing with a translation function). <br />
*'''Select by Z-score'''<br />
*: Number of standard deviations (sigmas) over the mean (the Z-score). <br />
*: Absolute significance test. Not all searches will produce output if the cutoff value is too high (e.g. 5 sigma). <br />
*'''Select by Number'''<br />
*: Number of top peaks to select. <br />
*: If the distribution is very flat then it might be better to select a fixed large number (e.g. 1000) of top rotation peaks for testing in the translation function.<br />
*'''No selection'''<br />
*: All peaks are selected. <br />
*: Enables full 6 dimensional searches, where all the solutions from the rotation function are output for testing in the translation function. This should never be necessary; it would be much faster and probably just as likely to work if the top 1000 peaks were used in this way.<br />
<br />
[[Image:Phaser_selection.gif| Selection criteria]]<br />
<br />
Peaks can also be clustered or not clustered prior to selection in steps 1 and 2.<br />
*'''Clustering Off'''<br />
: All high peaks on the search grid are selected<br />
*'''Clustering On'''<br />
: Points on the search grid with higher neighbouring points are removed from the selection<br />
<br />
<br />
[[Image:Phaser_clustering.gif| Clustering]]<br />
<br />
==How to Control Output==<br />
The output of Phaser can be controlled with optional keywords. <br />
<br />
The ROOT keyword is not compulsory (the default root filename is "PHASER"), but should always be given, so that your jobs have separate and meaningful output filenames.<br />
<br />
The TOPFiles keyword controls the number of potential MR solutions for which PDB and (in the appropriate modes) MTZ files are produced.<br />
<br />
For the MR_AUTO, MR_RNP and MR_LLG modes, unless HKLOut OFF is given as an optional keyword, Phaser produces an MTZ file with "SigmaA" type weighted Fourier map coefficients for producing electron density maps for rebuilding.<br />
<br />
{| class="wikitable" style="text-align:left" width=100%<br />
|-<br />
! MTZ Column Labels !! Description<br />
|-<br />
| FWT/PHWT || Amplitude and phase for 2''m''&#124;F<sub>obs</sub>&#124;-''D''&#124;F<sub>calc</sub>&#124; exp(''i''&alpha;<sub>calc</sub>) map<br />
|-<br />
| DELFWT/PHDELWT || Amplitude and phase for ''m''&#124;F<sub>obs</sub>&#124;-''D''&#124;F<sub>calc</sub>&#124; exp(''i''&alpha;<sub>calc</sub>) map<br />
|-<br />
| FOM || ''m'', analogous to the "Sim" weight, to estimate the reliability of &alpha;<sub>calc</sub><br />
|-<br />
| HLA/HLB/HLC/HLD || Hendrickson-Lattman coefficients encoding the phase probability distribution<br />
|}<br />
<br />
==Translational Non-crystallographic Symmetry==<br />
<br />
<span style="color:crimson">'''*Warning*''' Solution by MR in the presence of translational non-crystallographic symmetry is not fully automated.</span><br />
<br />
Phaser calculates correction factors for the expected intensities in the presence of translational non-crystallographic symmetry (tNCS), and is able to solve structures with complex patterns of tNCS. '''However, the use of Phaser in the presence of tNCS requires the nature of the tNCS to be understood by the user.''' In simple cases, solution is no more difficult than solution without tNCS, but in complex cases, separate Phaser runs with tNCS turned on and off, and/or the use of different tNCS vectors, may be necessary.<br />
<br />
The output of Phaser will help the user in detecting and understanding the tNCS, but '''the tNCS is not completely characterised by Phaser'''. The default behaviour may or may not be correct for the particular crystal under study.<br />
<br />
Characterization of the tNCS involves understanding the number of copies of the molecule in the asymmetric unit and the translation vectors between them. Molecules related by a tNCS vector will have an associated peak in the native Patterson. Phaser calculates the native Patterson (MODE TNCS) and lists the peaks that are more than 20% of the origin peak. Any given crystal with tNCS may have one or more peaks meeting this criteria.<br />
<br />
===Default tNCS detection and correction===<br />
<span style="color:crimson">Documentation for Phaser-2.7.16 and above</span><br />
<br />
====No tNCS====<br />
No tNCS correction is applied by default if there is<br />
# no peak in the native Patterson <br />
# more than one peak in the native Patterson over 20% of the origin and these peaks are not all the result of a commensurate modulation<br />
<br />
====Pairs of molecules====<br />
By default, if Phaser detects a peak in the native Patterson then Phaser will search for molecules in pairs related by the tNCS vector given by the peak in the native Patterson.<br />
<br />
This will be the correct behaviour if and only if there are an even number of copies of the molecule in the asymmetric unit, clustered into two groups related by a single tNCS vector. There will only be one significant peak in the native Patterson. Fortunately, this is a reasonably common scenario.<br />
<br />
Phaser refines the relative orientation of the molecules in the two groups (rotations of up to 10 degrees will still give rise to a significant native Patterson peak) and uses this information to generate expected intensity factors for the reflections. Solution should be straightforward, with the usual caveat for MR that there is a sufficiently good model.<br />
<br />
Where there is a single peak in the native Patterson, it is often located at a position half way along a unit cell axis or diagonal, representing a pseudo-halving of the unit cell dimensions. However, Phaser is by no means restricted to these sorts of pseudo-cells in its handling of two-fold tNCS, and the tNCS vector can be in a general position.<br />
<br />
===Non-default tNCS correction===<br />
====Higher order tNCS====<br />
Frequently, tNCS does not associate 2 clusters of molecules in the asymmetric unit, but rather there are 3 or more (n) clusters of molecules associated by a series of vectors that are multiples of 1, 2, 3 ... (n-1) times a basic translation vector. Where n times the basic translation vector equates to (very close to) integer multiples of unit cell axes, the tNCS represents a pseudo-cell, and this case is known as commensurate modulation. <br />
<br />
Phaser attempts to automatically detect commensurate modulation. The peaks of the native Patterson are analyzed to find the n-fold relationship. The series will not generally have all peaks the same height. Lower peaks in the series represent relationships where the relative rotations between related molecules are larger. Missing peaks in the series may be below the default 20% of origin cut-off. This can be lowered with TNCS PATT PERCENT <x><br />
<br />
Phaser then sets TNCS NMOL <n> and the vector for the tNCS, and searches for ensembles in multiples of NMOL.<br />
<br />
When there are more than two molecules related by tNCS, Phaser does not refine the orientations between the molecules related by the tNCS.<br />
<br />
However, as for two-fold tNCS, Phaser is not restricted to these sorts of pseudo-cells and the basic tNCS vector can be in a general position, as can the number of copies.<br />
<br />
'''The automatic detection may not give the true tNCS relationship'''. For example, the true commensurate modulation may be a factor of the NMOL automatically detected by Phaser, or there may not be commensurate modulation at all, or commensurate modulation may not be found with the default Pattesron peak height cutoff. In difficult cases, please inspect the Patterson for peaks.<br />
<br />
====Complex tNCS====<br />
If there are many molecules in the asymmetric unit but they are not all related by tNCS, or there are sub-groups of molecules related by different tNCS vectors, then the modulations of the expected intensities due to the tNCS will be much less significant than the cases described above. '''In these cases it is possible that structure solution will be achieved without any tNCS correction factors being applied.''' Indeed, searching for all the copies as tNCS-related multiples when some molecules are not related by tNCS will cause structure solution to fail. To turn off the automatic detection and use of tNCS use the keyword TNCS USE OFF.<br />
<br />
If turning off the TNCS correction factors fails to give a solution, then a good approach is to proceed step-wise. Consider the highest native Patterson peak first and determine that nature of the tNCS associated with it. Use the appropriate correction factors to locate all the molecules with this tNCS. Then take the second independent native Patterson peak and apply the correction factors associated with it to find the second set of molecules, fixing the first, etc. Finally, turn TNCS off to find any orphan molecules.</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Molecular_Replacement&diff=2379Molecular Replacement2016-11-28T11:02:36Z<p>Airlie: /* Default tNCS detection and correction */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
'''Quicklink to example scripts''' → [[MR using keyword input]]<br />
<br />
'''Quicklink to phaser.famos (find_alt_orig_sym_mate) documentation''' → [[Famos]]<br />
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Phaser should be able to solve most structures with the Automated Molecular Replacement mode, and this is the first mode that you should try. Give Phaser your data ([[#How to Define Data|How to Define Data]]) and your models ([[#How to Define Models|How to Define Models]]), tell Phaser what to search for, and a list of possible spacegroups (in the same point group).<br />
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If this doesn't work (see [[#Has Phaser Solved It?| Has Phaser Solved It?]]), you can try selecting peaks of lower significance in the rotation function in case the real orientation was not within the selection criteria. By default peaks above 75% of the top peak are selected (see [[#How to Select Peaks| How to Select Peaks]]). See [[#What to do in Difficult Cases| What to do in Difficult Cases]] for more hints and tips. If the automated molecular replacement mode doesn't work even with non-default input you need to run the modes of Phaser separately. The possibilities are endless - you can even try exhaustive searches (translations of all orientations) if you want - but experience has shown that most structures that can be solved by Phaser can be solved by relatively simple strategies.<br />
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==Automated Molecular Replacement==<br />
Automated Molecular Replacement combines the anisotropy correction, likelihood enhanced fast rotation function, likelihood enhanced fast translation function, packing and refinement modes for multiple search models and a set of possible spacegroups to automatically solve a structure by molecular replacement. Top solutions are output to the files FILEROOT.sol, FILEROOT.#.mtz and FILEROOT.#.pdb (where "#" refers to the sorted solution number, 1 being the best, and only 1 is output by default). Many structures can be solved by running an automated molecular replacement search with defaults, giving the ensembles that you expect to be easiest to find first.<br />
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At the completion of Molecular Replacement you may wish to place your solutions on a common origin with a previous solution, for which [[Famos | Famos ]] can be used.<br />
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[[Image:Phaser_MR_auto.gif|Flow Diagram for Automated MR]]<br />
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==Should Phaser Solve It?==<br />
The difficulty of a molecular replacement problem depends primarily on two major factors: how well the model will be able to explain the diffraction data (which depends both on the accuracy of the model and on its completeness), and how many reflections can be explained, at least in part. Each reflection provides a piece of information that helps to identify correct MR solutions.<br />
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It is possible to make a reasonable prediction of whether or not a solution will be found. If the quality of the model (its accuracy and completeness) can be estimated, then the expected contribution of each reflection to the total LLG can also be estimated. From a large battery of tests, we know that an LLG of 40 or greater usually indicates a correct solution (at least in the absence of complicating factors such as translational non-crystallographic symmetry, tNCS). Building on this understanding, if it is estimated that the LLG will be 60 or less, then Phaser will assume that the problem is a difficult one, and will implement search procedures optimised for difficult problems.<br />
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==What Resolution of Data Should be Used?==<br />
The signal for a molecular replacement solution should be very clear if the expected value of the LLG is much higher than the minimum required to be fairly certain of a solution. Currently Phaser aims for a minimum LLG of 120 and, if it is possible to achieve an even higher value, given the quality of the model and the quantity of diffraction data, then the resolution for the initial search is limited to the value required to achieve an expected LLG of 120. Data to the full resolution are still used for a final rigid-body refinement, or in a second pass if a clear solution is not found in the first attempt.<br />
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However, if the model is expected to have a large RMS error (based usually on the correlation between sequence identity and RMS error), then data to high resolution will not contribute any significant signal. Regardless of the expected LLG at the highest resolution limit, the resolution used is limited to 1.8 times the estimated RMS error of the model, because this resolution limit gives about 99% of the LLG that could be achieved.<br />
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Because Phaser implements strategies designed to solve structures with as much confidence as possible, as efficiently as possible, it is best to leave the choice of resolution to Phaser, at least in the first instance.<br />
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==Has Phaser Solved It?==<br />
{| class="wikitable" style="text-align:center" align="right" style="margin-left: 30px" <br />
|-<br />
! TF Z-score !! Have I solved it?<br />
|-<br />
| less than 5 || no<br />
|-<br />
| 5 - 6 || unlikely<br />
|-<br />
| 6 - 7 || possibly<br />
|-<br />
| 7 - 8 || probably<br />
|-<br />
| more than 8* ||definitely<br />
|-<br />
|colspan="2" style="text-align: center;" | *''6 for 1st model in monoclinic space groups''<br />
|} <br />
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Ideally, a unique solution with a strong signal will be found at the end of the search. If you are searching for multiple components, then ideally the search for each component will also give a strong signal. However if the signal-to-noise of your search is low, there will be noise peaks and multiple ambiguous solutions. Signal-to-noise is judged using the '''Z-score''', which is computed by comparing the LLG values from the rotation or translation search with LLG values for a set of random rotations or translations. The mean and the RMS deviation from the mean are computed from the random set, then the Z-score for a search peak is defined as its LLG minus the mean, all divided by the RMS deviation, ''i.e. '' '''the number of standard deviations above (or below) the mean. '''<br />
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For a rotation function, the correct orientation may be well down the list with a Z-score (number of standard deviations above the mean value, or RFZ) under 4, and it is often not possible to identify the correct orientation until a translation function is performed and yields a clear solution. Note that the signal-to-noise of the rotation function drops with increasing number of primitive symmetry operations (the number of different orientations for symmetry-related molecules), because there is more uncertainty about how the structure factor contributions from symmetry-related copies will add up.<br />
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For a translation function the correct solution will generally have a Z-score (TFZ) over 5 and be well separated from the rest of the solutions. Of course, there will always be exceptions! The table gives a very rough guide to interpreting TFZ scores. This table will be updated, as we learn more from systematic molecular replacement trials.<br />
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When you are searching for multiple components, the signal may be low for the first few components but, as the model becomes more complete, the signal should become stronger. Finding a clear solution for a new component is a good sign that the partial solution to which that component was added was indeed correct.<br />
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You should always at least glance through the summary of the logfile. One thing to look for, in particular, is whether any translation solutions with a high Z-score have been rejected by the packing step. By default up to 5 percent of marker atoms (C-alpha atoms for protein) are allowed to be involved in clashes. A solution with more clashes may still be correct, and the clashes may arise only because of differences in small surface loops. If this happens, repeat the run allowing a suitable number of clashes. Note that, unless there is specific evidence in the logfile that a high TFZ-score solution is being rejected with a few clashes, it is much better to edit the model to remove the loops than to increase the number of allowed clashes. Packing criteria are a very powerful constraint on the translation function, and increasing the number of allowed clashes beyond the default will increase the search time enormously without the possibility of generating any correct solutions that would not have otherwise been found.<br />
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Note that, by default, Phaser will produce a single PDB file corresponding to the top solution found (if any), so finding a single PDB file in your output directory is not an indication that the search succeeded! You have to look, at least, at the summary of the logfile, or at the list of possible solutions in the .sol file that is produced if you run Phaser from ccp4i or command-line scripts.<br />
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==Annotation==<br />
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A highly compact summary of the history of the statistics of a solution is given in the SOLUTION SET in the .sol file. This is a good place to start your analysis of the output. The annotation gives the Z-score of the solution at each rotation and translation function, the number of clashes in the packing, and the refined LLG.<br />
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{| class="wikitable" style="text-align:center" style="margin-left: 30px" <br />
|-<br />
! Annotation !! Meaning<br />
|-<br />
| RFZ= || Rotation Function Z-score<br />
|-<br />
| TFZ= || Translation Function Z-score<br />
|-<br />
| PAK= || Number of packing clashes<br />
|-<br />
| LLG= || LLG after refinement. Will be repeated when a low resolution refinement is followed by a high resolution refinement.<br />
|-<br />
| TFZ== || Translation Function Z-score equivalent, only calculated for the top solution after refinement (or for the number of top files specified by TOPFILES)<br />
|-<br />
| RF++ || Rotation angle from previous strong solution has been used in the addition of next solution<br />
|-<br />
| RF*0 || Rotation angle 000 identified by low R-factor of input model<br />
|-<br />
| TFZ=* || First molecule in P1 (arbitrary origin, no Translation Function required)<br />
|-<br />
| TF*0 || Translation vector 000 identified by low R-factor of input model<br />
|-<br />
| (&&nbsp;... & ...) || Set of TFZ PAK and LLG values for placements that were amalgamated (more than one placement from a single Translation Function)<br />
|-<br />
| LLG+=(...&nbsp;&&nbsp;...)&nbsp;|| Set of LLG values calculated during amalgamation, which will always be increasing in value<br />
|-<br />
| +TNCS || Components added by Translational NCS relation<br />
|-<br />
| *T=<i>n</i> || Solution matches template solution <i>n</i><br />
|} <br />
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Two versions of TFZ (the translation function Z-score) now appear for each component. The first ("TFZ=") is the Z-score from the actual translation search, which depends on the accuracy of the orientation used for that search. The second ("TFZ==") is the TFZ-equivalent, which indicates what the TFZ score would have been with the correct (refined) orientation. You should see the TFZ-equivalent is high at least for the final components of the solution, and that the LLG (log-likelihood gain) increases as each component of the solution is added. For example, in the case of beta-blip the annotation for the single solution output in the .sol file shows these features<br />
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SOLU SET RFZ=10.7 TFZ=24.3 PAK=0 LLG=472 TFZ==24.7 RFZ=6.4 TFZ=24.4 PAK=0 LLG=1006 TFZ==29.7 LLG=1006 TFZ==29.7<br />
SOLU 6DIM ENSE beta EULER 200.849 41.269 183.909 FRAC -0.49604 -0.15830 -0.28092 BFAC 0.00000<br />
SOLU 6DIM ENSE blip EULER 43.749 80.793 117.292 FRAC -0.12289 0.29435 -0.09266 BFAC 0.00000<br />
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Note that the Euler angles in Phaser follow the same convention as those defined for the Crowther fast rotation function, i.e. z-y-z (rotate around the z-axis, followed by the new y-axis, followed by the new z-axis).<br />
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==History==<br />
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A highly compact summary of the history of the peak positions of a solution is given in the SOLUTION HISTORY in the .sol file. Together with the SOLUTION SET annotation, this is useful in your analysis of the output. <br />
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{| class="wikitable" style="text-align:center" style="margin-left: 30px" <br />
|-<br />
! History !! Meaning<br />
|-<br />
| RF/TF(r/t:n) || (r) Rotation Function peak number/(t) Translation Function peak number for the rotation function : (n) number of peak in final merged and sorted list<br />
|-<br />
| PAK(n:m) || (n) input solution number : (m) output solution number after packing condition applied<br />
|-<br />
| RNP(m,a,b,c,... : p) || All input peaks amalgamated after refinement to give output solution number (m and others): (p) output solution number<br />
|-<br />
| FUSE(A,B,C) || Solution numbers merged in amalgamation<br />
|} <br />
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For example, in the case of beta-blip the annotation for the single solution output in the .sol file shows these features<br />
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SOLU HISTORY RF/TF(1/1:1)PAK(1:1)RNP(1:1)RNP(1:1)<br />
SOLU 6DIM ENSE beta EULER 200.849 41.269 183.909 FRAC -0.49604 -0.15830 -0.28092 BFAC 0.00000<br />
SOLU 6DIM ENSE blip EULER 43.749 80.793 117.292 FRAC -0.12289 0.29435 -0.09266 BFAC 0.00000<br />
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A more complicated structure solution may have<br />
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SOLU HISTORY RF/TF(7/1:10)PAK(10:10)RNP(10,12,13,11,17,16,18,25,3,8,22,21,20,7,969,6,5,201,9,4,390,2,1,19:1)RNP(1:1)<br />
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==What to do in Difficult Cases==<br />
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Not every structure can be solved by molecular replacement, but the right strategy can push the limits. What to do when the default jobs fail depends on why your structure is difficult.<br />
*'''Flexible Structure'''<br />
*:The relative orientations of the domains may be different in your crystal than in the model. If that may be the case, break the model into separate PDB files containing rigid-body units, enter these as separate ensembles, and search for them separately. If you find a convincing solution for one domain, but fail to find a solution for the next domain, you can take advantage of the knowledge that its orientation is likely to be similar to that of the first domain. The ROTAte&nbsp;AROUnd option of the brute rotation search can be used to restrict the search to orientations within, say, 30 degrees of that of the known domain. Allow for close approach of the domains by increasing the allowed clashes with the PACK keyword by, say, 1 for each domain break that you introduce. Note that it is possible to use the brute rotation search as part of the automated molecular replacement pipeline, by changing the choice of the type of rotation search. Alternatively, you could try generating a series of models perturbed by normal modes, with the NMAPdb keyword. One of these may duplicate the hinge motion and provide a good single model.<br />
*'''Poor or Incomplete Model'''<br />
*:Signal-to-noise is reduced by coordinate errors or incompleteness of the model. Since the rotation search has lower signal to begin with than the translation search, it is usually more severely affected. For this reason, it can be very useful to use the subsequent translation search as a way to choose among many (say 1000) orientations. THe MR_AUTO FAST search mode automatically reduces the cutoff for accepting peaks from the fast rotation function if the decault pass does not find a solution with a high z-score, but you can manually reduce this further with the PEAKS and PURGE keywords. You can also try turning off the clustering of fast rotation function peaks because the correct orientation may sit on the shoulder of a peak in the rotation function. <br />
*:As shown convincingly by Schwarzenbacher ''et al.'' (Schwarzenbacher, Godzik, Grzechnik &amp; Jaroszewski, ''Acta Cryst.'' D'''60''', 1229-1236, 2004), judicious editing can make a significant difference in the quality of a distant model. In a number of tests with their data on models below 30% sequence identity, we have found that Phaser works best with a "mixed model" (non-identical sidechains longer than Ser replaced by Ser). In agreement with their results, the best models are generally derived using more sophisticated alignment protocols, such as their FFAS protocol. Use [http://www.phenix-online.org/documentation/sculptor.htm phenix.sculptor] to edit your model.<br />
*'''High Degree of Non-crystallographic Symmetry'''<br />
*:If there are clear peaks in the self-rotation function, you can expect orientations to be related by this known NCS. Methods to automatically use such information will be implemented in a future version of Phaser. In the meantime, you can work out for yourself the orientations that would be consistent with NCS and use the ROTAte&nbsp;AROUnd option to sample similar orientations. Alternatively, you may have an oligomeric model and expect similar NCS in the crystal. First search with the oligomeric model; if this fails, search with a monomer. If that succeeds, you can again use the ROTAte&nbsp;AROUnd option to force a subsequent monomer to adopt an orientation similar to the one you expect.<br />
*'''What <u>not</u> to do'''<br />
*:The automated mode of Phaser is fast when Phaser finds a high Z-score solution to your problem. When Phaser cannot find a solution with a significant Z-score, it "thrashes", meaning it maintains a list of 100-1000's of low Z-score potential solutions and tries to improve them. This can lead to exceptionally long Phaser runs (over a week of CPU time). Such runs are possible because the highly automated script allows many consecutive MR jobs to be run without you having to manually set 100-1000's of jobs running and keep track of the results. "Thrashing" generally does not produce a solution: solutions generally appear relatively quickly or not at all. It is more useful to go back and analyse your models and your data to see where improvements can be made. Your system manager will appreciate you terminating these jobs.<br />
