https://www.phaser.cimr.cam.ac.uk/api.php?action=feedcontributions&feedformat=atom&user=GaborbPhaserwiki - User contributions [en]2026-06-29T04:36:37ZUser contributionsMediaWiki 1.31.8https://www.phaser.cimr.cam.ac.uk/index.php?title=Molecular_replacement_with_MRage&diff=1833Molecular replacement with MRage2013-07-19T11:18:45Z<p>Gaborb: </p>
<hr />
<div>This tutorial explains how to use to run phaser.MRage from the [http://www.phenix-online.org Phenix GUI] (input files to run the same through the command line examples are also available).<br />
<br />
<br />
== Beta/blip ==<br />
<br />
This is a complex between beta lactamase (''beta'') and beta lactamase inhibitor (''blip''). There are good models available, but the space group is ambiguous. This tutorial shows basic MRage functionality with a two-component system.<br />
<br />
Experimental data for this tutorial is distributed with [http://www.phenix-online.org Phenix GUI] and is also available from the [http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials Tutorials] page.<br />
<br />
=== Input ===<br />
<br />
The MRage GUI is available from the main Phenix window under the '''Molecular replacement''' tab (select the ''Enable alpha features'' options under ''File/Preferences'' dialog for it to show up). On startup, the GUI presents the '''Basic options''' dialog.<br />
<br />
The following screenshot shows the this required settings to run the tutorial. Note, that almost everything is filled in automatically once the reflection file has been selected, or default. The only additional change one needs to make is to switch the '''space group exploration''' box to ''enantiomorph'' from its default value ''dataset'', as the space group is enantiomorphic, and it is not possible to know without solving the structure, which hand is the correct one. In this tutorial, only a single CPU is used, but feel free to use more if available! Note that the '''Overall count''' box has been left blank. This tells the program to determine the number of copies automatically.<br />
{| class="wikitable"<br />
|[[File:Bb-basic-options_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Basic-options.png]]<br />
|-<br />
|The '''Basic options''' dialog<br />
|}<br />
Next, we need to tell the program about the composition of the asymmetric unit and the available search models.<br />
<br />
First, the ''beta'' component is described with its sequence, and the only search model. Since there is no modification needed to this model (it is 100% identical), it is input through the '''Ensemble''' tab. This tells the program that there is one alternative model for the ''beta'' component.<br />
<br />
{|class="wikitable"<br />
|[[File:Bb-beta-composition_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/bb-beta-composition.png|centre]]<br />
||[[File:Bb-beta-ensembles_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/bb-beta-ensembles.png|centre]]<br />
|-<br />
|The '''Basic info''' dialog of '''Component1''' (''beta'')<br />
|The '''Ensembles''' dialog of '''Component1''' (''beta'')<br />
|}<br />
Then, a new component is created for ''blip'' (using the '''Add component''' button on the '''Basic info''' tab). This is filled out accordingly.<br />
{|class="wikitable"<br />
|[[File:Bb-blip-composition_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/bb-blip-composition.png|centre]]<br />
||[[File:Bb-blip-ensembles_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/bb-blip-ensembles.png|centre]]<br />
|-<br />
|The '''Basic info''' dialog of '''Component2''' (''blip'')<br />
|The '''Ensembles''' dialog of '''Component2''' (''blip'')<br />
|}<br />
The job is ready to run!<br />
<br />
;Running from the command line<br />
<br />
'''Input file''' (betablip.eff)<br />
<br />
hklin = beta_blip.mtz<br />
labin = Fobs,Sigma<br />
symmetry_exploration = enantiomorph<br />
<br />
composition<br />
{<br />
<br />
component<br />
{<br />
sequence = beta.seq<br />
ensemble<br />
{<br />
coordinates<br />
{<br />
pdb = beta.pdb<br />
identity = 1.00<br />
}<br />
}<br />
}<br />
<br />
component<br />
{<br />
sequence = blip.seq<br />
ensemble<br />
{<br />
coordinates<br />
{<br />
pdb = blip.pdb<br />
identity = 1.00<br />
}<br />
}<br />
}<br />
