Difference between revisions of "Phaser Crystallographic Software"
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| − | 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 | + | |
| + | 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. | ||
Use the '''sidebar''' to navigate through the extensive documentation for Phaser. | Use the '''sidebar''' to navigate through the extensive documentation for Phaser. | ||
| − | <!-- index.php/MediaWiki:Sidebar--> | + | <!-- https://www.phaser.cimr.cam.ac.uk/index.php/MediaWiki:Sidebar --> |
| + | |||
| + | ''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]'' | ||
| − | + | For Data Protection information see [http://www.cam.ac.uk/about-this-site/privacy-policy Cambridge University Privacy Policy] | |
==Currently Supported Releases== | ==Currently Supported Releases== | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | ====Phaser-2. | + | ====Phaser-2.8==== |
| − | :Download with Phenix Official Release 1. | + | :Download with Phenix Nightly Builds → [http://www.phenix-online.org/download/ Phenix ] |
| − | : | + | :Documentation → [[Phaser-2.8: Manual | Manual]] |
| − | : | + | |
| + | ====Phaser-2.7.17==== | ||
| + | :Download with Phenix Nightly Builds → [http://www.phenix-online.org/download/ Phenix ] | ||
| + | :Download with CCP4 Update 7.0.023 | ||
| + | :Documentation → [[Phaser-2.7.17: Manual | Manual]] | ||
| + | ''Changelog highlights'' | ||
| + | :* add feature to filter out data with low information content particularly in cases of high anisotropy | ||
| + | :* bugfixes | ||
| + | :: ''solution history formatting'' | ||
| + | :: ''R-value test with multiple search components failing'' | ||
| + | :: ''limit number of permutations in amalgamation to stop combinatorial explosion'' | ||
| + | :: ''correct handling of effect of experimental error in fast rotation function'' | ||
| + | :: ''search method full & permutations on had corrupted search ensemble copy numbers'' | ||
| + | |||
| + | ====Phaser-2.7.16==== | ||
| + | <!--:Download with Phenix Nightly Builds → [http://www.phenix-online.org/download/ Phenix ]--> | ||
| + | :Download with Phenix Official Release 1.11.1 (October 2016) → [http://www.phenix-online.org/download/ Phenix ] | ||
| + | :Documentation → [[Phaser-2.7.15: Manual | Manual]] | ||
| + | ''Changelog highlights'' | ||
| + | :* SOLUTION HISTORY tracks solution through positions in RF/TF/PAK/RNP peak lists | ||
| + | :* selection by CHAIN and MODEL for PDB coordinate entry | ||
| + | :* ensemble member rmsds adjusted to give values consistent with rmsd between members of an ensemble | ||
| + | :* automatic search number for search ensemble(s) | ||
| + | :* packing trace can be entered independently of coordinates and map (can mask larger volume than model) | ||
| + | :* read TNCS/anisotropy binary files to avoid refinement (non-python interface) | ||
| + | :* write TNCS and anisotropy parameters to binary files (non-python interface) | ||
| + | :* default reading of I (or failing that, F) from mtz file (LABIN optional) | ||
| + | :* trace for ensembles from maps = hexgrid of 1000+/-100 points | ||
| + | :* trace for ensembles from coordinates above 1000 C-alpha = hexgrid of 1000+/-100 points | ||
| + | :* trace for ensembles from coordinates between 1000 atoms and 1000 C-alpha = Calpha atoms | ||
| + | :* trace for ensembles from coordinates under 1000 atoms = all atoms | ||
| + | :* packing by pairwise percent only, other packing modes obsoleted | ||
| + | :* packing test during FTF run by default with 50% pairwise packing cutoff | ||
| + | :* automatic tNCS NMOL determination in presence of commensurate modulation | ||
| + | :* added MODE GIMBLE, which splits ensembles by chain for rigid body refinement | ||
| + | :* support for unicode | ||
| + | :* solution coordinates placed nearest to input coordinates if possible | ||
| + | |||
| + | <!--====Phaser-2.5.6-beta <span style="color:darkorange">''*unstable*''</span>==== --> | ||
| + | |||
| + | <!--:'''<span style="color:darkorange">CCP4 update coming soon</span>'''--> | ||
==Referencing Phaser== | ==Referencing Phaser== | ||
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If you solve a structure with Phaser, please cite | If you solve a structure with Phaser, please cite | ||
| − | ;Phaser crystallographic software | + | ;Phaser crystallographic software |
: McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ. | : McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ. | ||
| − | :J | + | :[http://scripts.iucr.org/cgi-bin/paper?he5368 '''J Appl Cryst'''] (2007). 40, 658-674. |
| − | |||
__NOTOC__ | __NOTOC__ | ||
Latest revision as of 16:08, 15 January 2020
Phaser is a program for phasing macromolecular crystal structures with maximum likelihood methods. It has been developed by Randy Read's group at the Cambridge Institute for Medical Research (CIMR) in the University of Cambridge and is available through the Phenix and CCP4 software suites.
Use the sidebar to navigate through the extensive documentation for Phaser.
This PhaserWiki supersedes the obsolete Phaser homepage, which now redirects to this wiki. A copy of the obsolete Phaser homepage can be found here
For Data Protection information see Cambridge University Privacy Policy
Currently Supported Releases
Phaser-2.8
Phaser-2.7.17
- Download with Phenix Nightly Builds → Phenix
- Download with CCP4 Update 7.0.023
- Documentation → Manual
Changelog highlights
- add feature to filter out data with low information content particularly in cases of high anisotropy
- bugfixes
- solution history formatting
- R-value test with multiple search components failing
- limit number of permutations in amalgamation to stop combinatorial explosion
- correct handling of effect of experimental error in fast rotation function
- search method full & permutations on had corrupted search ensemble copy numbers
Phaser-2.7.16
Changelog highlights
- SOLUTION HISTORY tracks solution through positions in RF/TF/PAK/RNP peak lists
- selection by CHAIN and MODEL for PDB coordinate entry
- ensemble member rmsds adjusted to give values consistent with rmsd between members of an ensemble
- automatic search number for search ensemble(s)
- packing trace can be entered independently of coordinates and map (can mask larger volume than model)
- read TNCS/anisotropy binary files to avoid refinement (non-python interface)
- write TNCS and anisotropy parameters to binary files (non-python interface)
- default reading of I (or failing that, F) from mtz file (LABIN optional)
- trace for ensembles from maps = hexgrid of 1000+/-100 points
- trace for ensembles from coordinates above 1000 C-alpha = hexgrid of 1000+/-100 points
- trace for ensembles from coordinates between 1000 atoms and 1000 C-alpha = Calpha atoms
- trace for ensembles from coordinates under 1000 atoms = all atoms
- packing by pairwise percent only, other packing modes obsoleted
- packing test during FTF run by default with 50% pairwise packing cutoff
- automatic tNCS NMOL determination in presence of commensurate modulation
- added MODE GIMBLE, which splits ensembles by chain for rigid body refinement
- support for unicode
- solution coordinates placed nearest to input coordinates if possible
Referencing Phaser
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.
If you solve a structure with Phaser, please cite
- Phaser crystallographic software
- McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ.
- J Appl Cryst (2007). 40, 658-674.