*:It is also not a good idea to effectively remove the packing test. Unless there is specific evidence in the logfile that a high TF-function Z-score solution is being rejected with a few clashes, it is much better to edit the model to remove the loops than to increase the number of allowed clashes. Packing criteria are a very powerful constraint on the translation function, and increasing the number of allowed clashes beyond a few (e.g. 1-5) will increase the search time enormously without the possibility of generating any correct solutions that would not have otherwise been found.<br />
*'''Other suggestions'''<br />
*:Phaser has powerful input, output and scripting facilities that allow a large number of possibilities for altering default behaviour and forcing Phaser to do what you think it should. However, you will need to read the information in the manual below to take advantage of these facilities!<br />
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==How to Define Data==<br />
You need to tell Phaser the name of the mtz file containing your data and the columns in the mtz file to be used using the HKLIn and LABIn keywords. Additional keywords (BINS CELL OUTLier RESOlution SPACegroup) define how the data are used.<br />
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==How to Define Models==<br />
Phaser must be given the models that it will use for molecular replacement. A model in Phaser is referred to as an "ensemble", even when it is described by a single file. This is because it is possible to provide a set of aligned structures as an ensemble, from which a statistically-weighted averaged model is calculated. A molecular replacement model is provided either as one or more aligned pdb files, or as an electron density map, entered as structure factors in an mtz file. Each ensemble is treated as a separate type of rigid body to be placed in the molecular replacement solution. An ensemble should only be defined once, even if there are several copies of the molecule in the asymmetric unit.<br />
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Fundamental to the way in which Phaser uses MR models (either from coordinates or maps) is to estimate how the accuracy of the model falls off as a function of resolution, represented by the Sigma(A) curve. To generate the Sigma(A) curve, Phaser needs to know the RMS coordinate error expected for the model and the fraction of the scattering power in the asymmetric unit that this model contributes.<br />
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A Babinet-style correction is used to account for the effects of disordered solvent on the completeness of the model at low resolution.<br />
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Molecular replacement models are defined with the ENSEmble keyword and the COMPosition keyword. The ENSEmble keyword gives (amongst other things) the RMS deviation for the Sigma(A) curve. The COMPosition keyword is used to deduce the fraction of the scattering power in the asymmetric unit that each ensemble contributes. The composition of the asymmetric unit is defined either by entering the molecular weights or sequences of the components in the asymmetric unit, and giving the number of copies of each. Expert users can also enter the fraction of the scattering of each component directly, although the composition must still be entered for the absolute scale calculation. Please note that the composition supplied to Phaser has to include everything in the asymmetric unit, not just what is being looked for in the current search!<br />
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===Building an Ensemble from Coordinates===<br />
The RMS deviation is determined directly from RMS or indirectly from IDENtity in the ENSEmble<br />
keyword using a formula that depends on the sequence identity and the number of residues in the model.<br />
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{| class="wikitable" style="text-align:center" align=right style="margin-left: 30px" <br />
|colspan="11" style="text-align: center;" | Initial estimate of RMS deviation<br />
|-<br />
|colspan="11" style="text-align: center;" | Number of residues in model versus sequence identity<br />
|-<br />
! !! #50 !! #100 !! #200 !! #300 !! #400 !! #600 !! #850 !! #1000 !! #1500 !! #2000<br />
|-<br />
|'''ID=0%''' || 1.579 || 1.689 || 1.875 || 2.030 || 2.164 || 2.391 || 2.625 || 2.748 || 3.093 || 3.375<br />
|-<br />
|'''ID=10%''' || 1.356 || 1.451 || 1.610 || 1.743 || 1.858 || 2.053 || 2.255 || 2.360 || 2.657 || 2.899<br />
|-<br />
|'''ID=20%''' || 1.165 || 1.246 || 1.383 || 1.497 || 1.596 || 1.764 || 1.936 || 2.027 || 2.281 || 2.489<br />
|-<br />
|'''ID=30%''' || 1.000 || 1.070 || 1.188 || 1.286 || 1.371 || 1.515 || 1.663 || 1.741 || 1.959 || 2.138<br />
|-<br />
|'''ID=40%''' || 0.859 || 0.919 || 1.020 || 1.104 || 1.177 || 1.301 || 1.428 || 1.495 || 1.683 || 1.836<br />
|-<br />
|'''ID=50%''' || 0.738 || 0.789 || 0.876 || 0.948 || 1.011 || 1.117 || 1.227 || 1.284 || 1.445 || 1.577<br />
|-<br />
|'''ID=60%''' || 0.634 || 0.678 || 0.752 || 0.814 || 0.868 || 0.959 || 1.053 || 1.103 || 1.241 || 1.354<br />
|-<br />
|'''ID=70%''' || 0.544 || 0.582 || 0.646 || 0.699 || 0.746 || 0.824 || 0.905 || 0.947 || 1.066 || 1.163<br />
|-<br />
|'''ID=80%''' || 0.467 || 0.500 || 0.555 || 0.601 || 0.640 || 0.708 || 0.777 || 0.813 || 0.915 || 0.999<br />
|-<br />
|'''ID=90%''' || 0.401 || 0.429 || 0.477 || 0.516 || 0.550 || 0.608 || 0.667 || 0.698 || 0.786 || 0.858<br />
|-<br />
|'''ID=100%''' || 0.345 || 0.369 || 0.409 || 0.443 || 0.472 || 0.522 || 0.573 || 0.600 || 0.675 || 0.737<br />
|-<br />
|}<br />
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The RMS deviation estimated from ID may be an underestimate of the true value if there is a slight conformational change between the model and target structures. To find a solution in these cases it may be necessary to increase the RMS from the default value generated from the ID, by say 0.5 Ångstroms. On the other hand, when Phaser succeeds in solving a structure from a model with sequence identity much below 30%, it is often found that the fold is preserved better than the average for that level of sequence identity. So it may be worth submitting a run in which the RMS error is set at, say, 1.5, even if the sequence identity is low. The table below can be used as a guide as to the default RMS value corresponding to ID.<br />
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If you construct a model by homology modelling, remember that the RMS error you expect is essentially the error you expect from the template structure (if not worse!). So specify the sequence identity of the template, not of the homology model.<br />
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Only the model with the highest sequence identity is reported in the output pdb file. Also, HETATM cards in the input pdb file are ignored in the calculation of the structure factors for the ensemble, but are carried through to the output pdb file. Thus, the phases on the output mtz file (which come from the structure factors of the ensemble) do not correspond to those that would be calculated from the output pdb file, when there is more than one pdb file in an ensemble and/or the pdbfile(s) have HETATM records.<br />
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====Coordinate Editing====<br />
=====HETATM/LIGANDS=====<br />
Phaser ignores the scattering from HETATM records. The HETATM records are carried though to output with occupancy set to zero. Ligands will therefore not contribute to the scattering used for molecular replacement. The exceptions to this rule are the HETATM records for MSE (seleno-methionine) MSO (seleno-methionine selenoxide) CSE (seleno-cysteine) CSO (seleno-cysteine selenoxide) ALY (acetyllysine) MLY (n-dimethyl-lysine) and MLZ (n-methyl-lysine) which are used in the scattering and carried through to output with their original occupancy. If you wish to include any HETATM records in the scattering the record name use the keyword ENSE modlid HETATOM ON<br />
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=====WATER=====<br />
Water molecules (identified by the residue name OW WAT HOH H2O OH2 MOH WTR or TIP) are deleted from the pdb file on input, are not used in the scattering and are not carried through to file output. If you want to retain water molecules you will need to change the residue name to something other than this (e.g. WWW) so that the atoms are not identified as water. To include the water molecules in the scattering, the HETATM records will also have to be changed to ATOM records as described above.<br />
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===Building an Ensemble from Electron Density===<br />
When using density as a model, it is necessary to specify both the extent (x,y,z limits) of the cut-out region of density, and the centre of this region. With coordinates, Phaser can work this out by itself. This information is needed, for instance, to decide how large rotational steps can be in the rotation search and to carry out the molecular transform interpolation correctly. In the case of electron density, the RMS value does not have the same physical meaning that it has when the model is specified by atomic coordinates, but it is used to judge how the accuracy of the calculated structure factors drops off with resolution. A suitable value for RMS can be obtained, in the case of density from an experimentally-phased map, by choosing a value that makes the SigmaA curve fall off with resolution similarly to the mean figures-of-merit. In the case of density from an EM image reconstruction, the RMS value should make the SigmaA curve fall off similarly to a Fourier correlation curve used to judge the resolution of the EM image.<br />
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For detailed information, including a tutorial with example scripts, see<br />
[[Using Electron Density as a Model| Using density as a model]]<br />
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==How to Define Composition==<br />
The composition defines the total amount of protein and nucleic acid that you have in the asymmetric unit not the fraction of the asymmetric unit that you are searching for.<br />
<br />
===Default Composition===<br />
For convenience, the composition defaults to 50% protein scattering by volume (the average for protein crystals). It is better to enter it explicitly, even if only to check that you have correctly deduced the probable content of your crystal. If your crystal has higher or lower solvent content than this, or contains nucleic acid, then the composition should be entered explicitly.<br />
===Composition by Solvent Content===<br />
Scattering is determined from the solvent content of the crystal, assuming that the crystal contains protein only, and the average distribution of amino acids in protein. If your crystal contains nucleic acid or your protein has an unusual amino acid distribution then the composition should be entered explicitly using the MW or sequence options.<br />
===Composition by Number of Residues in ASU===<br />
Scattering is determined from the number of residues in the asymmetric unit, assuming that the crystal contains protein only or nucleic acid only, and assuming an average distribution of residues for either. If your crystal contains a mixture then the composition should be entered explicitly using the MW or sequence options. If your crystal has an unusual residue distribution then the composition should be entered explicitly using the sequence options.<br />
===Composition by Molecular Weight===<br />
The composition is calculated from the molecular weight of the protein and nucleic acid assuming the protein and nucleic acid have the average distribution of amino acids and bases. If your protein or nucleic acid has an unusual amino acid or base distribution the composition should be entered by sequence. You can mix compositions entered by molecular weight with those entered by sequence.<br />
===Composition by Sequence===<br />
The composition is calculated from the amino acid sequence of the protein and the base sequence of the nucleic acid in fasta format. You can mix compositions entered by molecular weight with those entered by sequence. Individual atoms can be added to the composition with the COMPOSITION ATOM keyword. This allows the explicit addition of heavy atoms in the structure e.g. Fe atoms.<br />
===Composition by Percentage Scattering===<br />
The fraction scattering of each ensemble can be entered directly. The fraction scattering of each ensemble is normally automatically worked out from the average scattering from each ensemble (calculated from the pdb files if entered as coordinates, or from the protein and nucleic acid molecular weights if entered as a map) divided by the total scattering given by the composition, but entering the fraction scattering directly overrides this calculation. This option is for use when the pdb files of the models in the ensemble are unusual e.g. consist only of C-alpha atoms, or only of hydrogen atoms (as in the CLOUDS method for NMR).<br />
<br />
==How to Define Solutions==<br />
Phaser writes out files ending in ".sol" and ".rlist" that contain the solution information from the job. The root of the files is given by the ROOT keyword. By default, the root filename is PHASER. These files can be read back into subsequent runs of Phaser to build up solutions containing more than one molecule in the asymmetric unit.<br />
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"PHASER.sol" files are generated by all modes (rotation function modes with VERBOSE output), and contain the current idea of potential molecular replacement solutions.<br />
<br />
"PHASER.rlist" files are generated by the rotation function modes, and are used as input for performing translation functions.<br />
<br />
For simple MR cases you don't really need to know how to define molecular replacement solutions. However, for difficult cases you might need to edit the files "PHASER.sol" and "PHASER.rlist" files manually<br />
<br />
=== "sol" Files===<br />
SOLUtion 6DIM keywords describe Ensembles that have been oriented by a rotation search and positioned by a translation search. Each Ensemble in the asymmetric unit has its own SOLUtion keyword. When more than one (potential) molecular replacement solution is present, the solutions are separated with the SOLUTION SET keywords.<br />
<br />
==="rlist" Files===<br />
These files define a rotation function list. The peak list is given with a series of SOLUtion TRIAl keywords.<br />
<br />
If a partial solution is already known, then the information for the currently "known" parts of the asymmetric unit is given in the form used for the PHASER.sol file, followed by the list of trial orientations for which a translation function is to be performed.<br />
<br />
===Fixed partial structure===<br />
If you have the coordinates of a partial solution with the pdb coordinates of the known structure in the correct orientation and position, then you can force Phaser to use these coordinates. Use the SOLUTION keyword to fix a rotation of 0 0 0 and a position of 0 0 0 for these coordinates.<br />
<br />
==How to Select Peaks==<br />
<br />
<br />
<br />
The selection of peaks saved for output in the rotation and translation functions can be done in four different ways.<br />
*'''Select by Percentage'''<br />
*: Percentage of the top peak, where the value of the top peak is defined as 100% and the value of the mean is defined as 0%.<br />
*: Default, cutoff=75%. This criteria has the advantange that at least one peak (the top peak) always survives the selection. If the top solution is clear, then only the one solution will be output, but if the distribution of peaks is rather flat, then many peaks will be output for testing in the next part of the MR procedure (e.g. many peaks selected from the rotation function for testing with a translation function). <br />
*'''Select by Z-score'''<br />
*: Number of standard deviations (sigmas) over the mean (the Z-score). <br />
*: Absolute significance test. Not all searches will produce output if the cutoff value is too high (e.g. 5 sigma). <br />
*'''Select by Number'''<br />
*: Number of top peaks to select. <br />
*: If the distribution is very flat then it might be better to select a fixed large number (e.g. 1000) of top rotation peaks for testing in the translation function.<br />
*'''No selection'''<br />
*: All peaks are selected. <br />
*: Enables full 6 dimensional searches, where all the solutions from the rotation function are output for testing in the translation function. This should never be necessary; it would be much faster and probably just as likely to work if the top 1000 peaks were used in this way.<br />
<br />
[[Image:Phaser_selection.gif| Selection criteria]]<br />
<br />
Peaks can also be clustered or not clustered prior to selection in steps 1 and 2.<br />
*'''Clustering Off'''<br />
: All high peaks on the search grid are selected<br />
*'''Clustering On'''<br />
: Points on the search grid with higher neighbouring points are removed from the selection<br />
<br />
<br />
[[Image:Phaser_clustering.gif| Clustering]]<br />
<br />
==How to Control Output==<br />
The output of Phaser can be controlled with optional keywords. <br />
<br />
The ROOT keyword is not compulsory (the default root filename is "PHASER"), but should always be given, so that your jobs have separate and meaningful output filenames.<br />
<br />
The TOPFiles keyword controls the number of potential MR solutions for which PDB and (in the appropriate modes) MTZ files are produced.<br />
<br />
For the MR_AUTO, MR_RNP and MR_LLG modes, unless HKLOut OFF is given as an optional keyword, Phaser produces an MTZ file with "SigmaA" type weighted Fourier map coefficients for producing electron density maps for rebuilding.<br />
<br />
{| class="wikitable" style="text-align:left" width=100%<br />
|-<br />
! MTZ Column Labels !! Description<br />
|-<br />
| FWT/PHWT || Amplitude and phase for 2''m''&#124;F<sub>obs</sub>&#124;-''D''&#124;F<sub>calc</sub>&#124; exp(''i''&alpha;<sub>calc</sub>) map<br />
|-<br />
| DELFWT/PHDELWT || Amplitude and phase for ''m''&#124;F<sub>obs</sub>&#124;-''D''&#124;F<sub>calc</sub>&#124; exp(''i''&alpha;<sub>calc</sub>) map<br />
|-<br />
| FOM || ''m'', analogous to the "Sim" weight, to estimate the reliability of &alpha;<sub>calc</sub><br />
|-<br />
| HLA/HLB/HLC/HLD || Hendrickson-Lattman coefficients encoding the phase probability distribution<br />
|}<br />
<br />
==Translational Non-crystallographic Symmetry==<br />
<br />
<span style="color:crimson">'''*Warning*''' Solution by MR in the presence of translational non-crystallographic symmetry is not fully automated.</span><br />
<br />
Phaser calculates correction factors for the expected intensities in the presence of translational non-crystallographic symmetry (tNCS), and is able to solve structures with complex patterns of tNCS. '''However, the use of Phaser in the presence of tNCS requires the nature of the tNCS to be understood by the user.''' In simple cases, solution is no more difficult than solution without tNCS, but in complex cases, separate Phaser runs with tNCS turned on and off, and/or the use of different tNCS vectors, may be necessary.<br />
<br />
The output of Phaser will help the user in detecting and understanding the tNCS, but '''the tNCS is not completely characterised by Phaser'''. The default behaviour may or may not be correct for the particular crystal under study.<br />
<br />
Characterization of the tNCS involves understanding the number of copies of the molecule in the asymmetric unit and the translation vectors between them. Molecules related by a tNCS vector will have an associated peak in the native Patterson. Phaser calculates the native Patterson (MODE TNCS) and lists the peaks that are more than 20% of the origin peak. Any given crystal with tNCS may have one or more peaks meeting this criteria.<br />
<br />
===Default tNCS detection and correction===<br />
Documentation for Phaser-2.7.16 and above<br />
<br />
====No tNCS====<br />
No tNCS correction is applied by default if there is<br />
# no peak in the native Patterson <br />
# more than one peak in the native Patterson over 20% of the origin and these peaks are not all the result of a commensurate modulation<br />
<br />
====Pairs of molecules====<br />
By default, if Phaser detects a peak in the native Patterson then Phaser will search for molecules in pairs related by the tNCS vector given by the peak in the native Patterson.<br />
<br />
This will be the correct behaviour if and only if there are an even number of copies of the molecule in the asymmetric unit, clustered into two groups related by a single tNCS vector. There will only be one significant peak in the native Patterson. Fortunately, this is a reasonably common scenario.<br />
<br />
Phaser refines the relative orientation of the molecules in the two groups (rotations of up to 10 degrees will still give rise to a significant native Patterson peak) and uses this information to generate expected intensity factors for the reflections. Solution should be straightforward, with the usual caveat for MR that there is a sufficiently good model.<br />
<br />
Where there is a single peak in the native Patterson, it is often located at a position half way along a unit cell axis or diagonal, representing a pseudo-halving of the unit cell dimensions. However, Phaser is by no means restricted to these sorts of pseudo-cells in its handling of two-fold tNCS, and the tNCS vector can be in a general position.<br />
<br />
===Non-default tNCS correction===<br />
====Higher order tNCS====<br />
Frequently, tNCS does not associate 2 clusters of molecules in the asymmetric unit, but rather there are 3 or more (n) clusters of molecules associated by a series of vectors that are multiples of 1, 2, 3 ... (n-1) times a basic translation vector. Where n times the basic translation vector equates to (very close to) integer multiples of unit cell axes, the tNCS represents a pseudo-cell, and this case is known as commensurate modulation. <br />
<br />
Phaser attempts to automatically detect commensurate modulation. The peaks of the native Patterson are analyzed to find the n-fold relationship. The series will not generally have all peaks the same height. Lower peaks in the series represent relationships where the relative rotations between related molecules are larger. Missing peaks in the series may be below the default 20% of origin cut-off. This can be lowered with TNCS PATT PERCENT <x><br />
<br />
Phaser then sets TNCS NMOL <n> and the vector for the tNCS, and searches for ensembles in multiples of NMOL.<br />
<br />
When there are more than two molecules related by tNCS, Phaser does not refine the orientations between the molecules related by the tNCS.<br />
<br />
However, as for two-fold tNCS, Phaser is not restricted to these sorts of pseudo-cells and the basic tNCS vector can be in a general position, as can the number of copies.<br />
<br />
'''The automatic detection may not give the true tNCS relationship'''. For example, the true commensurate modulation may be a factor of the NMOL automatically detected by Phaser, or there may not be commensurate modulation at all, or commensurate modulation may not be found with the default Pattesron peak height cutoff. In difficult cases, please inspect the Patterson for peaks.<br />
<br />
====Complex tNCS====<br />
If there are many molecules in the asymmetric unit but they are not all related by tNCS, or there are sub-groups of molecules related by different tNCS vectors, then the modulations of the expected intensities due to the tNCS will be much less significant than the cases described above. '''In these cases it is possible that structure solution will be achieved without any tNCS correction factors being applied.''' Indeed, searching for all the copies as tNCS-related multiples when some molecules are not related by tNCS will cause structure solution to fail. To turn off the automatic detection and use of tNCS use the keyword TNCS USE OFF.<br />
<br />
If turning off the TNCS correction factors fails to give a solution, then a good approach is to proceed step-wise. Consider the highest native Patterson peak first and determine that nature of the tNCS associated with it. Use the appropriate correction factors to locate all the molecules with this tNCS. Then take the second independent native Patterson peak and apply the correction factors associated with it to find the second set of molecules, fixing the first, etc. Finally, turn TNCS off to find any orphan molecules.</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Molecular_Replacement&diff=2378Molecular Replacement2016-11-28T11:01:20Z<p>Airlie: /* Higher order tNCS */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
'''Quicklink to example scripts''' → [[MR using keyword input]]<br />
<br />
'''Quicklink to phaser.famos (find_alt_orig_sym_mate) documentation''' → [[Famos]]<br />
<br />
Phaser should be able to solve most structures with the Automated Molecular Replacement mode, and this is the first mode that you should try. Give Phaser your data ([[#How to Define Data|How to Define Data]]) and your models ([[#How to Define Models|How to Define Models]]), tell Phaser what to search for, and a list of possible spacegroups (in the same point group).<br />
<br />
If this doesn't work (see [[#Has Phaser Solved It?| Has Phaser Solved It?]]), you can try selecting peaks of lower significance in the rotation function in case the real orientation was not within the selection criteria. By default peaks above 75% of the top peak are selected (see [[#How to Select Peaks| How to Select Peaks]]). See [[#What to do in Difficult Cases| What to do in Difficult Cases]] for more hints and tips. If the automated molecular replacement mode doesn't work even with non-default input you need to run the modes of Phaser separately. The possibilities are endless - you can even try exhaustive searches (translations of all orientations) if you want - but experience has shown that most structures that can be solved by Phaser can be solved by relatively simple strategies.<br />
<br />
==Automated Molecular Replacement==<br />
Automated Molecular Replacement combines the anisotropy correction, likelihood enhanced fast rotation function, likelihood enhanced fast translation function, packing and refinement modes for multiple search models and a set of possible spacegroups to automatically solve a structure by molecular replacement. Top solutions are output to the files FILEROOT.sol, FILEROOT.#.mtz and FILEROOT.#.pdb (where "#" refers to the sorted solution number, 1 being the best, and only 1 is output by default). Many structures can be solved by running an automated molecular replacement search with defaults, giving the ensembles that you expect to be easiest to find first.<br />
<br />
At the completion of Molecular Replacement you may wish to place your solutions on a common origin with a previous solution, for which [[Famos | Famos ]] can be used.<br />
<br />
[[Image:Phaser_MR_auto.gif|Flow Diagram for Automated MR]]<br />
<br />
==Should Phaser Solve It?==<br />
The difficulty of a molecular replacement problem depends primarily on two major factors: how well the model will be able to explain the diffraction data (which depends both on the accuracy of the model and on its completeness), and how many reflections can be explained, at least in part. Each reflection provides a piece of information that helps to identify correct MR solutions.<br />
<br />