<br />
}<br />
<br />
'''Command line'''<br />
phaser.MRage --verbosity=VERBOSE betablip.eff<br />
<br />
<br />
=== Output ===<br />
<br />
The GUI displays the program output in the logfile window. First, the program starts searching in both possible space groups.<br />
{|class="wikitable"<br />
|[[File:Bb-log-first-round-start_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Beta-blip-log-first-round-start.png|centre]]<br />
||[[File:Bb-log-space-group-evaluation_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Beta-blip-log-space-group-evaluation.png|centre]]<br />
||[[File:Bb-log-second-round-start_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Beta-blip-log-second-round-start.png|centre]]<br />
||[[File:Bb-log-final_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Beta-blip-log-finish.png|centre]]<br />
||[[File:Bb-solutions_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Beta-blip-solutions.png|centre]]<br />
|-<br />
|Initially, search starts in both P3₁21 and P3₂21<br />
|After finding the first component, the search in P3₁21 is dropped...<br />
|...and only P3₂21 is propagated with the partial solutions found.<br />
|The final solution: evaluation shows a high probability for it to be correct.<br />
|Final solution shown in the GUI '''Top solution''' tab with possible further steps.<br />
|}<br />
== Lysozyme ==<br />
<br />
As a frequently used test protein, there are good models for lysozyme. This tutorial demonstrates how to solve lysozyme starting from a homology search.<br />
<br />
=== Input ===<br />
{|class="wikitable"<br />
|[[File:Lyso-basic-options_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-basic-options.png|centre]]<br />
||[[File:Lyso-composition_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-composition.png|centre]]<br />
||[[File:Lyso-homology-searches_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-homology-searches.png|centre]]<br />
|-<br />
|Basic options dialog. Note that the space group is enantiomorphic, but we pretend we know the correct space group P4₃2₁2 to save time<br />
|Setting up composition. It would be possible to tick the '''NCBI Blast''' option and run, but we want to avoid overloading the NCBI and provide a saved homology search file<br />
|Specifying the homology search file. There are many hits, and the GUI by default selects the first three. Selecting any larger number, however, makes no difference!<br />
|}<br />
;Running from the command line<br />
<br />
'''Input file''' (lysozyme.eff)<br />
<br />
hklin = lyso.mtz<br />
labin = "F_New,SIGF_New,DANO_New,SIGDANO_New,ISYM_New"<br />
<br />
composition<br />
{<br />
component<br />
{<br />
sequence = hewl.seq<br />
homology<br />
{<br />
file_name = hewl_ebi_wu_blast.xml<br />
max_hits = 3<br />
}<br />
}<br />
}<br />
<br />
'''Command line'''<br />
phaser.MRage --verbosity=VERBOSE lysozyme.eff<br />
<br />
=== Output ===<br />
{|class="wikitable"<br />
|[[File:Lyso-fetch-1lsg_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-fetch-1lsg.png|centre]]<br />
||[[File:Lyso-sculptor-1lsg_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-sculptor-1lsg.png|centre]]<br />
||[[File:Lyso-finish_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-finish.png|centre]]<br />
|-<br />
|The program fetches the first homologue...<br />
|...then processes it with sculptor. Note that although all 13 protocols in sculptor are active, it only creates 7 models, because remaining protocols create models that are identical to the ones used.<br />
|This model gives a clear solution, and processing stops. Although 3 hits were specified, the second and the third was never downloaded, because the first gave a clear solution.<br />
|}</div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Molecular_replacement_with_MRage&diff=1832Molecular replacement with MRage2013-07-19T11:13:21Z<p>Gaborb: </p>
<hr />
<div>This tutorial explains how to use to run phaser.MRage from the [http://www.phenix-online.org Phenix GUI] (input files to run the same through the command line examples are also available).<br />
<br />
<br />
== Beta/blip ==<br />
<br />