It is possible to make a reasonable prediction of whether or not a solution will be found. If the quality of the model (its accuracy and completeness) can be estimated, then the expected contribution of each reflection to the total LLG can also be estimated. From a large battery of tests, we know that an LLG of 40 or greater usually indicates a correct solution (at least in the absence of complicating factors such as translational non-crystallographic symmetry, tNCS). Building on this understanding, if it is estimated that the LLG will be 60 or less, then Phaser will assume that the problem is a difficult one, and will implement search procedures optimised for difficult problems.<br />
<br />
==What Resolution of Data Should be Used?==<br />
The signal for a molecular replacement solution should be very clear if the expected value of the LLG is much higher than the minimum required to be fairly certain of a solution. Currently Phaser aims for a minimum LLG of 120 and, if it is possible to achieve an even higher value, given the quality of the model and the quantity of diffraction data, then the resolution for the initial search is limited to the value required to achieve an expected LLG of 120. Data to the full resolution are still used for a final rigid-body refinement, or in a second pass if a clear solution is not found in the first attempt.<br />
<br />
However, if the model is expected to have a large RMS error (based usually on the correlation between sequence identity and RMS error), then data to high resolution will not contribute any significant signal. Regardless of the expected LLG at the highest resolution limit, the resolution used is limited to 1.8 times the estimated RMS error of the model, because this resolution limit gives about 99% of the LLG that could be achieved.<br />
<br />
Because Phaser implements strategies designed to solve structures with as much confidence as possible, as efficiently as possible, it is best to leave the choice of resolution to Phaser, at least in the first instance.<br />
<br />
==Has Phaser Solved It?==<br />
{| class="wikitable" style="text-align:center" align="right" style="margin-left: 30px" <br />
|-<br />
! TF Z-score !! Have I solved it?<br />
|-<br />
| less than 5 || no<br />
|-<br />
| 5 - 6 || unlikely<br />
|-<br />
| 6 - 7 || possibly<br />
|-<br />
| 7 - 8 || probably<br />
|-<br />
| more than 8* ||definitely<br />
|-<br />
|colspan="2" style="text-align: center;" | *''6 for 1st model in monoclinic space groups''<br />
|} <br />
<br />
Ideally, a unique solution with a strong signal will be found at the end of the search. If you are searching for multiple components, then ideally the search for each component will also give a strong signal. However if the signal-to-noise of your search is low, there will be noise peaks and multiple ambiguous solutions. Signal-to-noise is judged using the '''Z-score''', which is computed by comparing the LLG values from the rotation or translation search with LLG values for a set of random rotations or translations. The mean and the RMS deviation from the mean are computed from the random set, then the Z-score for a search peak is defined as its LLG minus the mean, all divided by the RMS deviation, ''i.e. '' '''the number of standard deviations above (or below) the mean. '''<br />
<br />
For a rotation function, the correct orientation may be well down the list with a Z-score (number of standard deviations above the mean value, or RFZ) under 4, and it is often not possible to identify the correct orientation until a translation function is performed and yields a clear solution. Note that the signal-to-noise of the rotation function drops with increasing number of primitive symmetry operations (the number of different orientations for symmetry-related molecules), because there is more uncertainty about how the structure factor contributions from symmetry-related copies will add up.<br />
<br />
For a translation function the correct solution will generally have a Z-score (TFZ) over 5 and be well separated from the rest of the solutions. Of course, there will always be exceptions! The table gives a very rough guide to interpreting TFZ scores. This table will be updated, as we learn more from systematic molecular replacement trials.<br />
<br />
When you are searching for multiple components, the signal may be low for the first few components but, as the model becomes more complete, the signal should become stronger. Finding a clear solution for a new component is a good sign that the partial solution to which that component was added was indeed correct.<br />
<br />
You should always at least glance through the summary of the logfile. One thing to look for, in particular, is whether any translation solutions with a high Z-score have been rejected by the packing step. By default up to 5 percent of marker atoms (C-alpha atoms for protein) are allowed to be involved in clashes. A solution with more clashes may still be correct, and the clashes may arise only because of differences in small surface loops. If this happens, repeat the run allowing a suitable number of clashes. Note that, unless there is specific evidence in the logfile that a high TFZ-score solution is being rejected with a few clashes, it is much better to edit the model to remove the loops than to increase the number of allowed clashes. Packing criteria are a very powerful constraint on the translation function, and increasing the number of allowed clashes beyond the default will increase the search time enormously without the possibility of generating any correct solutions that would not have otherwise been found.<br />
<br />
Note that, by default, Phaser will produce a single PDB file corresponding to the top solution found (if any), so finding a single PDB file in your output directory is not an indication that the search succeeded! You have to look, at least, at the summary of the logfile, or at the list of possible solutions in the .sol file that is produced if you run Phaser from ccp4i or command-line scripts.<br />
<br />
==Annotation==<br />
<br />
A highly compact summary of the history of the statistics of a solution is given in the SOLUTION SET in the .sol file. This is a good place to start your analysis of the output. The annotation gives the Z-score of the solution at each rotation and translation function, the number of clashes in the packing, and the refined LLG.<br />
<br />
{| class="wikitable" style="text-align:center" style="margin-left: 30px" <br />
|-<br />
! Annotation !! Meaning<br />
|-<br />
| RFZ= || Rotation Function Z-score<br />
|-<br />
| TFZ= || Translation Function Z-score<br />
|-<br />
| PAK= || Number of packing clashes<br />
|-<br />
| LLG= || LLG after refinement. Will be repeated when a low resolution refinement is followed by a high resolution refinement.<br />
|-<br />
| TFZ== || Translation Function Z-score equivalent, only calculated for the top solution after refinement (or for the number of top files specified by TOPFILES)<br />
|-<br />
| RF++ || Rotation angle from previous strong solution has been used in the addition of next solution<br />
|-<br />
| RF*0 || Rotation angle 000 identified by low R-factor of input model<br />
|-<br />
| TFZ=* || First molecule in P1 (arbitrary origin, no Translation Function required)<br />
|-<br />
| TF*0 || Translation vector 000 identified by low R-factor of input model<br />
|-<br />
| (&&nbsp;... & ...) || Set of TFZ PAK and LLG values for placements that were amalgamated (more than one placement from a single Translation Function)<br />
|-<br />
| LLG+=(...&nbsp;&&nbsp;...)&nbsp;|| Set of LLG values calculated during amalgamation, which will always be increasing in value<br />
|-<br />
| +TNCS || Components added by Translational NCS relation<br />
|-<br />
| *T=<i>n</i> || Solution matches template solution <i>n</i><br />
|} <br />
<br />
Two versions of TFZ (the translation function Z-score) now appear for each component. The first ("TFZ=") is the Z-score from the actual translation search, which depends on the accuracy of the orientation used for that search. The second ("TFZ==") is the TFZ-equivalent, which indicates what the TFZ score would have been with the correct (refined) orientation. You should see the TFZ-equivalent is high at least for the final components of the solution, and that the LLG (log-likelihood gain) increases as each component of the solution is added. For example, in the case of beta-blip the annotation for the single solution output in the .sol file shows these features<br />
<br />
SOLU SET RFZ=10.7 TFZ=24.3 PAK=0 LLG=472 TFZ==24.7 RFZ=6.4 TFZ=24.4 PAK=0 LLG=1006 TFZ==29.7 LLG=1006 TFZ==29.7<br />
SOLU 6DIM ENSE beta EULER 200.849 41.269 183.909 FRAC -0.49604 -0.15830 -0.28092 BFAC 0.00000<br />
SOLU 6DIM ENSE blip EULER 43.749 80.793 117.292 FRAC -0.12289 0.29435 -0.09266 BFAC 0.00000<br />
<br />
Note that the Euler angles in Phaser follow the same convention as those defined for the Crowther fast rotation function, i.e. z-y-z (rotate around the z-axis, followed by the new y-axis, followed by the new z-axis).<br />
<br />
==History==<br />
<br />
A highly compact summary of the history of the peak positions of a solution is given in the SOLUTION HISTORY in the .sol file. Together with the SOLUTION SET annotation, this is useful in your analysis of the output. <br />
<br />
{| class="wikitable" style="text-align:center" style="margin-left: 30px" <br />
|-<br />
! History !! Meaning<br />
|-<br />
| RF/TF(r/t:n) || (r) Rotation Function peak number/(t) Translation Function peak number for the rotation function : (n) number of peak in final merged and sorted list<br />
|-<br />
| PAK(n:m) || (n) input solution number : (m) output solution number after packing condition applied<br />
|-<br />
| RNP(m,a,b,c,... : p) || All input peaks amalgamated after refinement to give output solution number (m and others): (p) output solution number<br />
|-<br />
| FUSE(A,B,C) || Solution numbers merged in amalgamation<br />
|} <br />
<br />
For example, in the case of beta-blip the annotation for the single solution output in the .sol file shows these features<br />
<br />
SOLU HISTORY RF/TF(1/1:1)PAK(1:1)RNP(1:1)RNP(1:1)<br />
SOLU 6DIM ENSE beta EULER 200.849 41.269 183.909 FRAC -0.49604 -0.15830 -0.28092 BFAC 0.00000<br />
SOLU 6DIM ENSE blip EULER 43.749 80.793 117.292 FRAC -0.12289 0.29435 -0.09266 BFAC 0.00000<br />
<br />
A more complicated structure solution may have<br />
<br />
SOLU HISTORY RF/TF(7/1:10)PAK(10:10)RNP(10,12,13,11,17,16,18,25,3,8,22,21,20,7,969,6,5,201,9,4,390,2,1,19:1)RNP(1:1)<br />
<br />
==What to do in Difficult Cases==<br />
<br />
Not every structure can be solved by molecular replacement, but the right strategy can push the limits. What to do when the default jobs fail depends on why your structure is difficult.<br />
*'''Flexible Structure'''<br />
*:The relative orientations of the domains may be different in your crystal than in the model. If that may be the case, break the model into separate PDB files containing rigid-body units, enter these as separate ensembles, and search for them separately. If you find a convincing solution for one domain, but fail to find a solution for the next domain, you can take advantage of the knowledge that its orientation is likely to be similar to that of the first domain. The ROTAte&nbsp;AROUnd option of the brute rotation search can be used to restrict the search to orientations within, say, 30 degrees of that of the known domain. Allow for close approach of the domains by increasing the allowed clashes with the PACK keyword by, say, 1 for each domain break that you introduce. Note that it is possible to use the brute rotation search as part of the automated molecular replacement pipeline, by changing the choice of the type of rotation search. Alternatively, you could try generating a series of models perturbed by normal modes, with the NMAPdb keyword. One of these may duplicate the hinge motion and provide a good single model.<br />
*'''Poor or Incomplete Model'''<br />
*:Signal-to-noise is reduced by coordinate errors or incompleteness of the model. Since the rotation search has lower signal to begin with than the translation search, it is usually more severely affected. For this reason, it can be very useful to use the subsequent translation search as a way to choose among many (say 1000) orientations. THe MR_AUTO FAST search mode automatically reduces the cutoff for accepting peaks from the fast rotation function if the decault pass does not find a solution with a high z-score, but you can manually reduce this further with the PEAKS and PURGE keywords. You can also try turning off the clustering of fast rotation function peaks because the correct orientation may sit on the shoulder of a peak in the rotation function. <br />
*:As shown convincingly by Schwarzenbacher ''et al.'' (Schwarzenbacher, Godzik, Grzechnik &amp; Jaroszewski, ''Acta Cryst.'' D'''60''', 1229-1236, 2004), judicious editing can make a significant difference in the quality of a distant model. In a number of tests with their data on models below 30% sequence identity, we have found that Phaser works best with a "mixed model" (non-identical sidechains longer than Ser replaced by Ser). In agreement with their results, the best models are generally derived using more sophisticated alignment protocols, such as their FFAS protocol. Use [http://www.phenix-online.org/documentation/sculptor.htm phenix.sculptor] to edit your model.<br />
*'''High Degree of Non-crystallographic Symmetry'''<br />
*:If there are clear peaks in the self-rotation function, you can expect orientations to be related by this known NCS. Methods to automatically use such information will be implemented in a future version of Phaser. In the meantime, you can work out for yourself the orientations that would be consistent with NCS and use the ROTAte&nbsp;AROUnd option to sample similar orientations. Alternatively, you may have an oligomeric model and expect similar NCS in the crystal. First search with the oligomeric model; if this fails, search with a monomer. If that succeeds, you can again use the ROTAte&nbsp;AROUnd option to force a subsequent monomer to adopt an orientation similar to the one you expect.<br />
*'''What <u>not</u> to do'''<br />
*:The automated mode of Phaser is fast when Phaser finds a high Z-score solution to your problem. When Phaser cannot find a solution with a significant Z-score, it "thrashes", meaning it maintains a list of 100-1000's of low Z-score potential solutions and tries to improve them. This can lead to exceptionally long Phaser runs (over a week of CPU time). Such runs are possible because the highly automated script allows many consecutive MR jobs to be run without you having to manually set 100-1000's of jobs running and keep track of the results. "Thrashing" generally does not produce a solution: solutions generally appear relatively quickly or not at all. It is more useful to go back and analyse your models and your data to see where improvements can be made. Your system manager will appreciate you terminating these jobs.<br />
*:It is also not a good idea to effectively remove the packing test. Unless there is specific evidence in the logfile that a high TF-function Z-score solution is being rejected with a few clashes, it is much better to edit the model to remove the loops than to increase the number of allowed clashes. Packing criteria are a very powerful constraint on the translation function, and increasing the number of allowed clashes beyond a few (e.g. 1-5) will increase the search time enormously without the possibility of generating any correct solutions that would not have otherwise been found.<br />
*'''Other suggestions'''<br />
*:Phaser has powerful input, output and scripting facilities that allow a large number of possibilities for altering default behaviour and forcing Phaser to do what you think it should. However, you will need to read the information in the manual below to take advantage of these facilities!<br />
<br />
==How to Define Data==<br />
You need to tell Phaser the name of the mtz file containing your data and the columns in the mtz file to be used using the HKLIn and LABIn keywords. Additional keywords (BINS CELL OUTLier RESOlution SPACegroup) define how the data are used.<br />
<br />
==How to Define Models==<br />
Phaser must be given the models that it will use for molecular replacement. A model in Phaser is referred to as an "ensemble", even when it is described by a single file. This is because it is possible to provide a set of aligned structures as an ensemble, from which a statistically-weighted averaged model is calculated. A molecular replacement model is provided either as one or more aligned pdb files, or as an electron density map, entered as structure factors in an mtz file. Each ensemble is treated as a separate type of rigid body to be placed in the molecular replacement solution. An ensemble should only be defined once, even if there are several copies of the molecule in the asymmetric unit.<br />
<br />
Fundamental to the way in which Phaser uses MR models (either from coordinates or maps) is to estimate how the accuracy of the model falls off as a function of resolution, represented by the Sigma(A) curve. To generate the Sigma(A) curve, Phaser needs to know the RMS coordinate error expected for the model and the fraction of the scattering power in the asymmetric unit that this model contributes.<br />
<br />
A Babinet-style correction is used to account for the effects of disordered solvent on the completeness of the model at low resolution.<br />
<br />
Molecular replacement models are defined with the ENSEmble keyword and the COMPosition keyword. The ENSEmble keyword gives (amongst other things) the RMS deviation for the Sigma(A) curve. The COMPosition keyword is used to deduce the fraction of the scattering power in the asymmetric unit that each ensemble contributes. The composition of the asymmetric unit is defined either by entering the molecular weights or sequences of the components in the asymmetric unit, and giving the number of copies of each. Expert users can also enter the fraction of the scattering of each component directly, although the composition must still be entered for the absolute scale calculation. Please note that the composition supplied to Phaser has to include everything in the asymmetric unit, not just what is being looked for in the current search!<br />
<br />
===Building an Ensemble from Coordinates===<br />
The RMS deviation is determined directly from RMS or indirectly from IDENtity in the ENSEmble<br />
keyword using a formula that depends on the sequence identity and the number of residues in the model.<br />
<br />
{| class="wikitable" style="text-align:center" align=right style="margin-left: 30px" <br />
|colspan="11" style="text-align: center;" | Initial estimate of RMS deviation<br />
|-<br />
|colspan="11" style="text-align: center;" | Number of residues in model versus sequence identity<br />
|-<br />
! !! #50 !! #100 !! #200 !! #300 !! #400 !! #600 !! #850 !! #1000 !! #1500 !! #2000<br />
|-<br />
|'''ID=0%''' || 1.579 || 1.689 || 1.875 || 2.030 || 2.164 || 2.391 || 2.625 || 2.748 || 3.093 || 3.375<br />
|-<br />
|'''ID=10%''' || 1.356 || 1.451 || 1.610 || 1.743 || 1.858 || 2.053 || 2.255 || 2.360 || 2.657 || 2.899<br />
|-<br />
|'''ID=20%''' || 1.165 || 1.246 || 1.383 || 1.497 || 1.596 || 1.764 || 1.936 || 2.027 || 2.281 || 2.489<br />
|-<br />
|'''ID=30%''' || 1.000 || 1.070 || 1.188 || 1.286 || 1.371 || 1.515 || 1.663 || 1.741 || 1.959 || 2.138<br />
|-<br />
|'''ID=40%''' || 0.859 || 0.919 || 1.020 || 1.104 || 1.177 || 1.301 || 1.428 || 1.495 || 1.683 || 1.836<br />
|-<br />
|'''ID=50%''' || 0.738 || 0.789 || 0.876 || 0.948 || 1.011 || 1.117 || 1.227 || 1.284 || 1.445 || 1.577<br />
|-<br />
|'''ID=60%''' || 0.634 || 0.678 || 0.752 || 0.814 || 0.868 || 0.959 || 1.053 || 1.103 || 1.241 || 1.354<br />
|-<br />
|'''ID=70%''' || 0.544 || 0.582 || 0.646 || 0.699 || 0.746 || 0.824 || 0.905 || 0.947 || 1.066 || 1.163<br />
|-<br />
|'''ID=80%''' || 0.467 || 0.500 || 0.555 || 0.601 || 0.640 || 0.708 || 0.777 || 0.813 || 0.915 || 0.999<br />
|-<br />
|'''ID=90%''' || 0.401 || 0.429 || 0.477 || 0.516 || 0.550 || 0.608 || 0.667 || 0.698 || 0.786 || 0.858<br />
|-<br />
|'''ID=100%''' || 0.345 || 0.369 || 0.409 || 0.443 || 0.472 || 0.522 || 0.573 || 0.600 || 0.675 || 0.737<br />
|-<br />
|}<br />
<br />
The RMS deviation estimated from ID may be an underestimate of the true value if there is a slight conformational change between the model and target structures. To find a solution in these cases it may be necessary to increase the RMS from the default value generated from the ID, by say 0.5 Ångstroms. On the other hand, when Phaser succeeds in solving a structure from a model with sequence identity much below 30%, it is often found that the fold is preserved better than the average for that level of sequence identity. So it may be worth submitting a run in which the RMS error is set at, say, 1.5, even if the sequence identity is low. The table below can be used as a guide as to the default RMS value corresponding to ID.<br />
<br />
If you construct a model by homology modelling, remember that the RMS error you expect is essentially the error you expect from the template structure (if not worse!). So specify the sequence identity of the template, not of the homology model.<br />
<br />
Only the model with the highest sequence identity is reported in the output pdb file. Also, HETATM cards in the input pdb file are ignored in the calculation of the structure factors for the ensemble, but are carried through to the output pdb file. Thus, the phases on the output mtz file (which come from the structure factors of the ensemble) do not correspond to those that would be calculated from the output pdb file, when there is more than one pdb file in an ensemble and/or the pdbfile(s) have HETATM records.<br />
<br />
====Coordinate Editing====<br />
=====HETATM/LIGANDS=====<br />
Phaser ignores the scattering from HETATM records. The HETATM records are carried though to output with occupancy set to zero. Ligands will therefore not contribute to the scattering used for molecular replacement. The exceptions to this rule are the HETATM records for MSE (seleno-methionine) MSO (seleno-methionine selenoxide) CSE (seleno-cysteine) CSO (seleno-cysteine selenoxide) ALY (acetyllysine) MLY (n-dimethyl-lysine) and MLZ (n-methyl-lysine) which are used in the scattering and carried through to output with their original occupancy. If you wish to include any HETATM records in the scattering the record name use the keyword ENSE modlid HETATOM ON<br />
<br />
=====WATER=====<br />
Water molecules (identified by the residue name OW WAT HOH H2O OH2 MOH WTR or TIP) are deleted from the pdb file on input, are not used in the scattering and are not carried through to file output. If you want to retain water molecules you will need to change the residue name to something other than this (e.g. WWW) so that the atoms are not identified as water. To include the water molecules in the scattering, the HETATM records will also have to be changed to ATOM records as described above.<br />
<br />
===Building an Ensemble from Electron Density===<br />
When using density as a model, it is necessary to specify both the extent (x,y,z limits) of the cut-out region of density, and the centre of this region. With coordinates, Phaser can work this out by itself. This information is needed, for instance, to decide how large rotational steps can be in the rotation search and to carry out the molecular transform interpolation correctly. In the case of electron density, the RMS value does not have the same physical meaning that it has when the model is specified by atomic coordinates, but it is used to judge how the accuracy of the calculated structure factors drops off with resolution. A suitable value for RMS can be obtained, in the case of density from an experimentally-phased map, by choosing a value that makes the SigmaA curve fall off with resolution similarly to the mean figures-of-merit. In the case of density from an EM image reconstruction, the RMS value should make the SigmaA curve fall off similarly to a Fourier correlation curve used to judge the resolution of the EM image.<br />
<br />
For detailed information, including a tutorial with example scripts, see<br />
[[Using Electron Density as a Model| Using density as a model]]<br />
<br />
==How to Define Composition==<br />
The composition defines the total amount of protein and nucleic acid that you have in the asymmetric unit not the fraction of the asymmetric unit that you are searching for.<br />
<br />
===Default Composition===<br />
For convenience, the composition defaults to 50% protein scattering by volume (the average for protein crystals). It is better to enter it explicitly, even if only to check that you have correctly deduced the probable content of your crystal. If your crystal has higher or lower solvent content than this, or contains nucleic acid, then the composition should be entered explicitly.<br />
===Composition by Solvent Content===<br />
Scattering is determined from the solvent content of the crystal, assuming that the crystal contains protein only, and the average distribution of amino acids in protein. If your crystal contains nucleic acid or your protein has an unusual amino acid distribution then the composition should be entered explicitly using the MW or sequence options.<br />
===Composition by Number of Residues in ASU===<br />
Scattering is determined from the number of residues in the asymmetric unit, assuming that the crystal contains protein only or nucleic acid only, and assuming an average distribution of residues for either. If your crystal contains a mixture then the composition should be entered explicitly using the MW or sequence options. If your crystal has an unusual residue distribution then the composition should be entered explicitly using the sequence options.<br />
===Composition by Molecular Weight===<br />
The composition is calculated from the molecular weight of the protein and nucleic acid assuming the protein and nucleic acid have the average distribution of amino acids and bases. If your protein or nucleic acid has an unusual amino acid or base distribution the composition should be entered by sequence. You can mix compositions entered by molecular weight with those entered by sequence.<br />
===Composition by Sequence===<br />
The composition is calculated from the amino acid sequence of the protein and the base sequence of the nucleic acid in fasta format. You can mix compositions entered by molecular weight with those entered by sequence. Individual atoms can be added to the composition with the COMPOSITION ATOM keyword. This allows the explicit addition of heavy atoms in the structure e.g. Fe atoms.<br />
===Composition by Percentage Scattering===<br />
The fraction scattering of each ensemble can be entered directly. The fraction scattering of each ensemble is normally automatically worked out from the average scattering from each ensemble (calculated from the pdb files if entered as coordinates, or from the protein and nucleic acid molecular weights if entered as a map) divided by the total scattering given by the composition, but entering the fraction scattering directly overrides this calculation. This option is for use when the pdb files of the models in the ensemble are unusual e.g. consist only of C-alpha atoms, or only of hydrogen atoms (as in the CLOUDS method for NMR).<br />
<br />
==How to Define Solutions==<br />
Phaser writes out files ending in ".sol" and ".rlist" that contain the solution information from the job. The root of the files is given by the ROOT keyword. By default, the root filename is PHASER. These files can be read back into subsequent runs of Phaser to build up solutions containing more than one molecule in the asymmetric unit.<br />
<br />