This is a complex between beta lactamase (''beta'') and beta lactamase inhibitor (''blip''). There are good models available, but the space group is ambiguous. This tutorial shows basic MRage functionality with a two-component system.<br />
<br />
Experimental data for this tutorial is distributed with [http://www.phenix-online.org Phenix GUI] and is also available from the [http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials Tutorials] page.<br />
<br />
=== Input ===<br />
<br />
The MRage GUI is available from the main Phenix window under the '''Molecular replacement''' tab (select the ''Enable alpha features'' options under ''File/Preferences'' dialog for it to show up). On startup, the GUI presents the '''Basic options''' dialog.<br />
<br />
The following screenshot shows the this required settings to run the tutorial. Note, that almost everything is filled in automatically once the reflection file has been selected, or default. The only additional change one needs to make is to switch the '''space group exploration''' box to ''enantiomorph'' from its default value ''dataset'', as the space group is enantiomorphic, and it is not possible to know without solving the structure, which hand is the correct one. In this tutorial, only a single CPU is used, but feel free to use more if available! Note that the '''Overall count''' box has been left blank. This tells the program to determine the number of copies automatically.<br />
{| class="wikitable"<br />
|[[File:Bb-basic-options_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Basic-options.png]]<br />
|-<br />
|The '''Basic options''' dialog<br />
|}<br />
Next, we need to tell the program about the composition of the asymmetric unit and the available search models.<br />
<br />
First, the ''beta'' component is described with its sequence, and the only search model. Since there is no modification needed to this model (it is 100% identical), it is input through the '''Ensemble''' tab. This tells the program that there is one alternative model for the ''beta'' component.<br />
<br />
{|class="wikitable"<br />
|[[File:Bb-beta-composition_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/bb-beta-composition.png|centre]]<br />
||[[File:Bb-beta-ensembles_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/bb-beta-ensembles.png|centre]]<br />
|-<br />
|The '''Basic info''' dialog of '''Component1''' (''beta'')<br />
|The '''Ensembles''' dialog of '''Component1''' (''beta'')<br />
|}<br />
Then, a new component is created for ''blip'' (using the '''Add component''' button on the '''Basic info''' tab). This is filled out accordingly.<br />
{|class="wikitable"<br />
|[[File:Bb-blip-composition_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/bb-blip-composition.png|centre]]<br />
||[[File:Bb-blip-ensembles_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/bb-blip-ensembles.png|centre]]<br />
|-<br />
|The '''Basic info''' dialog of '''Component2''' (''blip'')<br />
|The '''Ensembles''' dialog of '''Component2''' (''blip'')<br />
|}<br />
The job is ready to run!<br />
<br />
;Running from the command line<br />
<br />
'''Input file''' (betablip.eff)<br />
<br />
hklin = beta_blip.mtz<br />
labin = Fobs,Sigma<br />
symmetry_exploration = enantiomorph<br />
<br />
composition<br />
{<br />
<br />
component<br />
{<br />
sequence = beta.seq<br />
ensemble<br />
{<br />
coordinates<br />
{<br />
pdb = beta.pdb<br />
identity = 1.00<br />
}<br />
}<br />
}<br />
<br />
component<br />
{<br />
sequence = blip.seq<br />
ensemble<br />
{<br />
coordinates<br />
{<br />
pdb = blip.pdb<br />
identity = 1.00<br />
}<br />
}<br />
}<br />
<br />
}<br />
<br />
'''Command line'''<br />
phaser.MRage --verbosity=VERBOSE betablip.eff<br />
<br />
<br />
=== Output ===<br />
<br />
The GUI displays the program output in the logfile window. First, the program starts searching in both possible space groups.<br />
{|class="wikitable"<br />
|[[File:Bb-log-first-round-start_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Beta-blip-log-first-round-start.png|centre]]<br />
||[[File:Bb-log-space-group-evaluation_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Beta-blip-log-space-group-evaluation.png|centre]]<br />
||[[File:Bb-log-second-round-start_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Beta-blip-log-second-round-start.png|centre]]<br />
||[[File:Bb-log-final_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Beta-blip-log-finish.png|centre]]<br />
||[[File:Bb-solutions_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Beta-blip-solutions.png|centre]]<br />
|-<br />
|Initially, search starts in both P3₁21 and P3₂21<br />
|After finding the first component, the search in P3₁21 is dropped...<br />
|...and only P3₂21 is propagated with the partial solutions found.<br />
|The final solution: evaluation shows a high probability for it to be correct.<br />
|Final solution shown in the GUI '''Top solution''' tab with possible further steps.<br />
|}<br />
== Lysozyme ==<br />
<br />
As a frequently used test protein, there are good models for lysozyme. This tutorial demonstrates how to solve lysozyme starting from a homology search.<br />
<br />
=== Input ===<br />
{|<br />
|[[File:Lyso-basic-options_thumb.png|frame|centre|text-bottom|Basic options dialog. Note that the space group is enantiomorphic, but we pretend we know the correct space group P4₃2₁2 to save time [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-basic-options.png Large]]]<br />
||[[File:Lyso-composition_thumb.png|frame|centre|text-bottom|Setting up composition. It would be possible to tick the '''NCBI Blast''' option and run, but we want to avoid overloading the NCBI and provide a saved homology search file [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-composition.png Large]]]<br />
||[[File:Lyso-homology-searches_thumb.png|frame|centre|text-bottom|Specifying the homology search file. There are many hits, and the GUI by default selects the first three. Selecting any larger number, however, makes no difference! [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-homology-searches.png Large]]]<br />
|}<br />
;Running from the command line<br />
<br />
'''Input file''' (lysozyme.eff)<br />
<br />
hklin = lyso.mtz<br />
labin = "F_New,SIGF_New,DANO_New,SIGDANO_New,ISYM_New"<br />
<br />
composition<br />
{<br />
component<br />
{<br />
sequence = hewl.seq<br />
homology<br />
{<br />
file_name = hewl_ebi_wu_blast.xml<br />
max_hits = 3<br />
}<br />
}<br />
}<br />
<br />
'''Command line'''<br />
phaser.MRage --verbosity=VERBOSE lysozyme.eff<br />
<br />
=== Output ===<br />
{|<br />
|[[File:Lyso-fetch-1lsg_thumb.png|frame|centre|text-bottom|The program fetches the first homologue... [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-fetch-1lsg.png Large]]]<br />
||[[File:Lyso-sculptor-1lsg_thumb.png|frame|centre|text-bottom|...then processes it with sculptor. Note that although all 13 protocols in sculptor are active, it only creates 7 models, because remaining protocols create models that are identical to the ones used. [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-sculptor-1lsg.png Large]]]<br />
||[[File:Lyso-finish_thumb.png|frame|centre|text-bottom|This model gives a clear solution, and processing stops. Although 3 hits were specified, the second and the third was never downloaded, because the first gave a clear solution [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-finish.png Large]]]<br />
|}</div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Molecular_replacement_with_MRage&diff=1831Molecular replacement with MRage2013-07-19T10:45:21Z<p>Gaborb: </p>
<hr />
<div>This tutorial explains how to use to run phaser.MRage from the [http://www.phenix-online.org Phenix GUI] (input files to run the same through the command line examples are also available).<br />
<br />
<br />
== Beta/blip ==<br />
<br />
This is a complex between beta lactamase (''beta'') and beta lactamase inhibitor (''blip''). There are good models available, but the space group is ambiguous. This tutorial shows basic MRage functionality with a two-component system.<br />
<br />
Experimental data for this tutorial is distributed with [http://www.phenix-online.org Phenix GUI] and is also available from the [http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials Tutorials] page.<br />
<br />
=== Input ===<br />
<br />
The MRage GUI is available from the main Phenix window under the '''Molecular replacement''' tab (select the ''Enable alpha features'' options under ''File/Preferences'' dialog for it to show up). On startup, the GUI presents the '''Basic options''' dialog.<br />