"PHASER.sol" files are generated by all modes (rotation function modes with VERBOSE output), and contain the current idea of potential molecular replacement solutions.<br />
<br />
"PHASER.rlist" files are generated by the rotation function modes, and are used as input for performing translation functions.<br />
<br />
For simple MR cases you don't really need to know how to define molecular replacement solutions. However, for difficult cases you might need to edit the files "PHASER.sol" and "PHASER.rlist" files manually<br />
<br />
=== "sol" Files===<br />
SOLUtion 6DIM keywords describe Ensembles that have been oriented by a rotation search and positioned by a translation search. Each Ensemble in the asymmetric unit has its own SOLUtion keyword. When more than one (potential) molecular replacement solution is present, the solutions are separated with the SOLUTION SET keywords.<br />
<br />
==="rlist" Files===<br />
These files define a rotation function list. The peak list is given with a series of SOLUtion TRIAl keywords.<br />
<br />
If a partial solution is already known, then the information for the currently "known" parts of the asymmetric unit is given in the form used for the PHASER.sol file, followed by the list of trial orientations for which a translation function is to be performed.<br />
<br />
===Fixed partial structure===<br />
If you have the coordinates of a partial solution with the pdb coordinates of the known structure in the correct orientation and position, then you can force Phaser to use these coordinates. Use the SOLUTION keyword to fix a rotation of 0 0 0 and a position of 0 0 0 for these coordinates.<br />
<br />
==How to Select Peaks==<br />
<br />
<br />
<br />
The selection of peaks saved for output in the rotation and translation functions can be done in four different ways.<br />
*'''Select by Percentage'''<br />
*: Percentage of the top peak, where the value of the top peak is defined as 100% and the value of the mean is defined as 0%.<br />
*: Default, cutoff=75%. This criteria has the advantange that at least one peak (the top peak) always survives the selection. If the top solution is clear, then only the one solution will be output, but if the distribution of peaks is rather flat, then many peaks will be output for testing in the next part of the MR procedure (e.g. many peaks selected from the rotation function for testing with a translation function). <br />
*'''Select by Z-score'''<br />
*: Number of standard deviations (sigmas) over the mean (the Z-score). <br />
*: Absolute significance test. Not all searches will produce output if the cutoff value is too high (e.g. 5 sigma). <br />
*'''Select by Number'''<br />
*: Number of top peaks to select. <br />
*: If the distribution is very flat then it might be better to select a fixed large number (e.g. 1000) of top rotation peaks for testing in the translation function.<br />
*'''No selection'''<br />
*: All peaks are selected. <br />
*: Enables full 6 dimensional searches, where all the solutions from the rotation function are output for testing in the translation function. This should never be necessary; it would be much faster and probably just as likely to work if the top 1000 peaks were used in this way.<br />
<br />
[[Image:Phaser_selection.gif| Selection criteria]]<br />
<br />
Peaks can also be clustered or not clustered prior to selection in steps 1 and 2.<br />
*'''Clustering Off'''<br />
: All high peaks on the search grid are selected<br />
*'''Clustering On'''<br />
: Points on the search grid with higher neighbouring points are removed from the selection<br />
<br />
<br />
[[Image:Phaser_clustering.gif| Clustering]]<br />
<br />
==How to Control Output==<br />
The output of Phaser can be controlled with optional keywords. <br />
<br />
The ROOT keyword is not compulsory (the default root filename is "PHASER"), but should always be given, so that your jobs have separate and meaningful output filenames.<br />
<br />
The TOPFiles keyword controls the number of potential MR solutions for which PDB and (in the appropriate modes) MTZ files are produced.<br />
<br />
For the MR_AUTO, MR_RNP and MR_LLG modes, unless HKLOut OFF is given as an optional keyword, Phaser produces an MTZ file with "SigmaA" type weighted Fourier map coefficients for producing electron density maps for rebuilding.<br />
<br />
{| class="wikitable" style="text-align:left" width=100%<br />
|-<br />
! MTZ Column Labels !! Description<br />
|-<br />
| FWT/PHWT || Amplitude and phase for 2''m''&#124;F<sub>obs</sub>&#124;-''D''&#124;F<sub>calc</sub>&#124; exp(''i''&alpha;<sub>calc</sub>) map<br />
|-<br />
| DELFWT/PHDELWT || Amplitude and phase for ''m''&#124;F<sub>obs</sub>&#124;-''D''&#124;F<sub>calc</sub>&#124; exp(''i''&alpha;<sub>calc</sub>) map<br />
|-<br />
| FOM || ''m'', analogous to the "Sim" weight, to estimate the reliability of &alpha;<sub>calc</sub><br />
|-<br />
| HLA/HLB/HLC/HLD || Hendrickson-Lattman coefficients encoding the phase probability distribution<br />
|}<br />
<br />
==Translational Non-crystallographic Symmetry==<br />
<br />
<span style="color:crimson">'''*Warning*''' Solution by MR in the presence of translational non-crystallographic symmetry is not fully automated.</span><br />
<br />
Phaser calculates correction factors for the expected intensities in the presence of translational non-crystallographic symmetry (tNCS), and is able to solve structures with complex patterns of tNCS. '''However, the use of Phaser in the presence of tNCS requires the nature of the tNCS to be understood by the user.''' In simple cases, solution is no more difficult than solution without tNCS, but in complex cases, separate Phaser runs with tNCS turned on and off, and/or the use of different tNCS vectors, may be necessary.<br />
<br />
The output of Phaser will help the user in detecting and understanding the tNCS, but '''the tNCS is not completely characterised by Phaser'''. The default behaviour may or may not be correct for the particular crystal under study.<br />
<br />
Characterization of the tNCS involves understanding the number of copies of the molecule in the asymmetric unit and the translation vectors between them. Molecules related by a tNCS vector will have an associated peak in the native Patterson. Phaser calculates the native Patterson (MODE TNCS) and lists the peaks that are more than 20% of the origin peak. Any given crystal with tNCS may have one or more peaks meeting this criteria.<br />
<br />
===Default tNCS detection and correction===<br />
====No tNCS====<br />
No tNCS correction is applied by default if there is<br />
# no peak in the native Patterson <br />
# more than one peak in the native Patterson over 20% of the origin and these peaks are not all the result of a commensurate modulation<br />
<br />
====Pairs of molecules====<br />
By default, if Phaser detects a peak in the native Patterson then Phaser will search for molecules in pairs related by the tNCS vector given by the peak in the native Patterson.<br />
<br />
This will be the correct behaviour if and only if there are an even number of copies of the molecule in the asymmetric unit, clustered into two groups related by a single tNCS vector. There will only be one significant peak in the native Patterson. Fortunately, this is a reasonably common scenario.<br />
<br />
Phaser refines the relative orientation of the molecules in the two groups (rotations of up to 10 degrees will still give rise to a significant native Patterson peak) and uses this information to generate expected intensity factors for the reflections. Solution should be straightforward, with the usual caveat for MR that there is a sufficiently good model.<br />
<br />
Where there is a single peak in the native Patterson, it is often located at a position half way along a unit cell axis or diagonal, representing a pseudo-halving of the unit cell dimensions. However, Phaser is by no means restricted to these sorts of pseudo-cells in its handling of two-fold tNCS, and the tNCS vector can be in a general position.<br />
<br />
===Non-default tNCS correction===<br />
====Higher order tNCS====<br />
Frequently, tNCS does not associate 2 clusters of molecules in the asymmetric unit, but rather there are 3 or more (n) clusters of molecules associated by a series of vectors that are multiples of 1, 2, 3 ... (n-1) times a basic translation vector. Where n times the basic translation vector equates to (very close to) integer multiples of unit cell axes, the tNCS represents a pseudo-cell, and this case is known as commensurate modulation. <br />
<br />
Phaser attempts to automatically detect commensurate modulation. The peaks of the native Patterson are analyzed to find the n-fold relationship. The series will not generally have all peaks the same height. Lower peaks in the series represent relationships where the relative rotations between related molecules are larger. Missing peaks in the series may be below the default 20% of origin cut-off. This can be lowered with TNCS PATT PERCENT <x><br />
<br />
Phaser then sets TNCS NMOL <n> and the vector for the tNCS, and searches for ensembles in multiples of NMOL.<br />
<br />
When there are more than two molecules related by tNCS, Phaser does not refine the orientations between the molecules related by the tNCS.<br />
<br />
However, as for two-fold tNCS, Phaser is not restricted to these sorts of pseudo-cells and the basic tNCS vector can be in a general position, as can the number of copies.<br />
<br />
'''The automatic detection may not give the true tNCS relationship'''. For example, the true commensurate modulation may be a factor of the NMOL automatically detected by Phaser, or there may not be commensurate modulation at all, or commensurate modulation may not be found with the default Pattesron peak height cutoff. In difficult cases, please inspect the Patterson for peaks.<br />
<br />
====Complex tNCS====<br />
If there are many molecules in the asymmetric unit but they are not all related by tNCS, or there are sub-groups of molecules related by different tNCS vectors, then the modulations of the expected intensities due to the tNCS will be much less significant than the cases described above. '''In these cases it is possible that structure solution will be achieved without any tNCS correction factors being applied.''' Indeed, searching for all the copies as tNCS-related multiples when some molecules are not related by tNCS will cause structure solution to fail. To turn off the automatic detection and use of tNCS use the keyword TNCS USE OFF.<br />
<br />
If turning off the TNCS correction factors fails to give a solution, then a good approach is to proceed step-wise. Consider the highest native Patterson peak first and determine that nature of the tNCS associated with it. Use the appropriate correction factors to locate all the molecules with this tNCS. Then take the second independent native Patterson peak and apply the correction factors associated with it to find the second set of molecules, fixing the first, etc. Finally, turn TNCS off to find any orphan molecules.</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Molecular_Replacement&diff=2377Molecular Replacement2016-11-28T10:49:54Z<p>Airlie: /* Pairs of molecules */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
'''Quicklink to example scripts''' → [[MR using keyword input]]<br />
<br />
'''Quicklink to phaser.famos (find_alt_orig_sym_mate) documentation''' → [[Famos]]<br />
<br />
Phaser should be able to solve most structures with the Automated Molecular Replacement mode, and this is the first mode that you should try. Give Phaser your data ([[#How to Define Data|How to Define Data]]) and your models ([[#How to Define Models|How to Define Models]]), tell Phaser what to search for, and a list of possible spacegroups (in the same point group).<br />
<br />
If this doesn't work (see [[#Has Phaser Solved It?| Has Phaser Solved It?]]), you can try selecting peaks of lower significance in the rotation function in case the real orientation was not within the selection criteria. By default peaks above 75% of the top peak are selected (see [[#How to Select Peaks| How to Select Peaks]]). See [[#What to do in Difficult Cases| What to do in Difficult Cases]] for more hints and tips. If the automated molecular replacement mode doesn't work even with non-default input you need to run the modes of Phaser separately. The possibilities are endless - you can even try exhaustive searches (translations of all orientations) if you want - but experience has shown that most structures that can be solved by Phaser can be solved by relatively simple strategies.<br />
<br />
==Automated Molecular Replacement==<br />
Automated Molecular Replacement combines the anisotropy correction, likelihood enhanced fast rotation function, likelihood enhanced fast translation function, packing and refinement modes for multiple search models and a set of possible spacegroups to automatically solve a structure by molecular replacement. Top solutions are output to the files FILEROOT.sol, FILEROOT.#.mtz and FILEROOT.#.pdb (where "#" refers to the sorted solution number, 1 being the best, and only 1 is output by default). Many structures can be solved by running an automated molecular replacement search with defaults, giving the ensembles that you expect to be easiest to find first.<br />
<br />
At the completion of Molecular Replacement you may wish to place your solutions on a common origin with a previous solution, for which [[Famos | Famos ]] can be used.<br />
<br />
[[Image:Phaser_MR_auto.gif|Flow Diagram for Automated MR]]<br />
<br />
==Should Phaser Solve It?==<br />
The difficulty of a molecular replacement problem depends primarily on two major factors: how well the model will be able to explain the diffraction data (which depends both on the accuracy of the model and on its completeness), and how many reflections can be explained, at least in part. Each reflection provides a piece of information that helps to identify correct MR solutions.<br />
<br />
It is possible to make a reasonable prediction of whether or not a solution will be found. If the quality of the model (its accuracy and completeness) can be estimated, then the expected contribution of each reflection to the total LLG can also be estimated. From a large battery of tests, we know that an LLG of 40 or greater usually indicates a correct solution (at least in the absence of complicating factors such as translational non-crystallographic symmetry, tNCS). Building on this understanding, if it is estimated that the LLG will be 60 or less, then Phaser will assume that the problem is a difficult one, and will implement search procedures optimised for difficult problems.<br />
<br />
==What Resolution of Data Should be Used?==<br />
The signal for a molecular replacement solution should be very clear if the expected value of the LLG is much higher than the minimum required to be fairly certain of a solution. Currently Phaser aims for a minimum LLG of 120 and, if it is possible to achieve an even higher value, given the quality of the model and the quantity of diffraction data, then the resolution for the initial search is limited to the value required to achieve an expected LLG of 120. Data to the full resolution are still used for a final rigid-body refinement, or in a second pass if a clear solution is not found in the first attempt.<br />
<br />
However, if the model is expected to have a large RMS error (based usually on the correlation between sequence identity and RMS error), then data to high resolution will not contribute any significant signal. Regardless of the expected LLG at the highest resolution limit, the resolution used is limited to 1.8 times the estimated RMS error of the model, because this resolution limit gives about 99% of the LLG that could be achieved.<br />
<br />
Because Phaser implements strategies designed to solve structures with as much confidence as possible, as efficiently as possible, it is best to leave the choice of resolution to Phaser, at least in the first instance.<br />
<br />
==Has Phaser Solved It?==<br />
{| class="wikitable" style="text-align:center" align="right" style="margin-left: 30px" <br />
|-<br />
! TF Z-score !! Have I solved it?<br />
|-<br />
| less than 5 || no<br />
|-<br />
| 5 - 6 || unlikely<br />
|-<br />
| 6 - 7 || possibly<br />
|-<br />
| 7 - 8 || probably<br />
|-<br />
| more than 8* ||definitely<br />
|-<br />
|colspan="2" style="text-align: center;" | *''6 for 1st model in monoclinic space groups''<br />
|} <br />
<br />
Ideally, a unique solution with a strong signal will be found at the end of the search. If you are searching for multiple components, then ideally the search for each component will also give a strong signal. However if the signal-to-noise of your search is low, there will be noise peaks and multiple ambiguous solutions. Signal-to-noise is judged using the '''Z-score''', which is computed by comparing the LLG values from the rotation or translation search with LLG values for a set of random rotations or translations. The mean and the RMS deviation from the mean are computed from the random set, then the Z-score for a search peak is defined as its LLG minus the mean, all divided by the RMS deviation, ''i.e. '' '''the number of standard deviations above (or below) the mean. '''<br />
<br />
For a rotation function, the correct orientation may be well down the list with a Z-score (number of standard deviations above the mean value, or RFZ) under 4, and it is often not possible to identify the correct orientation until a translation function is performed and yields a clear solution. Note that the signal-to-noise of the rotation function drops with increasing number of primitive symmetry operations (the number of different orientations for symmetry-related molecules), because there is more uncertainty about how the structure factor contributions from symmetry-related copies will add up.<br />
<br />
For a translation function the correct solution will generally have a Z-score (TFZ) over 5 and be well separated from the rest of the solutions. Of course, there will always be exceptions! The table gives a very rough guide to interpreting TFZ scores. This table will be updated, as we learn more from systematic molecular replacement trials.<br />
<br />
When you are searching for multiple components, the signal may be low for the first few components but, as the model becomes more complete, the signal should become stronger. Finding a clear solution for a new component is a good sign that the partial solution to which that component was added was indeed correct.<br />
<br />
You should always at least glance through the summary of the logfile. One thing to look for, in particular, is whether any translation solutions with a high Z-score have been rejected by the packing step. By default up to 5 percent of marker atoms (C-alpha atoms for protein) are allowed to be involved in clashes. A solution with more clashes may still be correct, and the clashes may arise only because of differences in small surface loops. If this happens, repeat the run allowing a suitable number of clashes. Note that, unless there is specific evidence in the logfile that a high TFZ-score solution is being rejected with a few clashes, it is much better to edit the model to remove the loops than to increase the number of allowed clashes. Packing criteria are a very powerful constraint on the translation function, and increasing the number of allowed clashes beyond the default will increase the search time enormously without the possibility of generating any correct solutions that would not have otherwise been found.<br />
<br />
Note that, by default, Phaser will produce a single PDB file corresponding to the top solution found (if any), so finding a single PDB file in your output directory is not an indication that the search succeeded! You have to look, at least, at the summary of the logfile, or at the list of possible solutions in the .sol file that is produced if you run Phaser from ccp4i or command-line scripts.<br />
<br />
==Annotation==<br />
<br />
A highly compact summary of the history of the statistics of a solution is given in the SOLUTION SET in the .sol file. This is a good place to start your analysis of the output. The annotation gives the Z-score of the solution at each rotation and translation function, the number of clashes in the packing, and the refined LLG.<br />
<br />
{| class="wikitable" style="text-align:center" style="margin-left: 30px" <br />
|-<br />
! Annotation !! Meaning<br />
|-<br />
| RFZ= || Rotation Function Z-score<br />
|-<br />
| TFZ= || Translation Function Z-score<br />
|-<br />
| PAK= || Number of packing clashes<br />
|-<br />
| LLG= || LLG after refinement. Will be repeated when a low resolution refinement is followed by a high resolution refinement.<br />
|-<br />
| TFZ== || Translation Function Z-score equivalent, only calculated for the top solution after refinement (or for the number of top files specified by TOPFILES)<br />
|-<br />
| RF++ || Rotation angle from previous strong solution has been used in the addition of next solution<br />
|-<br />
| RF*0 || Rotation angle 000 identified by low R-factor of input model<br />
|-<br />
| TFZ=* || First molecule in P1 (arbitrary origin, no Translation Function required)<br />
|-<br />
| TF*0 || Translation vector 000 identified by low R-factor of input model<br />
|-<br />
| (&&nbsp;... & ...) || Set of TFZ PAK and LLG values for placements that were amalgamated (more than one placement from a single Translation Function)<br />
|-<br />
| LLG+=(...&nbsp;&&nbsp;...)&nbsp;|| Set of LLG values calculated during amalgamation, which will always be increasing in value<br />
|-<br />
| +TNCS || Components added by Translational NCS relation<br />
|-<br />
| *T=<i>n</i> || Solution matches template solution <i>n</i><br />
|} <br />
<br />
Two versions of TFZ (the translation function Z-score) now appear for each component. The first ("TFZ=") is the Z-score from the actual translation search, which depends on the accuracy of the orientation used for that search. The second ("TFZ==") is the TFZ-equivalent, which indicates what the TFZ score would have been with the correct (refined) orientation. You should see the TFZ-equivalent is high at least for the final components of the solution, and that the LLG (log-likelihood gain) increases as each component of the solution is added. For example, in the case of beta-blip the annotation for the single solution output in the .sol file shows these features<br />
<br />
SOLU SET RFZ=10.7 TFZ=24.3 PAK=0 LLG=472 TFZ==24.7 RFZ=6.4 TFZ=24.4 PAK=0 LLG=1006 TFZ==29.7 LLG=1006 TFZ==29.7<br />
SOLU 6DIM ENSE beta EULER 200.849 41.269 183.909 FRAC -0.49604 -0.15830 -0.28092 BFAC 0.00000<br />
SOLU 6DIM ENSE blip EULER 43.749 80.793 117.292 FRAC -0.12289 0.29435 -0.09266 BFAC 0.00000<br />
<br />
Note that the Euler angles in Phaser follow the same convention as those defined for the Crowther fast rotation function, i.e. z-y-z (rotate around the z-axis, followed by the new y-axis, followed by the new z-axis).<br />
<br />
==History==<br />
<br />
A highly compact summary of the history of the peak positions of a solution is given in the SOLUTION HISTORY in the .sol file. Together with the SOLUTION SET annotation, this is useful in your analysis of the output. <br />
<br />
{| class="wikitable" style="text-align:center" style="margin-left: 30px" <br />
|-<br />
! History !! Meaning<br />
|-<br />
| RF/TF(r/t:n) || (r) Rotation Function peak number/(t) Translation Function peak number for the rotation function : (n) number of peak in final merged and sorted list<br />
|-<br />
| PAK(n:m) || (n) input solution number : (m) output solution number after packing condition applied<br />
|-<br />
| RNP(m,a,b,c,... : p) || All input peaks amalgamated after refinement to give output solution number (m and others): (p) output solution number<br />
|-<br />
| FUSE(A,B,C) || Solution numbers merged in amalgamation<br />
|} <br />
<br />
For example, in the case of beta-blip the annotation for the single solution output in the .sol file shows these features<br />
<br />
SOLU HISTORY RF/TF(1/1:1)PAK(1:1)RNP(1:1)RNP(1:1)<br />
SOLU 6DIM ENSE beta EULER 200.849 41.269 183.909 FRAC -0.49604 -0.15830 -0.28092 BFAC 0.00000<br />
SOLU 6DIM ENSE blip EULER 43.749 80.793 117.292 FRAC -0.12289 0.29435 -0.09266 BFAC 0.00000<br />
<br />
A more complicated structure solution may have<br />
<br />
SOLU HISTORY RF/TF(7/1:10)PAK(10:10)RNP(10,12,13,11,17,16,18,25,3,8,22,21,20,7,969,6,5,201,9,4,390,2,1,19:1)RNP(1:1)<br />
<br />
==What to do in Difficult Cases==<br />
<br />
Not every structure can be solved by molecular replacement, but the right strategy can push the limits. What to do when the default jobs fail depends on why your structure is difficult.<br />
*'''Flexible Structure'''<br />
*:The relative orientations of the domains may be different in your crystal than in the model. If that may be the case, break the model into separate PDB files containing rigid-body units, enter these as separate ensembles, and search for them separately. If you find a convincing solution for one domain, but fail to find a solution for the next domain, you can take advantage of the knowledge that its orientation is likely to be similar to that of the first domain. The ROTAte&nbsp;AROUnd option of the brute rotation search can be used to restrict the search to orientations within, say, 30 degrees of that of the known domain. Allow for close approach of the domains by increasing the allowed clashes with the PACK keyword by, say, 1 for each domain break that you introduce. Note that it is possible to use the brute rotation search as part of the automated molecular replacement pipeline, by changing the choice of the type of rotation search. Alternatively, you could try generating a series of models perturbed by normal modes, with the NMAPdb keyword. One of these may duplicate the hinge motion and provide a good single model.<br />
*'''Poor or Incomplete Model'''<br />
*:Signal-to-noise is reduced by coordinate errors or incompleteness of the model. Since the rotation search has lower signal to begin with than the translation search, it is usually more severely affected. For this reason, it can be very useful to use the subsequent translation search as a way to choose among many (say 1000) orientations. THe MR_AUTO FAST search mode automatically reduces the cutoff for accepting peaks from the fast rotation function if the decault pass does not find a solution with a high z-score, but you can manually reduce this further with the PEAKS and PURGE keywords. You can also try turning off the clustering of fast rotation function peaks because the correct orientation may sit on the shoulder of a peak in the rotation function. <br />
*:As shown convincingly by Schwarzenbacher ''et al.'' (Schwarzenbacher, Godzik, Grzechnik &amp; Jaroszewski, ''Acta Cryst.'' D'''60''', 1229-1236, 2004), judicious editing can make a significant difference in the quality of a distant model. In a number of tests with their data on models below 30% sequence identity, we have found that Phaser works best with a "mixed model" (non-identical sidechains longer than Ser replaced by Ser). In agreement with their results, the best models are generally derived using more sophisticated alignment protocols, such as their FFAS protocol. Use [http://www.phenix-online.org/documentation/sculptor.htm phenix.sculptor] to edit your model.<br />
*'''High Degree of Non-crystallographic Symmetry'''<br />
*:If there are clear peaks in the self-rotation function, you can expect orientations to be related by this known NCS. Methods to automatically use such information will be implemented in a future version of Phaser. In the meantime, you can work out for yourself the orientations that would be consistent with NCS and use the ROTAte&nbsp;AROUnd option to sample similar orientations. Alternatively, you may have an oligomeric model and expect similar NCS in the crystal. First search with the oligomeric model; if this fails, search with a monomer. If that succeeds, you can again use the ROTAte&nbsp;AROUnd option to force a subsequent monomer to adopt an orientation similar to the one you expect.<br />
*'''What <u>not</u> to do'''<br />
*:The automated mode of Phaser is fast when Phaser finds a high Z-score solution to your problem. When Phaser cannot find a solution with a significant Z-score, it "thrashes", meaning it maintains a list of 100-1000's of low Z-score potential solutions and tries to improve them. This can lead to exceptionally long Phaser runs (over a week of CPU time). Such runs are possible because the highly automated script allows many consecutive MR jobs to be run without you having to manually set 100-1000's of jobs running and keep track of the results. "Thrashing" generally does not produce a solution: solutions generally appear relatively quickly or not at all. It is more useful to go back and analyse your models and your data to see where improvements can be made. Your system manager will appreciate you terminating these jobs.<br />
*:It is also not a good idea to effectively remove the packing test. Unless there is specific evidence in the logfile that a high TF-function Z-score solution is being rejected with a few clashes, it is much better to edit the model to remove the loops than to increase the number of allowed clashes. Packing criteria are a very powerful constraint on the translation function, and increasing the number of allowed clashes beyond a few (e.g. 1-5) will increase the search time enormously without the possibility of generating any correct solutions that would not have otherwise been found.<br />
*'''Other suggestions'''<br />
*:Phaser has powerful input, output and scripting facilities that allow a large number of possibilities for altering default behaviour and forcing Phaser to do what you think it should. However, you will need to read the information in the manual below to take advantage of these facilities!<br />
<br />
==How to Define Data==<br />
You need to tell Phaser the name of the mtz file containing your data and the columns in the mtz file to be used using the HKLIn and LABIn keywords. Additional keywords (BINS CELL OUTLier RESOlution SPACegroup) define how the data are used.<br />
<br />
==How to Define Models==<br />
Phaser must be given the models that it will use for molecular replacement. A model in Phaser is referred to as an "ensemble", even when it is described by a single file. This is because it is possible to provide a set of aligned structures as an ensemble, from which a statistically-weighted averaged model is calculated. A molecular replacement model is provided either as one or more aligned pdb files, or as an electron density map, entered as structure factors in an mtz file. Each ensemble is treated as a separate type of rigid body to be placed in the molecular replacement solution. An ensemble should only be defined once, even if there are several copies of the molecule in the asymmetric unit.<br />
<br />
Fundamental to the way in which Phaser uses MR models (either from coordinates or maps) is to estimate how the accuracy of the model falls off as a function of resolution, represented by the Sigma(A) curve. To generate the Sigma(A) curve, Phaser needs to know the RMS coordinate error expected for the model and the fraction of the scattering power in the asymmetric unit that this model contributes.<br />
<br />
A Babinet-style correction is used to account for the effects of disordered solvent on the completeness of the model at low resolution.<br />
<br />
Molecular replacement models are defined with the ENSEmble keyword and the COMPosition keyword. The ENSEmble keyword gives (amongst other things) the RMS deviation for the Sigma(A) curve. The COMPosition keyword is used to deduce the fraction of the scattering power in the asymmetric unit that each ensemble contributes. The composition of the asymmetric unit is defined either by entering the molecular weights or sequences of the components in the asymmetric unit, and giving the number of copies of each. Expert users can also enter the fraction of the scattering of each component directly, although the composition must still be entered for the absolute scale calculation. Please note that the composition supplied to Phaser has to include everything in the asymmetric unit, not just what is being looked for in the current search!<br />
<br />
===Building an Ensemble from Coordinates===<br />
The RMS deviation is determined directly from RMS or indirectly from IDENtity in the ENSEmble<br />
keyword using a formula that depends on the sequence identity and the number of residues in the model.<br />
<br />
{| class="wikitable" style="text-align:center" align=right style="margin-left: 30px" <br />
|colspan="11" style="text-align: center;" | Initial estimate of RMS deviation<br />
|-<br />
|colspan="11" style="text-align: center;" | Number of residues in model versus sequence identity<br />
|-<br />
! !! #50 !! #100 !! #200 !! #300 !! #400 !! #600 !! #850 !! #1000 !! #1500 !! #2000<br />
|-<br />
|'''ID=0%''' || 1.579 || 1.689 || 1.875 || 2.030 || 2.164 || 2.391 || 2.625 || 2.748 || 3.093 || 3.375<br />
|-<br />
|'''ID=10%''' || 1.356 || 1.451 || 1.610 || 1.743 || 1.858 || 2.053 || 2.255 || 2.360 || 2.657 || 2.899<br />
|-<br />
|'''ID=20%''' || 1.165 || 1.246 || 1.383 || 1.497 || 1.596 || 1.764 || 1.936 || 2.027 || 2.281 || 2.489<br />
|-<br />
|'''ID=30%''' || 1.000 || 1.070 || 1.188 || 1.286 || 1.371 || 1.515 || 1.663 || 1.741 || 1.959 || 2.138<br />
|-<br />
|'''ID=40%''' || 0.859 || 0.919 || 1.020 || 1.104 || 1.177 || 1.301 || 1.428 || 1.495 || 1.683 || 1.836<br />
|-<br />
|'''ID=50%''' || 0.738 || 0.789 || 0.876 || 0.948 || 1.011 || 1.117 || 1.227 || 1.284 || 1.445 || 1.577<br />
|-<br />
|'''ID=60%''' || 0.634 || 0.678 || 0.752 || 0.814 || 0.868 || 0.959 || 1.053 || 1.103 || 1.241 || 1.354<br />
|-<br />
|'''ID=70%''' || 0.544 || 0.582 || 0.646 || 0.699 || 0.746 || 0.824 || 0.905 || 0.947 || 1.066 || 1.163<br />
|-<br />
|'''ID=80%''' || 0.467 || 0.500 || 0.555 || 0.601 || 0.640 || 0.708 || 0.777 || 0.813 || 0.915 || 0.999<br />
|-<br />
|'''ID=90%''' || 0.401 || 0.429 || 0.477 || 0.516 || 0.550 || 0.608 || 0.667 || 0.698 || 0.786 || 0.858<br />
|-<br />
|'''ID=100%''' || 0.345 || 0.369 || 0.409 || 0.443 || 0.472 || 0.522 || 0.573 || 0.600 || 0.675 || 0.737<br />
|-<br />
|}<br />
<br />
The RMS deviation estimated from ID may be an underestimate of the true value if there is a slight conformational change between the model and target structures. To find a solution in these cases it may be necessary to increase the RMS from the default value generated from the ID, by say 0.5 Ångstroms. On the other hand, when Phaser succeeds in solving a structure from a model with sequence identity much below 30%, it is often found that the fold is preserved better than the average for that level of sequence identity. So it may be worth submitting a run in which the RMS error is set at, say, 1.5, even if the sequence identity is low. The table below can be used as a guide as to the default RMS value corresponding to ID.<br />
<br />
If you construct a model by homology modelling, remember that the RMS error you expect is essentially the error you expect from the template structure (if not worse!). So specify the sequence identity of the template, not of the homology model.<br />
<br />
Only the model with the highest sequence identity is reported in the output pdb file. Also, HETATM cards in the input pdb file are ignored in the calculation of the structure factors for the ensemble, but are carried through to the output pdb file. Thus, the phases on the output mtz file (which come from the structure factors of the ensemble) do not correspond to those that would be calculated from the output pdb file, when there is more than one pdb file in an ensemble and/or the pdbfile(s) have HETATM records.<br />
<br />
====Coordinate Editing====<br />
=====HETATM/LIGANDS=====<br />
Phaser ignores the scattering from HETATM records. The HETATM records are carried though to output with occupancy set to zero. Ligands will therefore not contribute to the scattering used for molecular replacement. The exceptions to this rule are the HETATM records for MSE (seleno-methionine) MSO (seleno-methionine selenoxide) CSE (seleno-cysteine) CSO (seleno-cysteine selenoxide) ALY (acetyllysine) MLY (n-dimethyl-lysine) and MLZ (n-methyl-lysine) which are used in the scattering and carried through to output with their original occupancy. If you wish to include any HETATM records in the scattering the record name use the keyword ENSE modlid HETATOM ON<br />
<br />
=====WATER=====<br />
Water molecules (identified by the residue name OW WAT HOH H2O OH2 MOH WTR or TIP) are deleted from the pdb file on input, are not used in the scattering and are not carried through to file output. If you want to retain water molecules you will need to change the residue name to something other than this (e.g. WWW) so that the atoms are not identified as water. To include the water molecules in the scattering, the HETATM records will also have to be changed to ATOM records as described above.<br />
<br />
===Building an Ensemble from Electron Density===<br />
When using density as a model, it is necessary to specify both the extent (x,y,z limits) of the cut-out region of density, and the centre of this region. With coordinates, Phaser can work this out by itself. This information is needed, for instance, to decide how large rotational steps can be in the rotation search and to carry out the molecular transform interpolation correctly. In the case of electron density, the RMS value does not have the same physical meaning that it has when the model is specified by atomic coordinates, but it is used to judge how the accuracy of the calculated structure factors drops off with resolution. A suitable value for RMS can be obtained, in the case of density from an experimentally-phased map, by choosing a value that makes the SigmaA curve fall off with resolution similarly to the mean figures-of-merit. In the case of density from an EM image reconstruction, the RMS value should make the SigmaA curve fall off similarly to a Fourier correlation curve used to judge the resolution of the EM image.<br />
<br />
For detailed information, including a tutorial with example scripts, see<br />
[[Using Electron Density as a Model| Using density as a model]]<br />
<br />
==How to Define Composition==<br />
The composition defines the total amount of protein and nucleic acid that you have in the asymmetric unit not the fraction of the asymmetric unit that you are searching for.<br />
<br />
===Default Composition===<br />
For convenience, the composition defaults to 50% protein scattering by volume (the average for protein crystals). It is better to enter it explicitly, even if only to check that you have correctly deduced the probable content of your crystal. If your crystal has higher or lower solvent content than this, or contains nucleic acid, then the composition should be entered explicitly.<br />
===Composition by Solvent Content===<br />
Scattering is determined from the solvent content of the crystal, assuming that the crystal contains protein only, and the average distribution of amino acids in protein. If your crystal contains nucleic acid or your protein has an unusual amino acid distribution then the composition should be entered explicitly using the MW or sequence options.<br />
===Composition by Number of Residues in ASU===<br />
Scattering is determined from the number of residues in the asymmetric unit, assuming that the crystal contains protein only or nucleic acid only, and assuming an average distribution of residues for either. If your crystal contains a mixture then the composition should be entered explicitly using the MW or sequence options. If your crystal has an unusual residue distribution then the composition should be entered explicitly using the sequence options.<br />
===Composition by Molecular Weight===<br />
The composition is calculated from the molecular weight of the protein and nucleic acid assuming the protein and nucleic acid have the average distribution of amino acids and bases. If your protein or nucleic acid has an unusual amino acid or base distribution the composition should be entered by sequence. You can mix compositions entered by molecular weight with those entered by sequence.<br />
===Composition by Sequence===<br />
The composition is calculated from the amino acid sequence of the protein and the base sequence of the nucleic acid in fasta format. You can mix compositions entered by molecular weight with those entered by sequence. Individual atoms can be added to the composition with the COMPOSITION ATOM keyword. This allows the explicit addition of heavy atoms in the structure e.g. Fe atoms.<br />
===Composition by Percentage Scattering===<br />
The fraction scattering of each ensemble can be entered directly. The fraction scattering of each ensemble is normally automatically worked out from the average scattering from each ensemble (calculated from the pdb files if entered as coordinates, or from the protein and nucleic acid molecular weights if entered as a map) divided by the total scattering given by the composition, but entering the fraction scattering directly overrides this calculation. This option is for use when the pdb files of the models in the ensemble are unusual e.g. consist only of C-alpha atoms, or only of hydrogen atoms (as in the CLOUDS method for NMR).<br />
<br />
==How to Define Solutions==<br />
Phaser writes out files ending in ".sol" and ".rlist" that contain the solution information from the job. The root of the files is given by the ROOT keyword. By default, the root filename is PHASER. These files can be read back into subsequent runs of Phaser to build up solutions containing more than one molecule in the asymmetric unit.<br />
<br />
"PHASER.sol" files are generated by all modes (rotation function modes with VERBOSE output), and contain the current idea of potential molecular replacement solutions.<br />
<br />
"PHASER.rlist" files are generated by the rotation function modes, and are used as input for performing translation functions.<br />
<br />
For simple MR cases you don't really need to know how to define molecular replacement solutions. However, for difficult cases you might need to edit the files "PHASER.sol" and "PHASER.rlist" files manually<br />
<br />
=== "sol" Files===<br />
SOLUtion 6DIM keywords describe Ensembles that have been oriented by a rotation search and positioned by a translation search. Each Ensemble in the asymmetric unit has its own SOLUtion keyword. When more than one (potential) molecular replacement solution is present, the solutions are separated with the SOLUTION SET keywords.<br />
<br />
==="rlist" Files===<br />
These files define a rotation function list. The peak list is given with a series of SOLUtion TRIAl keywords.<br />
<br />
If a partial solution is already known, then the information for the currently "known" parts of the asymmetric unit is given in the form used for the PHASER.sol file, followed by the list of trial orientations for which a translation function is to be performed.<br />
<br />
===Fixed partial structure===<br />
If you have the coordinates of a partial solution with the pdb coordinates of the known structure in the correct orientation and position, then you can force Phaser to use these coordinates. Use the SOLUTION keyword to fix a rotation of 0 0 0 and a position of 0 0 0 for these coordinates.<br />
<br />
==How to Select Peaks==<br />
<br />
<br />
<br />
The selection of peaks saved for output in the rotation and translation functions can be done in four different ways.<br />
*'''Select by Percentage'''<br />
*: Percentage of the top peak, where the value of the top peak is defined as 100% and the value of the mean is defined as 0%.<br />
*: Default, cutoff=75%. This criteria has the advantange that at least one peak (the top peak) always survives the selection. If the top solution is clear, then only the one solution will be output, but if the distribution of peaks is rather flat, then many peaks will be output for testing in the next part of the MR procedure (e.g. many peaks selected from the rotation function for testing with a translation function). <br />
*'''Select by Z-score'''<br />
*: Number of standard deviations (sigmas) over the mean (the Z-score). <br />
*: Absolute significance test. Not all searches will produce output if the cutoff value is too high (e.g. 5 sigma). <br />
*'''Select by Number'''<br />
*: Number of top peaks to select. <br />
*: If the distribution is very flat then it might be better to select a fixed large number (e.g. 1000) of top rotation peaks for testing in the translation function.<br />
*'''No selection'''<br />
*: All peaks are selected. <br />
*: Enables full 6 dimensional searches, where all the solutions from the rotation function are output for testing in the translation function. This should never be necessary; it would be much faster and probably just as likely to work if the top 1000 peaks were used in this way.<br />
<br />
[[Image:Phaser_selection.gif| Selection criteria]]<br />
<br />
Peaks can also be clustered or not clustered prior to selection in steps 1 and 2.<br />
*'''Clustering Off'''<br />
: All high peaks on the search grid are selected<br />
*'''Clustering On'''<br />
: Points on the search grid with higher neighbouring points are removed from the selection<br />
<br />
<br />
[[Image:Phaser_clustering.gif| Clustering]]<br />
<br />
==How to Control Output==<br />
The output of Phaser can be controlled with optional keywords. <br />
<br />
The ROOT keyword is not compulsory (the default root filename is "PHASER"), but should always be given, so that your jobs have separate and meaningful output filenames.<br />
<br />
The TOPFiles keyword controls the number of potential MR solutions for which PDB and (in the appropriate modes) MTZ files are produced.<br />
<br />
For the MR_AUTO, MR_RNP and MR_LLG modes, unless HKLOut OFF is given as an optional keyword, Phaser produces an MTZ file with "SigmaA" type weighted Fourier map coefficients for producing electron density maps for rebuilding.<br />
<br />
{| class="wikitable" style="text-align:left" width=100%<br />
|-<br />
! MTZ Column Labels !! Description<br />
|-<br />
| FWT/PHWT || Amplitude and phase for 2''m''&#124;F<sub>obs</sub>&#124;-''D''&#124;F<sub>calc</sub>&#124; exp(''i''&alpha;<sub>calc</sub>) map<br />
|-<br />
| DELFWT/PHDELWT || Amplitude and phase for ''m''&#124;F<sub>obs</sub>&#124;-''D''&#124;F<sub>calc</sub>&#124; exp(''i''&alpha;<sub>calc</sub>) map<br />
|-<br />
| FOM || ''m'', analogous to the "Sim" weight, to estimate the reliability of &alpha;<sub>calc</sub><br />
|-<br />
| HLA/HLB/HLC/HLD || Hendrickson-Lattman coefficients encoding the phase probability distribution<br />
|}<br />
<br />
==Translational Non-crystallographic Symmetry==<br />
<br />
<span style="color:crimson">'''*Warning*''' Solution by MR in the presence of translational non-crystallographic symmetry is not fully automated.</span><br />
<br />
Phaser calculates correction factors for the expected intensities in the presence of translational non-crystallographic symmetry (tNCS), and is able to solve structures with complex patterns of tNCS. '''However, the use of Phaser in the presence of tNCS requires the nature of the tNCS to be understood by the user.''' In simple cases, solution is no more difficult than solution without tNCS, but in complex cases, separate Phaser runs with tNCS turned on and off, and/or the use of different tNCS vectors, may be necessary.<br />
<br />
The output of Phaser will help the user in detecting and understanding the tNCS, but '''the tNCS is not completely characterised by Phaser'''. The default behaviour may or may not be correct for the particular crystal under study.<br />
<br />
Characterization of the tNCS involves understanding the number of copies of the molecule in the asymmetric unit and the translation vectors between them. Molecules related by a tNCS vector will have an associated peak in the native Patterson. Phaser calculates the native Patterson (MODE TNCS) and lists the peaks that are more than 20% of the origin peak. Any given crystal with tNCS may have one or more peaks meeting this criteria.<br />
<br />
===Default tNCS detection and correction===<br />
====No tNCS====<br />
No tNCS correction is applied by default if there is<br />
# no peak in the native Patterson <br />
# more than one peak in the native Patterson over 20% of the origin and these peaks are not all the result of a commensurate modulation<br />
<br />
====Pairs of molecules====<br />
By default, if Phaser detects a peak in the native Patterson then Phaser will search for molecules in pairs related by the tNCS vector given by the peak in the native Patterson.<br />
<br />
This will be the correct behaviour if and only if there are an even number of copies of the molecule in the asymmetric unit, clustered into two groups related by a single tNCS vector. There will only be one significant peak in the native Patterson. Fortunately, this is a reasonably common scenario.<br />
<br />
Phaser refines the relative orientation of the molecules in the two groups (rotations of up to 10 degrees will still give rise to a significant native Patterson peak) and uses this information to generate expected intensity factors for the reflections. Solution should be straightforward, with the usual caveat for MR that there is a sufficiently good model.<br />
<br />
Where there is a single peak in the native Patterson, it is often located at a position half way along a unit cell axis or diagonal, representing a pseudo-halving of the unit cell dimensions. However, Phaser is by no means restricted to these sorts of pseudo-cells in its handling of two-fold tNCS, and the tNCS vector can be in a general position.<br />
<br />
===Non-default tNCS correction===<br />
====Higher order tNCS====<br />
Frequently, tNCS does not associate 2 clusters of molecules in the asymmetric unit, but rather there are 3 or more (n) clusters of molecules associated by a series of vectors that are multiples of 1, 2, 3 ... (n-1) times a basic translation vector. The integer n is the order of the tNCS and is entered using the keyword TNCS NMOL <n>. <br />
<br />
Phaser does not automatically detect these cases. The peaks of the native Patterson must be inspected to find the n-fold relationship, which can be subtle; for instance, a peak at 0.2,0.4,0 can be interpreted in terms of a vector that is twice a vector of 0.6,0.2,0 (taking unit cell translations into account). The series will not generally have all peaks the same height. Lower peaks in the series represent relationships where the relative rotations between related molecules are larger. Missing peaks in the series may be below the default 20% of origin cut-off. This can be lowered with TNCS PATT PERCENT <x><br />
<br />
Phaser can account for this form of tNCS with the use of the keywords TNCS NMOL <n> '''and entering the number of search copies as a multiple of n.''' The vector for the tNCS should either be input using TNCS TRA VECTOR <x,y,z>, or set the TNCS PATT PERCENT <x> value so that only one peak is selected (if this peak represents the appropriate base vector for the tNCS).<br />
<br />
When there are more than two molecules related by tNCS, Phaser does not refine the orientations between the molecules related by the tNCS.<br />
<br />
Where n times the basic translation vector equates to (integer multiples of) unit cell axes, the tNCS represents a pseudo-cell, and this case is known as commensurate modulation. However, as for two-fold tNCS, Phaser is not restricted to these sorts of pseudo-cells and the basic tNCS vector can be in a general position.<br />
<br />
====Complex tNCS====<br />
If there are many molecules in the asymmetric unit but they are not all related by tNCS, or there are sub-groups of molecules related by different tNCS vectors, then the modulations of the expected intensities due to the tNCS will be much less significant than the cases described above. '''In these cases it is possible that structure solution will be achieved without any tNCS correction factors being applied.''' Indeed, searching for all the copies as tNCS-related multiples when some molecules are not related by tNCS will cause structure solution to fail. To turn off the automatic detection and use of tNCS use the keyword TNCS USE OFF.<br />
<br />
If turning off the TNCS correction factors fails to give a solution, then a good approach is to proceed step-wise. Consider the highest native Patterson peak first and determine that nature of the tNCS associated with it. Use the appropriate correction factors to locate all the molecules with this tNCS. Then take the second independent native Patterson peak and apply the correction factors associated with it to find the second set of molecules, fixing the first, etc. Finally, turn TNCS off to find any orphan molecules.</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Molecular_Replacement&diff=2376Molecular Replacement2016-11-28T10:48:30Z<p>Airlie: /* No tNCS */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
'''Quicklink to example scripts''' → [[MR using keyword input]]<br />
<br />
'''Quicklink to phaser.famos (find_alt_orig_sym_mate) documentation''' → [[Famos]]<br />
<br />
Phaser should be able to solve most structures with the Automated Molecular Replacement mode, and this is the first mode that you should try. Give Phaser your data ([[#How to Define Data|How to Define Data]]) and your models ([[#How to Define Models|How to Define Models]]), tell Phaser what to search for, and a list of possible spacegroups (in the same point group).<br />
<br />
If this doesn't work (see [[#Has Phaser Solved It?| Has Phaser Solved It?]]), you can try selecting peaks of lower significance in the rotation function in case the real orientation was not within the selection criteria. By default peaks above 75% of the top peak are selected (see [[#How to Select Peaks| How to Select Peaks]]). See [[#What to do in Difficult Cases| What to do in Difficult Cases]] for more hints and tips. If the automated molecular replacement mode doesn't work even with non-default input you need to run the modes of Phaser separately. The possibilities are endless - you can even try exhaustive searches (translations of all orientations) if you want - but experience has shown that most structures that can be solved by Phaser can be solved by relatively simple strategies.<br />
<br />
==Automated Molecular Replacement==<br />
Automated Molecular Replacement combines the anisotropy correction, likelihood enhanced fast rotation function, likelihood enhanced fast translation function, packing and refinement modes for multiple search models and a set of possible spacegroups to automatically solve a structure by molecular replacement. Top solutions are output to the files FILEROOT.sol, FILEROOT.#.mtz and FILEROOT.#.pdb (where "#" refers to the sorted solution number, 1 being the best, and only 1 is output by default). Many structures can be solved by running an automated molecular replacement search with defaults, giving the ensembles that you expect to be easiest to find first.<br />
<br />
At the completion of Molecular Replacement you may wish to place your solutions on a common origin with a previous solution, for which [[Famos | Famos ]] can be used.<br />
<br />
[[Image:Phaser_MR_auto.gif|Flow Diagram for Automated MR]]<br />
<br />
==Should Phaser Solve It?==<br />
The difficulty of a molecular replacement problem depends primarily on two major factors: how well the model will be able to explain the diffraction data (which depends both on the accuracy of the model and on its completeness), and how many reflections can be explained, at least in part. Each reflection provides a piece of information that helps to identify correct MR solutions.<br />
<br />
It is possible to make a reasonable prediction of whether or not a solution will be found. If the quality of the model (its accuracy and completeness) can be estimated, then the expected contribution of each reflection to the total LLG can also be estimated. From a large battery of tests, we know that an LLG of 40 or greater usually indicates a correct solution (at least in the absence of complicating factors such as translational non-crystallographic symmetry, tNCS). Building on this understanding, if it is estimated that the LLG will be 60 or less, then Phaser will assume that the problem is a difficult one, and will implement search procedures optimised for difficult problems.<br />
<br />
==What Resolution of Data Should be Used?==<br />
The signal for a molecular replacement solution should be very clear if the expected value of the LLG is much higher than the minimum required to be fairly certain of a solution. Currently Phaser aims for a minimum LLG of 120 and, if it is possible to achieve an even higher value, given the quality of the model and the quantity of diffraction data, then the resolution for the initial search is limited to the value required to achieve an expected LLG of 120. Data to the full resolution are still used for a final rigid-body refinement, or in a second pass if a clear solution is not found in the first attempt.<br />
<br />
However, if the model is expected to have a large RMS error (based usually on the correlation between sequence identity and RMS error), then data to high resolution will not contribute any significant signal. Regardless of the expected LLG at the highest resolution limit, the resolution used is limited to 1.8 times the estimated RMS error of the model, because this resolution limit gives about 99% of the LLG that could be achieved.<br />
<br />
Because Phaser implements strategies designed to solve structures with as much confidence as possible, as efficiently as possible, it is best to leave the choice of resolution to Phaser, at least in the first instance.<br />
<br />
==Has Phaser Solved It?==<br />
{| class="wikitable" style="text-align:center" align="right" style="margin-left: 30px" <br />
|-<br />
! TF Z-score !! Have I solved it?<br />
|-<br />
| less than 5 || no<br />
|-<br />
| 5 - 6 || unlikely<br />
|-<br />
| 6 - 7 || possibly<br />
|-<br />
| 7 - 8 || probably<br />
|-<br />
| more than 8* ||definitely<br />
|-<br />
|colspan="2" style="text-align: center;" | *''6 for 1st model in monoclinic space groups''<br />
|} <br />
<br />
Ideally, a unique solution with a strong signal will be found at the end of the search. If you are searching for multiple components, then ideally the search for each component will also give a strong signal. However if the signal-to-noise of your search is low, there will be noise peaks and multiple ambiguous solutions. Signal-to-noise is judged using the '''Z-score''', which is computed by comparing the LLG values from the rotation or translation search with LLG values for a set of random rotations or translations. The mean and the RMS deviation from the mean are computed from the random set, then the Z-score for a search peak is defined as its LLG minus the mean, all divided by the RMS deviation, ''i.e. '' '''the number of standard deviations above (or below) the mean. '''<br />
<br />
For a rotation function, the correct orientation may be well down the list with a Z-score (number of standard deviations above the mean value, or RFZ) under 4, and it is often not possible to identify the correct orientation until a translation function is performed and yields a clear solution. Note that the signal-to-noise of the rotation function drops with increasing number of primitive symmetry operations (the number of different orientations for symmetry-related molecules), because there is more uncertainty about how the structure factor contributions from symmetry-related copies will add up.<br />
<br />
For a translation function the correct solution will generally have a Z-score (TFZ) over 5 and be well separated from the rest of the solutions. Of course, there will always be exceptions! The table gives a very rough guide to interpreting TFZ scores. This table will be updated, as we learn more from systematic molecular replacement trials.<br />
<br />
When you are searching for multiple components, the signal may be low for the first few components but, as the model becomes more complete, the signal should become stronger. Finding a clear solution for a new component is a good sign that the partial solution to which that component was added was indeed correct.<br />
<br />
You should always at least glance through the summary of the logfile. One thing to look for, in particular, is whether any translation solutions with a high Z-score have been rejected by the packing step. By default up to 5 percent of marker atoms (C-alpha atoms for protein) are allowed to be involved in clashes. A solution with more clashes may still be correct, and the clashes may arise only because of differences in small surface loops. If this happens, repeat the run allowing a suitable number of clashes. Note that, unless there is specific evidence in the logfile that a high TFZ-score solution is being rejected with a few clashes, it is much better to edit the model to remove the loops than to increase the number of allowed clashes. Packing criteria are a very powerful constraint on the translation function, and increasing the number of allowed clashes beyond the default will increase the search time enormously without the possibility of generating any correct solutions that would not have otherwise been found.<br />
<br />
Note that, by default, Phaser will produce a single PDB file corresponding to the top solution found (if any), so finding a single PDB file in your output directory is not an indication that the search succeeded! You have to look, at least, at the summary of the logfile, or at the list of possible solutions in the .sol file that is produced if you run Phaser from ccp4i or command-line scripts.<br />
<br />
==Annotation==<br />
<br />
A highly compact summary of the history of the statistics of a solution is given in the SOLUTION SET in the .sol file. This is a good place to start your analysis of the output. The annotation gives the Z-score of the solution at each rotation and translation function, the number of clashes in the packing, and the refined LLG.<br />
<br />
{| class="wikitable" style="text-align:center" style="margin-left: 30px" <br />
|-<br />
! Annotation !! Meaning<br />
|-<br />
| RFZ= || Rotation Function Z-score<br />
|-<br />
| TFZ= || Translation Function Z-score<br />
|-<br />
| PAK= || Number of packing clashes<br />
|-<br />
| LLG= || LLG after refinement. Will be repeated when a low resolution refinement is followed by a high resolution refinement.<br />
|-<br />
| TFZ== || Translation Function Z-score equivalent, only calculated for the top solution after refinement (or for the number of top files specified by TOPFILES)<br />
|-<br />
| RF++ || Rotation angle from previous strong solution has been used in the addition of next solution<br />
|-<br />
| RF*0 || Rotation angle 000 identified by low R-factor of input model<br />
|-<br />
| TFZ=* || First molecule in P1 (arbitrary origin, no Translation Function required)<br />
|-<br />
| TF*0 || Translation vector 000 identified by low R-factor of input model<br />
|-<br />
| (&&nbsp;... & ...) || Set of TFZ PAK and LLG values for placements that were amalgamated (more than one placement from a single Translation Function)<br />
|-<br />
| LLG+=(...&nbsp;&&nbsp;...)&nbsp;|| Set of LLG values calculated during amalgamation, which will always be increasing in value<br />
|-<br />
| +TNCS || Components added by Translational NCS relation<br />
|-<br />
| *T=<i>n</i> || Solution matches template solution <i>n</i><br />
|} <br />
<br />
Two versions of TFZ (the translation function Z-score) now appear for each component. The first ("TFZ=") is the Z-score from the actual translation search, which depends on the accuracy of the orientation used for that search. The second ("TFZ==") is the TFZ-equivalent, which indicates what the TFZ score would have been with the correct (refined) orientation. You should see the TFZ-equivalent is high at least for the final components of the solution, and that the LLG (log-likelihood gain) increases as each component of the solution is added. For example, in the case of beta-blip the annotation for the single solution output in the .sol file shows these features<br />
<br />
SOLU SET RFZ=10.7 TFZ=24.3 PAK=0 LLG=472 TFZ==24.7 RFZ=6.4 TFZ=24.4 PAK=0 LLG=1006 TFZ==29.7 LLG=1006 TFZ==29.7<br />
SOLU 6DIM ENSE beta EULER 200.849 41.269 183.909 FRAC -0.49604 -0.15830 -0.28092 BFAC 0.00000<br />
SOLU 6DIM ENSE blip EULER 43.749 80.793 117.292 FRAC -0.12289 0.29435 -0.09266 BFAC 0.00000<br />
<br />
Note that the Euler angles in Phaser follow the same convention as those defined for the Crowther fast rotation function, i.e. z-y-z (rotate around the z-axis, followed by the new y-axis, followed by the new z-axis).<br />
<br />
==History==<br />
<br />
A highly compact summary of the history of the peak positions of a solution is given in the SOLUTION HISTORY in the .sol file. Together with the SOLUTION SET annotation, this is useful in your analysis of the output. <br />
<br />
{| class="wikitable" style="text-align:center" style="margin-left: 30px" <br />
|-<br />
! History !! Meaning<br />
|-<br />
| RF/TF(r/t:n) || (r) Rotation Function peak number/(t) Translation Function peak number for the rotation function : (n) number of peak in final merged and sorted list<br />
|-<br />
| PAK(n:m) || (n) input solution number : (m) output solution number after packing condition applied<br />
|-<br />
| RNP(m,a,b,c,... : p) || All input peaks amalgamated after refinement to give output solution number (m and others): (p) output solution number<br />
|-<br />
| FUSE(A,B,C) || Solution numbers merged in amalgamation<br />
|} <br />
<br />
For example, in the case of beta-blip the annotation for the single solution output in the .sol file shows these features<br />
<br />
SOLU HISTORY RF/TF(1/1:1)PAK(1:1)RNP(1:1)RNP(1:1)<br />
SOLU 6DIM ENSE beta EULER 200.849 41.269 183.909 FRAC -0.49604 -0.15830 -0.28092 BFAC 0.00000<br />
SOLU 6DIM ENSE blip EULER 43.749 80.793 117.292 FRAC -0.12289 0.29435 -0.09266 BFAC 0.00000<br />
<br />
A more complicated structure solution may have<br />
<br />
SOLU HISTORY RF/TF(7/1:10)PAK(10:10)RNP(10,12,13,11,17,16,18,25,3,8,22,21,20,7,969,6,5,201,9,4,390,2,1,19:1)RNP(1:1)<br />
<br />
==What to do in Difficult Cases==<br />
<br />
Not every structure can be solved by molecular replacement, but the right strategy can push the limits. What to do when the default jobs fail depends on why your structure is difficult.<br />
*'''Flexible Structure'''<br />
*:The relative orientations of the domains may be different in your crystal than in the model. If that may be the case, break the model into separate PDB files containing rigid-body units, enter these as separate ensembles, and search for them separately. If you find a convincing solution for one domain, but fail to find a solution for the next domain, you can take advantage of the knowledge that its orientation is likely to be similar to that of the first domain. The ROTAte&nbsp;AROUnd option of the brute rotation search can be used to restrict the search to orientations within, say, 30 degrees of that of the known domain. Allow for close approach of the domains by increasing the allowed clashes with the PACK keyword by, say, 1 for each domain break that you introduce. Note that it is possible to use the brute rotation search as part of the automated molecular replacement pipeline, by changing the choice of the type of rotation search. Alternatively, you could try generating a series of models perturbed by normal modes, with the NMAPdb keyword. One of these may duplicate the hinge motion and provide a good single model.<br />
*'''Poor or Incomplete Model'''<br />
*:Signal-to-noise is reduced by coordinate errors or incompleteness of the model. Since the rotation search has lower signal to begin with than the translation search, it is usually more severely affected. For this reason, it can be very useful to use the subsequent translation search as a way to choose among many (say 1000) orientations. THe MR_AUTO FAST search mode automatically reduces the cutoff for accepting peaks from the fast rotation function if the decault pass does not find a solution with a high z-score, but you can manually reduce this further with the PEAKS and PURGE keywords. You can also try turning off the clustering of fast rotation function peaks because the correct orientation may sit on the shoulder of a peak in the rotation function. <br />
*:As shown convincingly by Schwarzenbacher ''et al.'' (Schwarzenbacher, Godzik, Grzechnik &amp; Jaroszewski, ''Acta Cryst.'' D'''60''', 1229-1236, 2004), judicious editing can make a significant difference in the quality of a distant model. In a number of tests with their data on models below 30% sequence identity, we have found that Phaser works best with a "mixed model" (non-identical sidechains longer than Ser replaced by Ser). In agreement with their results, the best models are generally derived using more sophisticated alignment protocols, such as their FFAS protocol. Use [http://www.phenix-online.org/documentation/sculptor.htm phenix.sculptor] to edit your model.<br />
*'''High Degree of Non-crystallographic Symmetry'''<br />
*:If there are clear peaks in the self-rotation function, you can expect orientations to be related by this known NCS. Methods to automatically use such information will be implemented in a future version of Phaser. In the meantime, you can work out for yourself the orientations that would be consistent with NCS and use the ROTAte&nbsp;AROUnd option to sample similar orientations. Alternatively, you may have an oligomeric model and expect similar NCS in the crystal. First search with the oligomeric model; if this fails, search with a monomer. If that succeeds, you can again use the ROTAte&nbsp;AROUnd option to force a subsequent monomer to adopt an orientation similar to the one you expect.<br />
*'''What <u>not</u> to do'''<br />
*:The automated mode of Phaser is fast when Phaser finds a high Z-score solution to your problem. When Phaser cannot find a solution with a significant Z-score, it "thrashes", meaning it maintains a list of 100-1000's of low Z-score potential solutions and tries to improve them. This can lead to exceptionally long Phaser runs (over a week of CPU time). Such runs are possible because the highly automated script allows many consecutive MR jobs to be run without you having to manually set 100-1000's of jobs running and keep track of the results. "Thrashing" generally does not produce a solution: solutions generally appear relatively quickly or not at all. It is more useful to go back and analyse your models and your data to see where improvements can be made. Your system manager will appreciate you terminating these jobs.<br />
*:It is also not a good idea to effectively remove the packing test. Unless there is specific evidence in the logfile that a high TF-function Z-score solution is being rejected with a few clashes, it is much better to edit the model to remove the loops than to increase the number of allowed clashes. Packing criteria are a very powerful constraint on the translation function, and increasing the number of allowed clashes beyond a few (e.g. 1-5) will increase the search time enormously without the possibility of generating any correct solutions that would not have otherwise been found.<br />
*'''Other suggestions'''<br />
*:Phaser has powerful input, output and scripting facilities that allow a large number of possibilities for altering default behaviour and forcing Phaser to do what you think it should. However, you will need to read the information in the manual below to take advantage of these facilities!<br />
<br />
==How to Define Data==<br />
You need to tell Phaser the name of the mtz file containing your data and the columns in the mtz file to be used using the HKLIn and LABIn keywords. Additional keywords (BINS CELL OUTLier RESOlution SPACegroup) define how the data are used.<br />
<br />
==How to Define Models==<br />
Phaser must be given the models that it will use for molecular replacement. A model in Phaser is referred to as an "ensemble", even when it is described by a single file. This is because it is possible to provide a set of aligned structures as an ensemble, from which a statistically-weighted averaged model is calculated. A molecular replacement model is provided either as one or more aligned pdb files, or as an electron density map, entered as structure factors in an mtz file. Each ensemble is treated as a separate type of rigid body to be placed in the molecular replacement solution. An ensemble should only be defined once, even if there are several copies of the molecule in the asymmetric unit.<br />
<br />
Fundamental to the way in which Phaser uses MR models (either from coordinates or maps) is to estimate how the accuracy of the model falls off as a function of resolution, represented by the Sigma(A) curve. To generate the Sigma(A) curve, Phaser needs to know the RMS coordinate error expected for the model and the fraction of the scattering power in the asymmetric unit that this model contributes.<br />
<br />
A Babinet-style correction is used to account for the effects of disordered solvent on the completeness of the model at low resolution.<br />
<br />
Molecular replacement models are defined with the ENSEmble keyword and the COMPosition keyword. The ENSEmble keyword gives (amongst other things) the RMS deviation for the Sigma(A) curve. The COMPosition keyword is used to deduce the fraction of the scattering power in the asymmetric unit that each ensemble contributes. The composition of the asymmetric unit is defined either by entering the molecular weights or sequences of the components in the asymmetric unit, and giving the number of copies of each. Expert users can also enter the fraction of the scattering of each component directly, although the composition must still be entered for the absolute scale calculation. Please note that the composition supplied to Phaser has to include everything in the asymmetric unit, not just what is being looked for in the current search!<br />
<br />
===Building an Ensemble from Coordinates===<br />
The RMS deviation is determined directly from RMS or indirectly from IDENtity in the ENSEmble<br />
keyword using a formula that depends on the sequence identity and the number of residues in the model.<br />
<br />
{| class="wikitable" style="text-align:center" align=right style="margin-left: 30px" <br />
|colspan="11" style="text-align: center;" | Initial estimate of RMS deviation<br />
|-<br />
|colspan="11" style="text-align: center;" | Number of residues in model versus sequence identity<br />
|-<br />
! !! #50 !! #100 !! #200 !! #300 !! #400 !! #600 !! #850 !! #1000 !! #1500 !! #2000<br />
|-<br />
|'''ID=0%''' || 1.579 || 1.689 || 1.875 || 2.030 || 2.164 || 2.391 || 2.625 || 2.748 || 3.093 || 3.375<br />
|-<br />
|'''ID=10%''' || 1.356 || 1.451 || 1.610 || 1.743 || 1.858 || 2.053 || 2.255 || 2.360 || 2.657 || 2.899<br />
|-<br />
|'''ID=20%''' || 1.165 || 1.246 || 1.383 || 1.497 || 1.596 || 1.764 || 1.936 || 2.027 || 2.281 || 2.489<br />
|-<br />
|'''ID=30%''' || 1.000 || 1.070 || 1.188 || 1.286 || 1.371 || 1.515 || 1.663 || 1.741 || 1.959 || 2.138<br />
|-<br />
|'''ID=40%''' || 0.859 || 0.919 || 1.020 || 1.104 || 1.177 || 1.301 || 1.428 || 1.495 || 1.683 || 1.836<br />
|-<br />
|'''ID=50%''' || 0.738 || 0.789 || 0.876 || 0.948 || 1.011 || 1.117 || 1.227 || 1.284 || 1.445 || 1.577<br />
|-<br />
|'''ID=60%''' || 0.634 || 0.678 || 0.752 || 0.814 || 0.868 || 0.959 || 1.053 || 1.103 || 1.241 || 1.354<br />
|-<br />
|'''ID=70%''' || 0.544 || 0.582 || 0.646 || 0.699 || 0.746 || 0.824 || 0.905 || 0.947 || 1.066 || 1.163<br />
|-<br />
|'''ID=80%''' || 0.467 || 0.500 || 0.555 || 0.601 || 0.640 || 0.708 || 0.777 || 0.813 || 0.915 || 0.999<br />
|-<br />
|'''ID=90%''' || 0.401 || 0.429 || 0.477 || 0.516 || 0.550 || 0.608 || 0.667 || 0.698 || 0.786 || 0.858<br />
|-<br />
|'''ID=100%''' || 0.345 || 0.369 || 0.409 || 0.443 || 0.472 || 0.522 || 0.573 || 0.600 || 0.675 || 0.737<br />
|-<br />
|}<br />
<br />
The RMS deviation estimated from ID may be an underestimate of the true value if there is a slight conformational change between the model and target structures. To find a solution in these cases it may be necessary to increase the RMS from the default value generated from the ID, by say 0.5 Ångstroms. On the other hand, when Phaser succeeds in solving a structure from a model with sequence identity much below 30%, it is often found that the fold is preserved better than the average for that level of sequence identity. So it may be worth submitting a run in which the RMS error is set at, say, 1.5, even if the sequence identity is low. The table below can be used as a guide as to the default RMS value corresponding to ID.<br />
<br />
If you construct a model by homology modelling, remember that the RMS error you expect is essentially the error you expect from the template structure (if not worse!). So specify the sequence identity of the template, not of the homology model.<br />
<br />
Only the model with the highest sequence identity is reported in the output pdb file. Also, HETATM cards in the input pdb file are ignored in the calculation of the structure factors for the ensemble, but are carried through to the output pdb file. Thus, the phases on the output mtz file (which come from the structure factors of the ensemble) do not correspond to those that would be calculated from the output pdb file, when there is more than one pdb file in an ensemble and/or the pdbfile(s) have HETATM records.<br />
<br />
====Coordinate Editing====<br />
=====HETATM/LIGANDS=====<br />
Phaser ignores the scattering from HETATM records. The HETATM records are carried though to output with occupancy set to zero. Ligands will therefore not contribute to the scattering used for molecular replacement. The exceptions to this rule are the HETATM records for MSE (seleno-methionine) MSO (seleno-methionine selenoxide) CSE (seleno-cysteine) CSO (seleno-cysteine selenoxide) ALY (acetyllysine) MLY (n-dimethyl-lysine) and MLZ (n-methyl-lysine) which are used in the scattering and carried through to output with their original occupancy. If you wish to include any HETATM records in the scattering the record name use the keyword ENSE modlid HETATOM ON<br />
<br />
=====WATER=====<br />
Water molecules (identified by the residue name OW WAT HOH H2O OH2 MOH WTR or TIP) are deleted from the pdb file on input, are not used in the scattering and are not carried through to file output. If you want to retain water molecules you will need to change the residue name to something other than this (e.g. WWW) so that the atoms are not identified as water. To include the water molecules in the scattering, the HETATM records will also have to be changed to ATOM records as described above.<br />
<br />
===Building an Ensemble from Electron Density===<br />
When using density as a model, it is necessary to specify both the extent (x,y,z limits) of the cut-out region of density, and the centre of this region. With coordinates, Phaser can work this out by itself. This information is needed, for instance, to decide how large rotational steps can be in the rotation search and to carry out the molecular transform interpolation correctly. In the case of electron density, the RMS value does not have the same physical meaning that it has when the model is specified by atomic coordinates, but it is used to judge how the accuracy of the calculated structure factors drops off with resolution. A suitable value for RMS can be obtained, in the case of density from an experimentally-phased map, by choosing a value that makes the SigmaA curve fall off with resolution similarly to the mean figures-of-merit. In the case of density from an EM image reconstruction, the RMS value should make the SigmaA curve fall off similarly to a Fourier correlation curve used to judge the resolution of the EM image.<br />
<br />
For detailed information, including a tutorial with example scripts, see<br />
[[Using Electron Density as a Model| Using density as a model]]<br />
<br />
==How to Define Composition==<br />
The composition defines the total amount of protein and nucleic acid that you have in the asymmetric unit not the fraction of the asymmetric unit that you are searching for.<br />
<br />
===Default Composition===<br />
For convenience, the composition defaults to 50% protein scattering by volume (the average for protein crystals). It is better to enter it explicitly, even if only to check that you have correctly deduced the probable content of your crystal. If your crystal has higher or lower solvent content than this, or contains nucleic acid, then the composition should be entered explicitly.<br />
===Composition by Solvent Content===<br />
Scattering is determined from the solvent content of the crystal, assuming that the crystal contains protein only, and the average distribution of amino acids in protein. If your crystal contains nucleic acid or your protein has an unusual amino acid distribution then the composition should be entered explicitly using the MW or sequence options.<br />
===Composition by Number of Residues in ASU===<br />
Scattering is determined from the number of residues in the asymmetric unit, assuming that the crystal contains protein only or nucleic acid only, and assuming an average distribution of residues for either. If your crystal contains a mixture then the composition should be entered explicitly using the MW or sequence options. If your crystal has an unusual residue distribution then the composition should be entered explicitly using the sequence options.<br />
===Composition by Molecular Weight===<br />
The composition is calculated from the molecular weight of the protein and nucleic acid assuming the protein and nucleic acid have the average distribution of amino acids and bases. If your protein or nucleic acid has an unusual amino acid or base distribution the composition should be entered by sequence. You can mix compositions entered by molecular weight with those entered by sequence.<br />
===Composition by Sequence===<br />
The composition is calculated from the amino acid sequence of the protein and the base sequence of the nucleic acid in fasta format. You can mix compositions entered by molecular weight with those entered by sequence. Individual atoms can be added to the composition with the COMPOSITION ATOM keyword. This allows the explicit addition of heavy atoms in the structure e.g. Fe atoms.<br />
===Composition by Percentage Scattering===<br />
The fraction scattering of each ensemble can be entered directly. The fraction scattering of each ensemble is normally automatically worked out from the average scattering from each ensemble (calculated from the pdb files if entered as coordinates, or from the protein and nucleic acid molecular weights if entered as a map) divided by the total scattering given by the composition, but entering the fraction scattering directly overrides this calculation. This option is for use when the pdb files of the models in the ensemble are unusual e.g. consist only of C-alpha atoms, or only of hydrogen atoms (as in the CLOUDS method for NMR).<br />
<br />
==How to Define Solutions==<br />
Phaser writes out files ending in ".sol" and ".rlist" that contain the solution information from the job. The root of the files is given by the ROOT keyword. By default, the root filename is PHASER. These files can be read back into subsequent runs of Phaser to build up solutions containing more than one molecule in the asymmetric unit.<br />
<br />
"PHASER.sol" files are generated by all modes (rotation function modes with VERBOSE output), and contain the current idea of potential molecular replacement solutions.<br />
<br />
"PHASER.rlist" files are generated by the rotation function modes, and are used as input for performing translation functions.<br />
<br />
For simple MR cases you don't really need to know how to define molecular replacement solutions. However, for difficult cases you might need to edit the files "PHASER.sol" and "PHASER.rlist" files manually<br />
<br />
=== "sol" Files===<br />
SOLUtion 6DIM keywords describe Ensembles that have been oriented by a rotation search and positioned by a translation search. Each Ensemble in the asymmetric unit has its own SOLUtion keyword. When more than one (potential) molecular replacement solution is present, the solutions are separated with the SOLUTION SET keywords.<br />
<br />
==="rlist" Files===<br />
These files define a rotation function list. The peak list is given with a series of SOLUtion TRIAl keywords.<br />
<br />
If a partial solution is already known, then the information for the currently "known" parts of the asymmetric unit is given in the form used for the PHASER.sol file, followed by the list of trial orientations for which a translation function is to be performed.<br />
<br />
===Fixed partial structure===<br />
If you have the coordinates of a partial solution with the pdb coordinates of the known structure in the correct orientation and position, then you can force Phaser to use these coordinates. Use the SOLUTION keyword to fix a rotation of 0 0 0 and a position of 0 0 0 for these coordinates.<br />
<br />
==How to Select Peaks==<br />
<br />
<br />
<br />
The selection of peaks saved for output in the rotation and translation functions can be done in four different ways.<br />
*'''Select by Percentage'''<br />
*: Percentage of the top peak, where the value of the top peak is defined as 100% and the value of the mean is defined as 0%.<br />
*: Default, cutoff=75%. This criteria has the advantange that at least one peak (the top peak) always survives the selection. If the top solution is clear, then only the one solution will be output, but if the distribution of peaks is rather flat, then many peaks will be output for testing in the next part of the MR procedure (e.g. many peaks selected from the rotation function for testing with a translation function). <br />
*'''Select by Z-score'''<br />
*: Number of standard deviations (sigmas) over the mean (the Z-score). <br />
*: Absolute significance test. Not all searches will produce output if the cutoff value is too high (e.g. 5 sigma). <br />
*'''Select by Number'''<br />
*: Number of top peaks to select. <br />
*: If the distribution is very flat then it might be better to select a fixed large number (e.g. 1000) of top rotation peaks for testing in the translation function.<br />
*'''No selection'''<br />
*: All peaks are selected. <br />
*: Enables full 6 dimensional searches, where all the solutions from the rotation function are output for testing in the translation function. This should never be necessary; it would be much faster and probably just as likely to work if the top 1000 peaks were used in this way.<br />
<br />
[[Image:Phaser_selection.gif| Selection criteria]]<br />
<br />
Peaks can also be clustered or not clustered prior to selection in steps 1 and 2.<br />
*'''Clustering Off'''<br />
: All high peaks on the search grid are selected<br />
*'''Clustering On'''<br />
: Points on the search grid with higher neighbouring points are removed from the selection<br />
<br />
<br />
[[Image:Phaser_clustering.gif| Clustering]]<br />
<br />
==How to Control Output==<br />
The output of Phaser can be controlled with optional keywords. <br />
<br />
The ROOT keyword is not compulsory (the default root filename is "PHASER"), but should always be given, so that your jobs have separate and meaningful output filenames.<br />
<br />
The TOPFiles keyword controls the number of potential MR solutions for which PDB and (in the appropriate modes) MTZ files are produced.<br />
<br />
For the MR_AUTO, MR_RNP and MR_LLG modes, unless HKLOut OFF is given as an optional keyword, Phaser produces an MTZ file with "SigmaA" type weighted Fourier map coefficients for producing electron density maps for rebuilding.<br />
<br />
{| class="wikitable" style="text-align:left" width=100%<br />
|-<br />
! MTZ Column Labels !! Description<br />
|-<br />
| FWT/PHWT || Amplitude and phase for 2''m''&#124;F<sub>obs</sub>&#124;-''D''&#124;F<sub>calc</sub>&#124; exp(''i''&alpha;<sub>calc</sub>) map<br />
|-<br />
| DELFWT/PHDELWT || Amplitude and phase for ''m''&#124;F<sub>obs</sub>&#124;-''D''&#124;F<sub>calc</sub>&#124; exp(''i''&alpha;<sub>calc</sub>) map<br />
|-<br />
| FOM || ''m'', analogous to the "Sim" weight, to estimate the reliability of &alpha;<sub>calc</sub><br />
|-<br />
| HLA/HLB/HLC/HLD || Hendrickson-Lattman coefficients encoding the phase probability distribution<br />
|}<br />
<br />
==Translational Non-crystallographic Symmetry==<br />
<br />
<span style="color:crimson">'''*Warning*''' Solution by MR in the presence of translational non-crystallographic symmetry is not fully automated.</span><br />
<br />
Phaser calculates correction factors for the expected intensities in the presence of translational non-crystallographic symmetry (tNCS), and is able to solve structures with complex patterns of tNCS. '''However, the use of Phaser in the presence of tNCS requires the nature of the tNCS to be understood by the user.''' In simple cases, solution is no more difficult than solution without tNCS, but in complex cases, separate Phaser runs with tNCS turned on and off, and/or the use of different tNCS vectors, may be necessary.<br />
<br />
The output of Phaser will help the user in detecting and understanding the tNCS, but '''the tNCS is not completely characterised by Phaser'''. The default behaviour may or may not be correct for the particular crystal under study.<br />
<br />
Characterization of the tNCS involves understanding the number of copies of the molecule in the asymmetric unit and the translation vectors between them. Molecules related by a tNCS vector will have an associated peak in the native Patterson. Phaser calculates the native Patterson (MODE TNCS) and lists the peaks that are more than 20% of the origin peak. Any given crystal with tNCS may have one or more peaks meeting this criteria.<br />
<br />
===Default tNCS detection and correction===<br />
====No tNCS====<br />
No tNCS correction is applied by default if there is<br />
# no peak in the native Patterson <br />
# more than one peak in the native Patterson over 20% of the origin and these peaks are not all the result of a commensurate modulation<br />
<br />
====Pairs of molecules====<br />
By default, if Phaser detects a peak in the native Patterson '''and the number of search copies is divisible by 2''' then Phaser will search for molecules in pairs related by the tNCS vector given by the peak in the native Patterson.<br />
<br />
This will be the correct behaviour if and only if there are an even number of copies of the molecule in the asymmetric unit, clustered into two groups related by a single tNCS vector. There will only be one significant peak in the native Patterson. Fortunately, this is a reasonably common scenario.<br />
<br />
Phaser refines the relative orientation of the molecules in the two groups (rotations of up to 10 degrees will still give rise to a significant native Patterson peak) and uses this information to generate expected intensity factors for the reflections. Solution should be straightforward, with the usual caveat for MR that there is a sufficiently good model.<br />
<br />
Where there is a single peak in the native Patterson, it is often located at a position half way along a unit cell axis or diagonal, representing a pseudo-halving of the unit cell dimensions. However, Phaser is by no means restricted to these sorts of pseudo-cells in its handling of two-fold tNCS, and the tNCS vector can be in a general position.<br />
<br />
===Non-default tNCS correction===<br />
====Higher order tNCS====<br />
Frequently, tNCS does not associate 2 clusters of molecules in the asymmetric unit, but rather there are 3 or more (n) clusters of molecules associated by a series of vectors that are multiples of 1, 2, 3 ... (n-1) times a basic translation vector. The integer n is the order of the tNCS and is entered using the keyword TNCS NMOL <n>. <br />
<br />
Phaser does not automatically detect these cases. The peaks of the native Patterson must be inspected to find the n-fold relationship, which can be subtle; for instance, a peak at 0.2,0.4,0 can be interpreted in terms of a vector that is twice a vector of 0.6,0.2,0 (taking unit cell translations into account). The series will not generally have all peaks the same height. Lower peaks in the series represent relationships where the relative rotations between related molecules are larger. Missing peaks in the series may be below the default 20% of origin cut-off. This can be lowered with TNCS PATT PERCENT <x><br />
<br />
Phaser can account for this form of tNCS with the use of the keywords TNCS NMOL <n> '''and entering the number of search copies as a multiple of n.''' The vector for the tNCS should either be input using TNCS TRA VECTOR <x,y,z>, or set the TNCS PATT PERCENT <x> value so that only one peak is selected (if this peak represents the appropriate base vector for the tNCS).<br />
<br />
When there are more than two molecules related by tNCS, Phaser does not refine the orientations between the molecules related by the tNCS.<br />
<br />
Where n times the basic translation vector equates to (integer multiples of) unit cell axes, the tNCS represents a pseudo-cell, and this case is known as commensurate modulation. However, as for two-fold tNCS, Phaser is not restricted to these sorts of pseudo-cells and the basic tNCS vector can be in a general position.<br />
<br />
====Complex tNCS====<br />
If there are many molecules in the asymmetric unit but they are not all related by tNCS, or there are sub-groups of molecules related by different tNCS vectors, then the modulations of the expected intensities due to the tNCS will be much less significant than the cases described above. '''In these cases it is possible that structure solution will be achieved without any tNCS correction factors being applied.''' Indeed, searching for all the copies as tNCS-related multiples when some molecules are not related by tNCS will cause structure solution to fail. To turn off the automatic detection and use of tNCS use the keyword TNCS USE OFF.<br />
<br />
If turning off the TNCS correction factors fails to give a solution, then a good approach is to proceed step-wise. Consider the highest native Patterson peak first and determine that nature of the tNCS associated with it. Use the appropriate correction factors to locate all the molecules with this tNCS. Then take the second independent native Patterson peak and apply the correction factors associated with it to find the second set of molecules, fixing the first, etc. Finally, turn TNCS off to find any orphan molecules.</div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Python_Example_Scripts&diff=2375Python Example Scripts2016-11-25T17:26:29Z<p>Airlie: /* Anisotropy Correction */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
See [[Python Interface]] for introduction to running phaser as a python library.<br />
<br />
Example scripts for the most popular modes of running Phaser. <br />
<br />
== Reading MTZ Files for Molecular Replacement==<br />
Example script for reading data from MTZ file beta_blip.mtz.<br />
<br />
Note that by default reflections are sorted into resolution order upon reading, to achieve a performance gain in the molecular replacement routines. If reflections are not being read from an MTZ file with this script, reflections should be pre-sorted into resolution order to achieve the same performance gain. Sorting is turned off with the setSORT(False) function.<br />
<br />
#beta_blip_data.py<br />
from phaser import *<br />
i = InputMR_DAT()<br />
HKLIN = "beta_blip_P3221.mtz"<br />
i.setHKLI(HKLIN)<br />
i.setMUTE(True)<br />
r = runMR_DAT(i)<br />
print r.logfile()<br />
if r.Success():<br />
hkl = r.getMiller()<br />
fobs = r.getF()<br />
sigma = r.getSIGF()<br />
nrefl = min(10,hkl.size())<br />
print "Data read from: " , HKLIN<br />
print "First ", nrefl , " reflections"<br />
print "%4s %4s %4s %10s %10s" % ("H","K","L",F,SIGF)<br />
for i in range(0,nrefl):<br />
print "%4d %4d %4d %10.4f %10.4f" % \<br />
(hkl[i][0],hkl[i][1],hkl[i][2],fobs[i],sigma[i])<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
<br />
==Automated Molecular Replacement==<br />
Example script for automated structure solution of BETA-BLIP<br />
<br />
#beta_blip_auto.py<br />
from phaser import *<br />
i = InputMR_DAT()<br />
i.setHKLI("beta_blip_P3221.mtz")<br />
i.setHIRES(6.0)<br />
i.setMUTE(True)<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputMR_AUTO()<br />
i.setREFL_DATA(r.getREFL_DATA())<br />
i.setROOT("beta_blip_auto")<br />
i.addENSE_PDB_ID("beta","beta.pdb",1.0)<br />
i.addENSE_PDB_ID("blip","blip.pdb",1.0)<br />
i.addCOMP_PROT_MW_NUM(28853,1)<br />
i.addCOMP_PROT_MW_NUM(17522,1)<br />
i.addSEAR_ENSE_NUM("beta",1)<br />
i.addSEAR_ENSE_NUM("blip",1)<br />
i.setMUTE(True)<br />
del(r)<br />
r = runMR_AUTO(i)<br />
if r.Success():<br />
if r.foundSolutions() :<br />
print "Phaser has found MR solutions"<br />
print "Top LLG = %f" % r.getTopLLG()<br />
print "Top PDB file = %s" % r.getTopPdbFile()<br />
else:<br />
print "Phaser has not found any MR solutions"<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
<br />
==Reading MTZ Files for Experimental Phasing==<br />
Example script for reading SAD data from MTZ file S-insulin.mtz<br />
<pre><br />
#insulin_data.py<br />
from phaser import *<br />
i = InputEP_DAT()<br />
HKLIN = "S-insulin.mtz"<br />
xtalid = "insulin"<br />
waveid = "cuka"<br />
i.setHKLI(HKLIN)<br />
i.addCRYS_ANOM_LABI(xtalid,waveid,"F(+)","SIGF(+)","F(-)","SIGF(-)")<br />
i.setMUTE(True)<br />
r = runEP_DAT(i)<br />
if r.Success():<br />
hkl = r.getMiller()<br />
Fpos = r.getFpos(xtalid,waveid)<br />
Ppos = r.getPpos(xtalid,waveid)<br />
Fneg = r.getFneg(xtalid,waveid)<br />
Pneg = r.getPneg(xtalid,waveid)<br />
print "Data read from: " , HKLIN<br />
print "Spacegroup Name (Hall symbol) = %s (%s)" % \<br />
(r.getSpaceGroupName(), r.getSpaceGroupHall())<br />
print "Unitcell = " , r.getUnitCell()<br />
nrefl = min(10,hkl.size())<br />
print "First ", nrefl , " reflections with anomalous differences"<br />
print "%4s %4s %4s %10s %10s %10s" % ("H","K","L","F(+)","F(-)","D")<br />
i = 0<br />
r = 0<br />
while r < nrefl:<br />
if Ppos[i] and Pneg[i] :<br />
D = abs(Fpos[i]-Fneg[i])<br />
if D > 0<br />
print "%4d %4d %4d %10.4f %10.4f %10.4f" % \<br />
(hkl[i][0],hkl[i][1],hkl[i][2],Fpos[i],Fneg[i],D)<br />
r=r+1<br />
i=i+1<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Automated Experimental Phasing==<br />
<br />
<br />
Example script for SAD phasing for insulin<br />
<pre><br />
#insulin_sad.py<br />
from phaser import *<br />
from cctbx import xray<br />
i = InputEP_DAT()<br />
HKLIN = "S-insulin.mtz"<br />
xtalid = "insulin"<br />
waveid = "cuka"<br />
i.setHKLI(HKLIN)<br />
i.addCRYS_ANOM_LABI(xtalid,waveid,"F(+)","SIGF(+)","F(-)","SIGF(-)")<br />
i.setMUTE(True)<br />
r = runEP_DAT(i)<br />
if r.Success():<br />
hkl = r.getMiller()<br />
Fpos = r.getFpos(xtalid,waveid)<br />
Spos = r.getSIGFpos(xtalid,waveid)<br />
Ppos = r.getPpos(xtalid,waveid)<br />
Fneg = r.getFneg(xtalid,waveid)<br />
Sneg = r.getSIGFneg(xtalid,waveid)<br />
Pneg = r.getPneg(xtalid,waveid)<br />
i = InputEP_AUTO()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL(r.getUnitCell())<br />
i.setCRYS_MILLER(hkl)<br />
i.addCRYS_ANOM_DATA(xtalid,waveid,Fpos,Spos,Ppos,Fneg,Sneg,Pneg)<br />
i.setATOM_PDB(xtalid,"S-insulin_hyss.pdb")<br />
i.setLLGC_CRYS_COMPLETE(xtalid,True)<br />
i.addLLGC_CRYS_SCAT_ELEMENT(xtalid,"S")<br />
i.addCOMP_PROT_FASTA_NUM("S-insulin.seq",1.)<br />
i.setHKLO(False)<br />
i.setSCRI(False)<br />
i.setXYZO(False)<br />
i.setMUTE(True)<br />
r = runEP_AUTO(i)<br />
if r.Success():<br />
print "SAD phasing"<br />
print "Data read from: " , HKLIN<br />
print "Data output to : " , r.getMtzFile()<br />
print "Spacegroup Name (Hall symbol) = %s (%s)" % \<br />
(r.getSpaceGroupName(), r.getSpaceGroupHall())<br />
print "Unitcell = " , r.getUnitCell()<br />
print "LogLikelihood = " , r.getLogLikelihood()<br />
atom = r.getAtoms(xtalid)<br />
print atom.size(), " refined atoms"<br />
print "%5s %10s %10s %10s %10s %10s" % \<br />
("atom","x","y","z","occupancy","u-iso")<br />
for i in range(0,atom.size()):<br />
print "%5s %10.4f %10.4f %10.4f %10.4f %10.4f" % \<br />
<br />
(atom[i].scattering_type,atom[i].site[0],atom[i].site[1],atom[i].site[2],atom[i].occupancy,atom[i].u_iso)<br />
hkl = r.getMiller();<br />
fwt = r.getFWT()<br />
phwt = r.getPHWT()<br />
fom = r.getFOM()<br />
nrefl = min(10,hkl.size())<br />
print "First ", nrefl , " reflections"<br />
print "%4s %4s %4s %10s %10s %10s" % \<br />
("H","K","L","FWT","PHWT","FOM")<br />
for i in range(0,nrefl):<br />
print "%4d %4d %4d %10.4f %10.4f %10.4f" % \<br />
(hkl[i][0],hkl[i][1],hkl[i][2],fwt[i],phwt[i],fom[i])<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Anisotropy Correction==<br />
Example script script for anisotropy correction of BETA-BLIP data<br />
<br />
#beta_blip_ano.py<br />
from phaser import *<br />
i = InputMR_DAT()<br />
HKLIn = "beta_blip_P3221.mtz"<br />
i.setHKLI(HKLIn)<br />
i.setMUTE(True)<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputANO()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setREFL_DATA(r.getREFL_DATA())<br />
i.setROOT("beta_blip_ano")<br />
i.setMUTE(True)<br />
del(r)<br />
r = runANO(i)<br />
if r.Success():<br />
print "Anisotropy Correction"<br />
print "Data read from: " , HKLIn<br />
print "Data output to : " , r.getMtzFile()<br />
print "Spacegroup Name (Hall symbol) = %s (%s)" % \<br />
(r.getSpaceGroupName(), r.getSpaceGroupHall())<br />
print "Unitcell = " , r.getUnitCell()<br />
print "Principal components = " , r.getEigenBs()<br />
print "Range of principal components = " , r.getAnisoDeltaB()<br />
print "Wilson Scale = " , r.getWilsonK()<br />
print "Wilson B-factor = " , r.getWilsonB()<br />
hkl = r.getMiller();<br />
f = r.getF()<br />
sigf = r.getSIGF()<br />
f_iso = r.getCorrectedF()<br />
sigf_iso = r.getCorrectedSIGF()<br />
corr = r.getCorrection()<br />
nrefl = min(10,hkl.size())<br />
print "First ", nrefl , " reflections"<br />
print "%4s %4s %4s %10s %10s %10s %10s %10s" % \<br />
("H","K","L","F","SIGF",r.getLaboutF(),r.getLaboutSIGF(),"Corr\'n")<br />
for i in range(0,nrefl):<br />
print "%4d %4d %4d %10.4f %10.4f %10.4f %10.4f %10.4f" % \<br />
(hkl[i][0],hkl[i][1],hkl[i][2],f[i],sigf[i],f_iso[i],sigf_iso[i],corr[i])<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
<br />
==Cell Content Analysis==<br />
Example script for cell content analysis of BETA-BLIP<br />
<pre><br />
#beta_blip_cca.py<br />
from phaser import *<br />
i = InputMR_DAT()<br />
HKLIN = "beta_blip.mtz"<br />
F = "Fobs"<br />
SIGF = "Sigma"<br />
i.setHKLI(HKLIN)<br />
i.setLABI_F_SIGF(F,SIGF)<br />
i.setMUTE(True)<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputCCA()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.addCOMP_PROT_MW_NUM(28853,1)<br />
i.addCOMP_PROT_MW_NUM(17522,1)<br />
i.setMUTE(True)<br />
del(r)<br />
r = runCCA(i)<br />
if r.Success():<br />
print "Cell Content Analysis"<br />
print "Molecular weight of assembly = " , r.getAssemblyMW()<br />
print "Best Z value = " , r.getBestZ()<br />
print "Best VM value = " , r.getBestVM()<br />
print "Probability of Best VM = " , r.getBestProb()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Translational NCS Analysis==<br />
Example script for translational NCS analysis of BETA-BLIP<br />
<pre><br />
#beta_blip_ncs.py<br />
from phaser import *<br />
i = InputMR_DAT()<br />
HKLIN = "beta_blip.mtz"<br />
F = "Fobs"<br />
SIGF = "Sigma"<br />
i.setHKLI(HKLIN)<br />
i.setLABI_F_SIGF(F,SIGF)<br />
i.setMUTE(True)<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputNCS()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.setREFL_F_SIGF(r.getMiller(),r.getF(),r.getSIGF())<br />
i.addCOMP_PROT_MW_NUM(28853,1)<br />
i.addCOMP_PROT_MW_NUM(17522,1)<br />
i.setMUTE(True)<br />
del(r)<br />
r = runNCS(i)<br />
if r.Success():<br />
print "Translational NCS analysis"<br />
print "Translational NCS present = ", r.hasTNCS()<br />
if r.hasTNCS():<br />
print "Translational NCS vecor = ", r.hasTNCS()<br />
print "Twinning alpha = ", r.getTwinAlpha()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Normal Mode Analysis==<br />
Example script for normal mode analysis of BETA-BLIP. Note that the space group and unit cell are not required, and so the MTZ file does not need to be read to extract these parameters.<br />
<pre><br />
#beta_nma.py<br />
from phaser import *<br />
i = InputNMA()<br />
i.setROOT("beta_nma")<br />
i.addENSE_PDB_ID("beta","beta.pdb",1.0)<br />
i.addNMA_MODE(4)<br />
i.setPERT_RMS_DIRE("FORWARD")<br />
i.setMUTE(True)<br />
r = runNMAXYZ(i)<br />
if r.Success():<br />
print "Normal Mode Analysis"<br />
for i in range(0,r.getNum()):<br />
print "PDB file = ", r.getPdbFile(i)<br />
displacement = r.getDisplacements(i)<br />
mode = r.getModes(i)<br />
for j in range(0,mode.size()):<br />
print " Mode = " , mode[j], " Displacement = ", displacement[j]<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Logfile Handling==<br />
<br />
Example of how to redirect phaser output to a python string for real-time viewing of output, but not via standard output. Output to standard out is silenced with setMUTE(True).<br />
<pre><br />
beta_blip_logfile.py<br />
from phaser import *<br />
from cStringIO import StringIO<br />
i = InputMR_DAT()<br />
i.setHKLI("beta_blip.mtz")<br />
i.setLABI_F_SIGF("Fobs","Sigma")<br />
i.setMUTE(True)<br />
o = Output()<br />
redirect_str = StringIO()<br />
o.setPackagePhenix(file_object=redirect_str)<br />
r = runMR_DAT(i,o)<br />
</pre></div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Python_Example_Scripts&diff=2374Python Example Scripts2016-11-25T17:20:37Z<p>Airlie: /* Reading MTZ Files for Molecular Replacement */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
See [[Python Interface]] for introduction to running phaser as a python library.<br />
<br />
Example scripts for the most popular modes of running Phaser. <br />
<br />
== Reading MTZ Files for Molecular Replacement==<br />
Example script for reading data from MTZ file beta_blip.mtz.<br />
<br />
Note that by default reflections are sorted into resolution order upon reading, to achieve a performance gain in the molecular replacement routines. If reflections are not being read from an MTZ file with this script, reflections should be pre-sorted into resolution order to achieve the same performance gain. Sorting is turned off with the setSORT(False) function.<br />
<br />
#beta_blip_data.py<br />
from phaser import *<br />
i = InputMR_DAT()<br />
HKLIN = "beta_blip_P3221.mtz"<br />
i.setHKLI(HKLIN)<br />
i.setMUTE(True)<br />
r = runMR_DAT(i)<br />
print r.logfile()<br />
if r.Success():<br />
hkl = r.getMiller()<br />
fobs = r.getF()<br />
sigma = r.getSIGF()<br />
nrefl = min(10,hkl.size())<br />
print "Data read from: " , HKLIN<br />
print "First ", nrefl , " reflections"<br />
print "%4s %4s %4s %10s %10s" % ("H","K","L",F,SIGF)<br />
for i in range(0,nrefl):<br />
print "%4d %4d %4d %10.4f %10.4f" % \<br />
(hkl[i][0],hkl[i][1],hkl[i][2],fobs[i],sigma[i])<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
<br />
==Automated Molecular Replacement==<br />
Example script for automated structure solution of BETA-BLIP<br />
<br />
#beta_blip_auto.py<br />
from phaser import *<br />
i = InputMR_DAT()<br />
i.setHKLI("beta_blip_P3221.mtz")<br />
i.setHIRES(6.0)<br />
i.setMUTE(True)<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputMR_AUTO()<br />
i.setREFL_DATA(r.getREFL_DATA())<br />
i.setROOT("beta_blip_auto")<br />
i.addENSE_PDB_ID("beta","beta.pdb",1.0)<br />
i.addENSE_PDB_ID("blip","blip.pdb",1.0)<br />
i.addCOMP_PROT_MW_NUM(28853,1)<br />
i.addCOMP_PROT_MW_NUM(17522,1)<br />
i.addSEAR_ENSE_NUM("beta",1)<br />
i.addSEAR_ENSE_NUM("blip",1)<br />
i.setMUTE(True)<br />
del(r)<br />
r = runMR_AUTO(i)<br />
if r.Success():<br />
if r.foundSolutions() :<br />
print "Phaser has found MR solutions"<br />
print "Top LLG = %f" % r.getTopLLG()<br />
print "Top PDB file = %s" % r.getTopPdbFile()<br />
else:<br />
print "Phaser has not found any MR solutions"<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
<br />
==Reading MTZ Files for Experimental Phasing==<br />
Example script for reading SAD data from MTZ file S-insulin.mtz<br />
<pre><br />
#insulin_data.py<br />
from phaser import *<br />
i = InputEP_DAT()<br />
HKLIN = "S-insulin.mtz"<br />
xtalid = "insulin"<br />
waveid = "cuka"<br />
i.setHKLI(HKLIN)<br />
i.addCRYS_ANOM_LABI(xtalid,waveid,"F(+)","SIGF(+)","F(-)","SIGF(-)")<br />
i.setMUTE(True)<br />
r = runEP_DAT(i)<br />
if r.Success():<br />
hkl = r.getMiller()<br />
Fpos = r.getFpos(xtalid,waveid)<br />
Ppos = r.getPpos(xtalid,waveid)<br />
Fneg = r.getFneg(xtalid,waveid)<br />
Pneg = r.getPneg(xtalid,waveid)<br />
print "Data read from: " , HKLIN<br />
print "Spacegroup Name (Hall symbol) = %s (%s)" % \<br />
(r.getSpaceGroupName(), r.getSpaceGroupHall())<br />
print "Unitcell = " , r.getUnitCell()<br />
nrefl = min(10,hkl.size())<br />
print "First ", nrefl , " reflections with anomalous differences"<br />
print "%4s %4s %4s %10s %10s %10s" % ("H","K","L","F(+)","F(-)","D")<br />
i = 0<br />
r = 0<br />
while r < nrefl:<br />
if Ppos[i] and Pneg[i] :<br />
D = abs(Fpos[i]-Fneg[i])<br />
if D > 0<br />
print "%4d %4d %4d %10.4f %10.4f %10.4f" % \<br />
(hkl[i][0],hkl[i][1],hkl[i][2],Fpos[i],Fneg[i],D)<br />
r=r+1<br />
i=i+1<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Automated Experimental Phasing==<br />
<br />
<br />
Example script for SAD phasing for insulin<br />
<pre><br />
#insulin_sad.py<br />
from phaser import *<br />
from cctbx import xray<br />
i = InputEP_DAT()<br />
HKLIN = "S-insulin.mtz"<br />
xtalid = "insulin"<br />
waveid = "cuka"<br />
i.setHKLI(HKLIN)<br />
i.addCRYS_ANOM_LABI(xtalid,waveid,"F(+)","SIGF(+)","F(-)","SIGF(-)")<br />
i.setMUTE(True)<br />
r = runEP_DAT(i)<br />
if r.Success():<br />
hkl = r.getMiller()<br />
Fpos = r.getFpos(xtalid,waveid)<br />
Spos = r.getSIGFpos(xtalid,waveid)<br />
Ppos = r.getPpos(xtalid,waveid)<br />
Fneg = r.getFneg(xtalid,waveid)<br />
Sneg = r.getSIGFneg(xtalid,waveid)<br />
Pneg = r.getPneg(xtalid,waveid)<br />
i = InputEP_AUTO()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL(r.getUnitCell())<br />
i.setCRYS_MILLER(hkl)<br />
i.addCRYS_ANOM_DATA(xtalid,waveid,Fpos,Spos,Ppos,Fneg,Sneg,Pneg)<br />
i.setATOM_PDB(xtalid,"S-insulin_hyss.pdb")<br />
i.setLLGC_CRYS_COMPLETE(xtalid,True)<br />
i.addLLGC_CRYS_SCAT_ELEMENT(xtalid,"S")<br />
i.addCOMP_PROT_FASTA_NUM("S-insulin.seq",1.)<br />
i.setHKLO(False)<br />
i.setSCRI(False)<br />
i.setXYZO(False)<br />
i.setMUTE(True)<br />
r = runEP_AUTO(i)<br />
if r.Success():<br />
print "SAD phasing"<br />
print "Data read from: " , HKLIN<br />
print "Data output to : " , r.getMtzFile()<br />
print "Spacegroup Name (Hall symbol) = %s (%s)" % \<br />
(r.getSpaceGroupName(), r.getSpaceGroupHall())<br />
print "Unitcell = " , r.getUnitCell()<br />
print "LogLikelihood = " , r.getLogLikelihood()<br />
atom = r.getAtoms(xtalid)<br />
print atom.size(), " refined atoms"<br />
print "%5s %10s %10s %10s %10s %10s" % \<br />
("atom","x","y","z","occupancy","u-iso")<br />
for i in range(0,atom.size()):<br />
print "%5s %10.4f %10.4f %10.4f %10.4f %10.4f" % \<br />
<br />
(atom[i].scattering_type,atom[i].site[0],atom[i].site[1],atom[i].site[2],atom[i].occupancy,atom[i].u_iso)<br />
hkl = r.getMiller();<br />
fwt = r.getFWT()<br />
phwt = r.getPHWT()<br />
fom = r.getFOM()<br />
nrefl = min(10,hkl.size())<br />
print "First ", nrefl , " reflections"<br />
print "%4s %4s %4s %10s %10s %10s" % \<br />
("H","K","L","FWT","PHWT","FOM")<br />
for i in range(0,nrefl):<br />
print "%4d %4d %4d %10.4f %10.4f %10.4f" % \<br />
(hkl[i][0],hkl[i][1],hkl[i][2],fwt[i],phwt[i],fom[i])<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Anisotropy Correction==<br />
Example script script for anisotropy correction of BETA-BLIP data<br />
<br />
<pre><br />
#beta_blip_ano.py<br />
from phaser import *<br />
i = InputMR_DAT()<br />
HKLIn = "beta_blip.mtz"<br />
F = "Fobs"<br />
SIGF = "Sigma"<br />
i.setHKLI(HKLIn)<br />
i.setLABI_F_SIGF(F,SIGF)<br />
i.setMUTE(True)<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputANO()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.setREFL_F_SIGF(r.getMiller(),r.getFobs(),r.getSigFobs())<br />
i.setLABI_F_SIGF(F,SIGF)<br />
i.setHKLI(HKLIn)<br />
i.setROOT("beta_blip_ano")<br />
i.setMUTE(True)<br />
del(r)<br />
r = runANO(i)<br />
if r.Success():<br />
print "Anisotropy Correction"<br />
print "Data read from: " , HKLIn<br />
print "Data output to : " , r.getMtzFile()<br />
print "Spacegroup Name (Hall symbol) = %s (%s)" % \<br />
(r.getSpaceGroupName(), r.getSpaceGroupHall())<br />
print "Unitcell = " , r.getUnitCell()<br />
print "Principal components = " , r.getEigenBs()<br />
print "Range of principal components = " , r.getAnisoDeltaB()<br />
print "Wilson Scale = " , r.getWilsonK()<br />
print "Wilson B-factor = " , r.getWilsonB()<br />
hkl = r.getMiller();<br />
f = r.getF()<br />
sigf = r.getSIGF()<br />
f_iso = r.getCorrectedF()<br />
sigf_iso = r.getCorrectedSIGF()<br />
corr = r.getCorrection()<br />
nrefl = min(10,hkl.size())<br />
print "First ", nrefl , " reflections"<br />
print "%4s %4s %4s %10s %10s %10s %10s %10s" % \<br />
("H","K","L",F,SIGF,r.getLaboutF(),r.getLaboutSIGF(),"Corr\'n")<br />
for i in range(0,nrefl):<br />
print "%4d %4d %4d %10.4f %10.4f %10.4f %10.4f %10.4f" % \<br />
(hkl[i][0],hkl[i][1],hkl[i][2],f[i],sigf[i],f_iso[i],sigf_iso[i],corr[i])<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Cell Content Analysis==<br />
Example script for cell content analysis of BETA-BLIP<br />
<pre><br />
#beta_blip_cca.py<br />
from phaser import *<br />
i = InputMR_DAT()<br />
HKLIN = "beta_blip.mtz"<br />
F = "Fobs"<br />
SIGF = "Sigma"<br />
i.setHKLI(HKLIN)<br />
i.setLABI_F_SIGF(F,SIGF)<br />
i.setMUTE(True)<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputCCA()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.addCOMP_PROT_MW_NUM(28853,1)<br />
i.addCOMP_PROT_MW_NUM(17522,1)<br />
i.setMUTE(True)<br />
del(r)<br />
r = runCCA(i)<br />
if r.Success():<br />
print "Cell Content Analysis"<br />
print "Molecular weight of assembly = " , r.getAssemblyMW()<br />
print "Best Z value = " , r.getBestZ()<br />
print "Best VM value = " , r.getBestVM()<br />
print "Probability of Best VM = " , r.getBestProb()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Translational NCS Analysis==<br />
Example script for translational NCS analysis of BETA-BLIP<br />
<pre><br />
#beta_blip_ncs.py<br />
from phaser import *<br />
i = InputMR_DAT()<br />
HKLIN = "beta_blip.mtz"<br />
F = "Fobs"<br />
SIGF = "Sigma"<br />
i.setHKLI(HKLIN)<br />
i.setLABI_F_SIGF(F,SIGF)<br />
i.setMUTE(True)<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputNCS()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.setREFL_F_SIGF(r.getMiller(),r.getF(),r.getSIGF())<br />
i.addCOMP_PROT_MW_NUM(28853,1)<br />
i.addCOMP_PROT_MW_NUM(17522,1)<br />
i.setMUTE(True)<br />
del(r)<br />
r = runNCS(i)<br />
if r.Success():<br />
print "Translational NCS analysis"<br />
print "Translational NCS present = ", r.hasTNCS()<br />
if r.hasTNCS():<br />
print "Translational NCS vecor = ", r.hasTNCS()<br />
print "Twinning alpha = ", r.getTwinAlpha()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Normal Mode Analysis==<br />
Example script for normal mode analysis of BETA-BLIP. Note that the space group and unit cell are not required, and so the MTZ file does not need to be read to extract these parameters.<br />
<pre><br />
#beta_nma.py<br />
from phaser import *<br />
i = InputNMA()<br />
i.setROOT("beta_nma")<br />
i.addENSE_PDB_ID("beta","beta.pdb",1.0)<br />
i.addNMA_MODE(4)<br />
i.setPERT_RMS_DIRE("FORWARD")<br />
i.setMUTE(True)<br />
r = runNMAXYZ(i)<br />
if r.Success():<br />
print "Normal Mode Analysis"<br />
for i in range(0,r.getNum()):<br />
print "PDB file = ", r.getPdbFile(i)<br />
displacement = r.getDisplacements(i)<br />
mode = r.getModes(i)<br />
for j in range(0,mode.size()):<br />
print " Mode = " , mode[j], " Displacement = ", displacement[j]<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Logfile Handling==<br />
<br />
Example of how to redirect phaser output to a python string for real-time viewing of output, but not via standard output. Output to standard out is silenced with setMUTE(True).<br />
<pre><br />
beta_blip_logfile.py<br />
from phaser import *<br />
from cStringIO import StringIO<br />
i = InputMR_DAT()<br />
i.setHKLI("beta_blip.mtz")<br />
i.setLABI_F_SIGF("Fobs","Sigma")<br />
i.setMUTE(True)<br />
o = Output()<br />
redirect_str = StringIO()<br />
o.setPackagePhenix(file_object=redirect_str)<br />
r = runMR_DAT(i,o)<br />
</pre></div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Python_Example_Scripts&diff=2373Python Example Scripts2016-11-25T17:20:18Z<p>Airlie: /* Automated Molecular Replacement */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
See [[Python Interface]] for introduction to running phaser as a python library.<br />
<br />
Example scripts for the most popular modes of running Phaser. <br />
<br />
== Reading MTZ Files for Molecular Replacement==<br />
Example script for reading data from MTZ file beta_blip.mtz.<br />
<br />
Note that by default reflections are sorted into resolution order upon reading, to achieve a performance gain in the molecular replacement routines. If reflections are not being read from an MTZ file with this script, reflections should be pre-sorted into resolution order to achieve the same performance gain. Sorting is turned off with the setSORT(False) function.<br />
<br />
#beta_blip_data.py<br />
from phaser import *<br />
i = InputMR_DAT()<br />
HKLIN = "beta_blip.mtz"<br />
i.setHKLI(HKLIN)<br />
i.setMUTE(True)<br />
r = runMR_DAT(i)<br />
print r.logfile()<br />
if r.Success():<br />
hkl = r.getMiller()<br />
fobs = r.getF()<br />
sigma = r.getSIGF()<br />
nrefl = min(10,hkl.size())<br />
print "Data read from: " , HKLIN<br />
print "First ", nrefl , " reflections"<br />
print "%4s %4s %4s %10s %10s" % ("H","K","L",F,SIGF)<br />
for i in range(0,nrefl):<br />
print "%4d %4d %4d %10.4f %10.4f" % \<br />
(hkl[i][0],hkl[i][1],hkl[i][2],fobs[i],sigma[i])<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
<br />
==Automated Molecular Replacement==<br />
Example script for automated structure solution of BETA-BLIP<br />
<br />
#beta_blip_auto.py<br />
from phaser import *<br />
i = InputMR_DAT()<br />
i.setHKLI("beta_blip_P3221.mtz")<br />
i.setHIRES(6.0)<br />
i.setMUTE(True)<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputMR_AUTO()<br />
i.setREFL_DATA(r.getREFL_DATA())<br />
i.setROOT("beta_blip_auto")<br />
i.addENSE_PDB_ID("beta","beta.pdb",1.0)<br />
i.addENSE_PDB_ID("blip","blip.pdb",1.0)<br />
i.addCOMP_PROT_MW_NUM(28853,1)<br />
i.addCOMP_PROT_MW_NUM(17522,1)<br />
i.addSEAR_ENSE_NUM("beta",1)<br />
i.addSEAR_ENSE_NUM("blip",1)<br />
i.setMUTE(True)<br />
del(r)<br />
r = runMR_AUTO(i)<br />
if r.Success():<br />
if r.foundSolutions() :<br />
print "Phaser has found MR solutions"<br />
print "Top LLG = %f" % r.getTopLLG()<br />
print "Top PDB file = %s" % r.getTopPdbFile()<br />
else:<br />
print "Phaser has not found any MR solutions"<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
<br />
==Reading MTZ Files for Experimental Phasing==<br />
Example script for reading SAD data from MTZ file S-insulin.mtz<br />
<pre><br />
#insulin_data.py<br />
from phaser import *<br />
i = InputEP_DAT()<br />
HKLIN = "S-insulin.mtz"<br />
xtalid = "insulin"<br />
waveid = "cuka"<br />
i.setHKLI(HKLIN)<br />
i.addCRYS_ANOM_LABI(xtalid,waveid,"F(+)","SIGF(+)","F(-)","SIGF(-)")<br />
i.setMUTE(True)<br />
r = runEP_DAT(i)<br />
if r.Success():<br />
hkl = r.getMiller()<br />
Fpos = r.getFpos(xtalid,waveid)<br />
Ppos = r.getPpos(xtalid,waveid)<br />
Fneg = r.getFneg(xtalid,waveid)<br />
Pneg = r.getPneg(xtalid,waveid)<br />
print "Data read from: " , HKLIN<br />
print "Spacegroup Name (Hall symbol) = %s (%s)" % \<br />
(r.getSpaceGroupName(), r.getSpaceGroupHall())<br />
print "Unitcell = " , r.getUnitCell()<br />
nrefl = min(10,hkl.size())<br />
print "First ", nrefl , " reflections with anomalous differences"<br />
print "%4s %4s %4s %10s %10s %10s" % ("H","K","L","F(+)","F(-)","D")<br />
i = 0<br />
r = 0<br />
while r < nrefl:<br />
if Ppos[i] and Pneg[i] :<br />
D = abs(Fpos[i]-Fneg[i])<br />
if D > 0<br />
print "%4d %4d %4d %10.4f %10.4f %10.4f" % \<br />
(hkl[i][0],hkl[i][1],hkl[i][2],Fpos[i],Fneg[i],D)<br />
r=r+1<br />
i=i+1<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Automated Experimental Phasing==<br />
<br />
<br />
Example script for SAD phasing for insulin<br />
<pre><br />
#insulin_sad.py<br />
from phaser import *<br />
from cctbx import xray<br />
i = InputEP_DAT()<br />
HKLIN = "S-insulin.mtz"<br />
xtalid = "insulin"<br />
waveid = "cuka"<br />
i.setHKLI(HKLIN)<br />
i.addCRYS_ANOM_LABI(xtalid,waveid,"F(+)","SIGF(+)","F(-)","SIGF(-)")<br />
i.setMUTE(True)<br />
r = runEP_DAT(i)<br />
if r.Success():<br />
hkl = r.getMiller()<br />
Fpos = r.getFpos(xtalid,waveid)<br />
Spos = r.getSIGFpos(xtalid,waveid)<br />
Ppos = r.getPpos(xtalid,waveid)<br />
Fneg = r.getFneg(xtalid,waveid)<br />
Sneg = r.getSIGFneg(xtalid,waveid)<br />
Pneg = r.getPneg(xtalid,waveid)<br />
i = InputEP_AUTO()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL(r.getUnitCell())<br />
i.setCRYS_MILLER(hkl)<br />
i.addCRYS_ANOM_DATA(xtalid,waveid,Fpos,Spos,Ppos,Fneg,Sneg,Pneg)<br />
i.setATOM_PDB(xtalid,"S-insulin_hyss.pdb")<br />
i.setLLGC_CRYS_COMPLETE(xtalid,True)<br />
i.addLLGC_CRYS_SCAT_ELEMENT(xtalid,"S")<br />
i.addCOMP_PROT_FASTA_NUM("S-insulin.seq",1.)<br />
i.setHKLO(False)<br />
i.setSCRI(False)<br />
i.setXYZO(False)<br />
i.setMUTE(True)<br />
r = runEP_AUTO(i)<br />
if r.Success():<br />
print "SAD phasing"<br />
print "Data read from: " , HKLIN<br />
print "Data output to : " , r.getMtzFile()<br />
print "Spacegroup Name (Hall symbol) = %s (%s)" % \<br />
(r.getSpaceGroupName(), r.getSpaceGroupHall())<br />
print "Unitcell = " , r.getUnitCell()<br />
print "LogLikelihood = " , r.getLogLikelihood()<br />
atom = r.getAtoms(xtalid)<br />
print atom.size(), " refined atoms"<br />
print "%5s %10s %10s %10s %10s %10s" % \<br />
("atom","x","y","z","occupancy","u-iso")<br />
for i in range(0,atom.size()):<br />
print "%5s %10.4f %10.4f %10.4f %10.4f %10.4f" % \<br />
<br />
(atom[i].scattering_type,atom[i].site[0],atom[i].site[1],atom[i].site[2],atom[i].occupancy,atom[i].u_iso)<br />
hkl = r.getMiller();<br />
fwt = r.getFWT()<br />
phwt = r.getPHWT()<br />
fom = r.getFOM()<br />
nrefl = min(10,hkl.size())<br />
print "First ", nrefl , " reflections"<br />
print "%4s %4s %4s %10s %10s %10s" % \<br />
("H","K","L","FWT","PHWT","FOM")<br />
for i in range(0,nrefl):<br />
print "%4d %4d %4d %10.4f %10.4f %10.4f" % \<br />
(hkl[i][0],hkl[i][1],hkl[i][2],fwt[i],phwt[i],fom[i])<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Anisotropy Correction==<br />
Example script script for anisotropy correction of BETA-BLIP data<br />
<br />
<pre><br />
#beta_blip_ano.py<br />
from phaser import *<br />
i = InputMR_DAT()<br />
HKLIn = "beta_blip.mtz"<br />
F = "Fobs"<br />
SIGF = "Sigma"<br />
i.setHKLI(HKLIn)<br />
i.setLABI_F_SIGF(F,SIGF)<br />
i.setMUTE(True)<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputANO()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.setREFL_F_SIGF(r.getMiller(),r.getFobs(),r.getSigFobs())<br />
i.setLABI_F_SIGF(F,SIGF)<br />
i.setHKLI(HKLIn)<br />
i.setROOT("beta_blip_ano")<br />
i.setMUTE(True)<br />
del(r)<br />
r = runANO(i)<br />
if r.Success():<br />
print "Anisotropy Correction"<br />
print "Data read from: " , HKLIn<br />
print "Data output to : " , r.getMtzFile()<br />
print "Spacegroup Name (Hall symbol) = %s (%s)" % \<br />
(r.getSpaceGroupName(), r.getSpaceGroupHall())<br />
print "Unitcell = " , r.getUnitCell()<br />
print "Principal components = " , r.getEigenBs()<br />
print "Range of principal components = " , r.getAnisoDeltaB()<br />
print "Wilson Scale = " , r.getWilsonK()<br />
print "Wilson B-factor = " , r.getWilsonB()<br />
hkl = r.getMiller();<br />
f = r.getF()<br />
sigf = r.getSIGF()<br />
f_iso = r.getCorrectedF()<br />
sigf_iso = r.getCorrectedSIGF()<br />
corr = r.getCorrection()<br />
nrefl = min(10,hkl.size())<br />
print "First ", nrefl , " reflections"<br />
print "%4s %4s %4s %10s %10s %10s %10s %10s" % \<br />
("H","K","L",F,SIGF,r.getLaboutF(),r.getLaboutSIGF(),"Corr\'n")<br />
for i in range(0,nrefl):<br />
print "%4d %4d %4d %10.4f %10.4f %10.4f %10.4f %10.4f" % \<br />
(hkl[i][0],hkl[i][1],hkl[i][2],f[i],sigf[i],f_iso[i],sigf_iso[i],corr[i])<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Cell Content Analysis==<br />
Example script for cell content analysis of BETA-BLIP<br />
<pre><br />
#beta_blip_cca.py<br />
from phaser import *<br />
i = InputMR_DAT()<br />
HKLIN = "beta_blip.mtz"<br />
F = "Fobs"<br />
SIGF = "Sigma"<br />
i.setHKLI(HKLIN)<br />
i.setLABI_F_SIGF(F,SIGF)<br />
i.setMUTE(True)<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputCCA()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.addCOMP_PROT_MW_NUM(28853,1)<br />
i.addCOMP_PROT_MW_NUM(17522,1)<br />
i.setMUTE(True)<br />
del(r)<br />
r = runCCA(i)<br />
if r.Success():<br />
print "Cell Content Analysis"<br />
print "Molecular weight of assembly = " , r.getAssemblyMW()<br />
print "Best Z value = " , r.getBestZ()<br />
print "Best VM value = " , r.getBestVM()<br />
print "Probability of Best VM = " , r.getBestProb()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Translational NCS Analysis==<br />
Example script for translational NCS analysis of BETA-BLIP<br />
<pre><br />
#beta_blip_ncs.py<br />
from phaser import *<br />
i = InputMR_DAT()<br />
HKLIN = "beta_blip.mtz"<br />
F = "Fobs"<br />
SIGF = "Sigma"<br />
i.setHKLI(HKLIN)<br />
i.setLABI_F_SIGF(F,SIGF)<br />
i.setMUTE(True)<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputNCS()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.setREFL_F_SIGF(r.getMiller(),r.getF(),r.getSIGF())<br />
i.addCOMP_PROT_MW_NUM(28853,1)<br />
i.addCOMP_PROT_MW_NUM(17522,1)<br />
i.setMUTE(True)<br />
del(r)<br />
r = runNCS(i)<br />
if r.Success():<br />
print "Translational NCS analysis"<br />
print "Translational NCS present = ", r.hasTNCS()<br />
if r.hasTNCS():<br />
print "Translational NCS vecor = ", r.hasTNCS()<br />
print "Twinning alpha = ", r.getTwinAlpha()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Normal Mode Analysis==<br />
Example script for normal mode analysis of BETA-BLIP. Note that the space group and unit cell are not required, and so the MTZ file does not need to be read to extract these parameters.<br />
<pre><br />
#beta_nma.py<br />
from phaser import *<br />
i = InputNMA()<br />
i.setROOT("beta_nma")<br />
i.addENSE_PDB_ID("beta","beta.pdb",1.0)<br />
i.addNMA_MODE(4)<br />
i.setPERT_RMS_DIRE("FORWARD")<br />
i.setMUTE(True)<br />
r = runNMAXYZ(i)<br />
if r.Success():<br />
print "Normal Mode Analysis"<br />
for i in range(0,r.getNum()):<br />
print "PDB file = ", r.getPdbFile(i)<br />
displacement = r.getDisplacements(i)<br />
mode = r.getModes(i)<br />
for j in range(0,mode.size()):<br />
print " Mode = " , mode[j], " Displacement = ", displacement[j]<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Logfile Handling==<br />
<br />
Example of how to redirect phaser output to a python string for real-time viewing of output, but not via standard output. Output to standard out is silenced with setMUTE(True).<br />
<pre><br />
beta_blip_logfile.py<br />
from phaser import *<br />
from cStringIO import StringIO<br />
i = InputMR_DAT()<br />
i.setHKLI("beta_blip.mtz")<br />
i.setLABI_F_SIGF("Fobs","Sigma")<br />
i.setMUTE(True)<br />
o = Output()<br />
redirect_str = StringIO()<br />
o.setPackagePhenix(file_object=redirect_str)<br />
r = runMR_DAT(i,o)<br />
</pre></div>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=Python_Example_Scripts&diff=2372Python Example Scripts2016-11-25T17:14:31Z<p>Airlie: /* Reading MTZ Files for Molecular Replacement */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
See [[Python Interface]] for introduction to running phaser as a python library.<br />
<br />
Example scripts for the most popular modes of running Phaser. <br />
<br />
== Reading MTZ Files for Molecular Replacement==<br />
Example script for reading data from MTZ file beta_blip.mtz.<br />
<br />
Note that by default reflections are sorted into resolution order upon reading, to achieve a performance gain in the molecular replacement routines. If reflections are not being read from an MTZ file with this script, reflections should be pre-sorted into resolution order to achieve the same performance gain. Sorting is turned off with the setSORT(False) function.<br />
<br />
#beta_blip_data.py<br />
from phaser import *<br />
i = InputMR_DAT()<br />
HKLIN = "beta_blip.mtz"<br />
i.setHKLI(HKLIN)<br />
i.setMUTE(True)<br />
r = runMR_DAT(i)<br />
print r.logfile()<br />
if r.Success():<br />
hkl = r.getMiller()<br />
fobs = r.getF()<br />
sigma = r.getSIGF()<br />
nrefl = min(10,hkl.size())<br />
print "Data read from: " , HKLIN<br />
print "First ", nrefl , " reflections"<br />
print "%4s %4s %4s %10s %10s" % ("H","K","L",F,SIGF)<br />
for i in range(0,nrefl):<br />
print "%4d %4d %4d %10.4f %10.4f" % \<br />
(hkl[i][0],hkl[i][1],hkl[i][2],fobs[i],sigma[i])<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
<br />
==Automated Molecular Replacement==<br />
Example script for automated structure solution of BETA-BLIP<br />
<pre><br />
#beta_blip_auto.py<br />
from phaser import *<br />
i = InputMR_DAT()<br />
i.setHKLI("beta_blip.mtz")<br />
i.setLABI_F_SIGF("Fobs","Sigma")<br />
i.setHIRES(6.0)<br />
i.setMUTE(True)<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputMR_AUTO()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.setREFL_F_SIGF(r.getMiller(),r.getFobs(),r.getSigFobs())<br />
i.setROOT("beta_blip_auto")<br />
i.addENSE_PDB_ID("beta","beta.pdb",1.0)<br />
i.addENSE_PDB_ID("blip","blip.pdb",1.0)<br />
i.addCOMP_PROT_MW_NUM(28853,1)<br />
i.addCOMP_PROT_MW_NUM(17522,1)<br />
i.addSEAR_ENSE_NUM("beta",1)<br />
i.addSEAR_ENSE_NUM("blip",1)<br />
i.setMUTE(True)<br />
del(r)<br />
r = runMR_AUTO(i)<br />
if r.Success():<br />
if r.foundSolutions() :<br />
print "Phaser has found MR solutions"<br />
print "Top LLG = %f" % r.getTopLLG()<br />
print "Top PDB file = %s" % r.getTopPdbFile()<br />
else:<br />
print "Phaser has not found any MR solutions"<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Reading MTZ Files for Experimental Phasing==<br />
Example script for reading SAD data from MTZ file S-insulin.mtz<br />
<pre><br />
#insulin_data.py<br />
from phaser import *<br />
i = InputEP_DAT()<br />
HKLIN = "S-insulin.mtz"<br />
xtalid = "insulin"<br />
waveid = "cuka"<br />
i.setHKLI(HKLIN)<br />
i.addCRYS_ANOM_LABI(xtalid,waveid,"F(+)","SIGF(+)","F(-)","SIGF(-)")<br />
i.setMUTE(True)<br />
r = runEP_DAT(i)<br />
if r.Success():<br />
hkl = r.getMiller()<br />
Fpos = r.getFpos(xtalid,waveid)<br />
Ppos = r.getPpos(xtalid,waveid)<br />
Fneg = r.getFneg(xtalid,waveid)<br />
Pneg = r.getPneg(xtalid,waveid)<br />
print "Data read from: " , HKLIN<br />
print "Spacegroup Name (Hall symbol) = %s (%s)" % \<br />
(r.getSpaceGroupName(), r.getSpaceGroupHall())<br />
print "Unitcell = " , r.getUnitCell()<br />
nrefl = min(10,hkl.size())<br />
print "First ", nrefl , " reflections with anomalous differences"<br />
print "%4s %4s %4s %10s %10s %10s" % ("H","K","L","F(+)","F(-)","D")<br />
i = 0<br />
r = 0<br />
while r < nrefl:<br />
if Ppos[i] and Pneg[i] :<br />
D = abs(Fpos[i]-Fneg[i])<br />
if D > 0<br />
print "%4d %4d %4d %10.4f %10.4f %10.4f" % \<br />
(hkl[i][0],hkl[i][1],hkl[i][2],Fpos[i],Fneg[i],D)<br />
r=r+1<br />
i=i+1<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Automated Experimental Phasing==<br />
<br />
<br />
Example script for SAD phasing for insulin<br />
<pre><br />
#insulin_sad.py<br />
from phaser import *<br />
from cctbx import xray<br />
i = InputEP_DAT()<br />
HKLIN = "S-insulin.mtz"<br />
xtalid = "insulin"<br />
waveid = "cuka"<br />
i.setHKLI(HKLIN)<br />
i.addCRYS_ANOM_LABI(xtalid,waveid,"F(+)","SIGF(+)","F(-)","SIGF(-)")<br />
i.setMUTE(True)<br />
r = runEP_DAT(i)<br />
if r.Success():<br />
hkl = r.getMiller()<br />
Fpos = r.getFpos(xtalid,waveid)<br />
Spos = r.getSIGFpos(xtalid,waveid)<br />
Ppos = r.getPpos(xtalid,waveid)<br />
Fneg = r.getFneg(xtalid,waveid)<br />
Sneg = r.getSIGFneg(xtalid,waveid)<br />
Pneg = r.getPneg(xtalid,waveid)<br />
i = InputEP_AUTO()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL(r.getUnitCell())<br />
i.setCRYS_MILLER(hkl)<br />
i.addCRYS_ANOM_DATA(xtalid,waveid,Fpos,Spos,Ppos,Fneg,Sneg,Pneg)<br />
i.setATOM_PDB(xtalid,"S-insulin_hyss.pdb")<br />
i.setLLGC_CRYS_COMPLETE(xtalid,True)<br />
i.addLLGC_CRYS_SCAT_ELEMENT(xtalid,"S")<br />
i.addCOMP_PROT_FASTA_NUM("S-insulin.seq",1.)<br />
i.setHKLO(False)<br />
i.setSCRI(False)<br />
i.setXYZO(False)<br />
i.setMUTE(True)<br />
r = runEP_AUTO(i)<br />
if r.Success():<br />
print "SAD phasing"<br />
print "Data read from: " , HKLIN<br />
print "Data output to : " , r.getMtzFile()<br />
print "Spacegroup Name (Hall symbol) = %s (%s)" % \<br />
(r.getSpaceGroupName(), r.getSpaceGroupHall())<br />
print "Unitcell = " , r.getUnitCell()<br />
print "LogLikelihood = " , r.getLogLikelihood()<br />
atom = r.getAtoms(xtalid)<br />
print atom.size(), " refined atoms"<br />
print "%5s %10s %10s %10s %10s %10s" % \<br />
("atom","x","y","z","occupancy","u-iso")<br />
for i in range(0,atom.size()):<br />
print "%5s %10.4f %10.4f %10.4f %10.4f %10.4f" % \<br />
<br />
(atom[i].scattering_type,atom[i].site[0],atom[i].site[1],atom[i].site[2],atom[i].occupancy,atom[i].u_iso)<br />
hkl = r.getMiller();<br />
fwt = r.getFWT()<br />
phwt = r.getPHWT()<br />
fom = r.getFOM()<br />
nrefl = min(10,hkl.size())<br />
print "First ", nrefl , " reflections"<br />
print "%4s %4s %4s %10s %10s %10s" % \<br />
("H","K","L","FWT","PHWT","FOM")<br />
for i in range(0,nrefl):<br />
print "%4d %4d %4d %10.4f %10.4f %10.4f" % \<br />
(hkl[i][0],hkl[i][1],hkl[i][2],fwt[i],phwt[i],fom[i])<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Anisotropy Correction==<br />
Example script script for anisotropy correction of BETA-BLIP data<br />
<br />
<pre><br />
#beta_blip_ano.py<br />
from phaser import *<br />
i = InputMR_DAT()<br />
HKLIn = "beta_blip.mtz"<br />
F = "Fobs"<br />
SIGF = "Sigma"<br />
i.setHKLI(HKLIn)<br />
i.setLABI_F_SIGF(F,SIGF)<br />
i.setMUTE(True)<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputANO()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.setREFL_F_SIGF(r.getMiller(),r.getFobs(),r.getSigFobs())<br />
i.setLABI_F_SIGF(F,SIGF)<br />
i.setHKLI(HKLIn)<br />
i.setROOT("beta_blip_ano")<br />
i.setMUTE(True)<br />
del(r)<br />
r = runANO(i)<br />
if r.Success():<br />
print "Anisotropy Correction"<br />
print "Data read from: " , HKLIn<br />
print "Data output to : " , r.getMtzFile()<br />
print "Spacegroup Name (Hall symbol) = %s (%s)" % \<br />
(r.getSpaceGroupName(), r.getSpaceGroupHall())<br />
print "Unitcell = " , r.getUnitCell()<br />
print "Principal components = " , r.getEigenBs()<br />
print "Range of principal components = " , r.getAnisoDeltaB()<br />
print "Wilson Scale = " , r.getWilsonK()<br />
print "Wilson B-factor = " , r.getWilsonB()<br />
hkl = r.getMiller();<br />
f = r.getF()<br />
sigf = r.getSIGF()<br />
f_iso = r.getCorrectedF()<br />
sigf_iso = r.getCorrectedSIGF()<br />
corr = r.getCorrection()<br />
nrefl = min(10,hkl.size())<br />
print "First ", nrefl , " reflections"<br />
print "%4s %4s %4s %10s %10s %10s %10s %10s" % \<br />
("H","K","L",F,SIGF,r.getLaboutF(),r.getLaboutSIGF(),"Corr\'n")<br />
for i in range(0,nrefl):<br />
print "%4d %4d %4d %10.4f %10.4f %10.4f %10.4f %10.4f" % \<br />
(hkl[i][0],hkl[i][1],hkl[i][2],f[i],sigf[i],f_iso[i],sigf_iso[i],corr[i])<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Cell Content Analysis==<br />
Example script for cell content analysis of BETA-BLIP<br />
<pre><br />
#beta_blip_cca.py<br />
from phaser import *<br />
i = InputMR_DAT()<br />
HKLIN = "beta_blip.mtz"<br />
F = "Fobs"<br />
SIGF = "Sigma"<br />
i.setHKLI(HKLIN)<br />
i.setLABI_F_SIGF(F,SIGF)<br />
i.setMUTE(True)<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputCCA()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.addCOMP_PROT_MW_NUM(28853,1)<br />
i.addCOMP_PROT_MW_NUM(17522,1)<br />
i.setMUTE(True)<br />
del(r)<br />
r = runCCA(i)<br />
if r.Success():<br />
print "Cell Content Analysis"<br />
print "Molecular weight of assembly = " , r.getAssemblyMW()<br />
print "Best Z value = " , r.getBestZ()<br />
print "Best VM value = " , r.getBestVM()<br />
print "Probability of Best VM = " , r.getBestProb()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Translational NCS Analysis==<br />
Example script for translational NCS analysis of BETA-BLIP<br />
<pre><br />
#beta_blip_ncs.py<br />
from phaser import *<br />
i = InputMR_DAT()<br />
HKLIN = "beta_blip.mtz"<br />
F = "Fobs"<br />
SIGF = "Sigma"<br />
i.setHKLI(HKLIN)<br />
i.setLABI_F_SIGF(F,SIGF)<br />
i.setMUTE(True)<br />
r = runMR_DAT(i)<br />
if r.Success():<br />
i = InputNCS()<br />
i.setSPAC_HALL(r.getSpaceGroupHall())<br />
i.setCELL6(r.getUnitCell())<br />
i.setREFL_F_SIGF(r.getMiller(),r.getF(),r.getSIGF())<br />
i.addCOMP_PROT_MW_NUM(28853,1)<br />
i.addCOMP_PROT_MW_NUM(17522,1)<br />
i.setMUTE(True)<br />
del(r)<br />
r = runNCS(i)<br />
if r.Success():<br />
print "Translational NCS analysis"<br />
print "Translational NCS present = ", r.hasTNCS()<br />
if r.hasTNCS():<br />
print "Translational NCS vecor = ", r.hasTNCS()<br />
print "Twinning alpha = ", r.getTwinAlpha()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Normal Mode Analysis==<br />
Example script for normal mode analysis of BETA-BLIP. Note that the space group and unit cell are not required, and so the MTZ file does not need to be read to extract these parameters.<br />
<pre><br />
#beta_nma.py<br />
from phaser import *<br />
i = InputNMA()<br />
i.setROOT("beta_nma")<br />
i.addENSE_PDB_ID("beta","beta.pdb",1.0)<br />
i.addNMA_MODE(4)<br />
i.setPERT_RMS_DIRE("FORWARD")<br />
i.setMUTE(True)<br />
r = runNMAXYZ(i)<br />
if r.Success():<br />
print "Normal Mode Analysis"<br />
for i in range(0,r.getNum()):<br />
print "PDB file = ", r.getPdbFile(i)<br />
displacement = r.getDisplacements(i)<br />
mode = r.getModes(i)<br />
for j in range(0,mode.size()):<br />
print " Mode = " , mode[j], " Displacement = ", displacement[j]<br />
else:<br />
print "Job exit status FAILURE"<br />
print r.ErrorName(), "ERROR :", r.ErrorMessage()<br />
</pre><br />
<br />
==Logfile Handling==<br />
<br />
Example of how to redirect phaser output to a python string for real-time viewing of output, but not via standard output. Output to standard out is silenced with setMUTE(True).<br />
<pre><br />
beta_blip_logfile.py<br />
from phaser import *<br />
from cStringIO import StringIO<br />
i = InputMR_DAT()<br />
i.setHKLI("beta_blip.mtz")<br />
i.setLABI_F_SIGF("Fobs","Sigma")<br />
i.setMUTE(True)<br />
o = Output()<br />
redirect_str = StringIO()<br />
o.setPackagePhenix(file_object=redirect_str)<br />
r = runMR_DAT(i,o)<br />
</pre></div>Airlie