<br />
The following screenshot shows the this required settings to run the tutorial. Note, that almost everything is filled in automatically once the reflection file has been selected, or default. The only additional change one needs to make is to switch the '''space group exploration''' box to ''enantiomorph'' from its default value ''dataset'', as the space group is enantiomorphic, and it is not possible to know without solving the structure, which hand is the correct one. In this tutorial, only a single CPU is used, but feel free to use more if available! Note that the '''Overall count''' box has been left blank. This tells the program to determine the number of copies automatically.<br />
{|<br />
|[[File:Bb-basic-options_thumb.png|frame|center|text-bottom|The '''Basic options''' dialog [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Basic-options.png Large]]]<br />
|}<br />
Next, we need to tell the program about the composition of the asymmetric unit and the available search models.<br />
<br />
First, the ''beta'' component is described with its sequence, and the only search model. Since there is no modification needed to this model (it is 100% identical), it is input through the '''Ensemble''' tab. This tells the program that there is one alternative model for the ''beta'' component.<br />
<br />
{|<br />
|[[File:Bb-beta-composition_thumb.png|frame|centre|text-bottom|The '''Basic info''' dialog of '''Component1''' (''beta'') [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/bb-beta-composition.png Large]]]<br />
||[[File:Bb-beta-ensembles_thumb.png|frame|centre|text-bottom|The '''Ensembles''' dialog of '''Component1''' (''beta'') [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/bb-beta-ensembles.png Large]]]<br />
|}<br />
Then, a new component is created for ''blip'' (using the '''Add component''' button on the '''Basic info''' tab). This is filled out accordingly.<br />
{|<br />
|[[File:Bb-blip-composition_thumb.png|frame|centre|text-bottom|The '''Basic info''' dialog of '''Component2''' (''blip'') [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/bb-blip-composition.png Large]]]<br />
||[[File:Bb-blip-ensembles_thumb.png|frame|centre|text-bottom|The '''Ensembles''' dialog of '''Component2''' (''blip'') [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/bb-blip-ensembles.png Large]]]<br />
|}<br />
The job is ready to run!<br />
<br />
;Running from the command line<br />
<br />
'''Input file''' (betablip.eff)<br />
<br />
hklin = beta_blip.mtz<br />
labin = Fobs,Sigma<br />
symmetry_exploration = enantiomorph<br />
<br />
composition<br />
{<br />
<br />
component<br />
{<br />
sequence = beta.seq<br />
ensemble<br />
{<br />
coordinates<br />
{<br />
pdb = beta.pdb<br />
identity = 1.00<br />
}<br />
}<br />
}<br />
<br />
component<br />
{<br />
sequence = blip.seq<br />
ensemble<br />
{<br />
coordinates<br />
{<br />
pdb = blip.pdb<br />
identity = 1.00<br />
}<br />
}<br />
}<br />
<br />
}<br />
<br />
'''Command line'''<br />
phaser.MRage --verbosity=VERBOSE betablip.eff<br />
<br />
<br />
=== Output ===<br />
<br />
The GUI displays the program output in the logfile window. First, the program starts searching in both possible space groups.<br />
{|[[File:Bb-log-first-round-start_thumb.png|frame|centre|text-bottom|Initially, search starts in both P3₁21 and P3₂21 [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Beta-blip-log-first-round-start.png Large]]]<br />
||[[File:Bb-log-space-group-evaluation_thumb.png|frame|centre|text-bottom|After finding the first component, the search in P3₁21 is dropped... [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Beta-blip-log-space-group-evaluation.png Large]]]<br />
||[[File:Bb-log-second-round-start_thumb.png|frame|centre|text-bottom|...and only P3₂21 is propagated with the partial solutions found. [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Beta-blip-log-second-round-start.png Large]]]<br />
||[[File:Bb-log-final_thumb.png|frame|centre|text-bottom|The final solution: evaluation shows a high probability for it to be correct. [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Beta-blip-log-finish.png Large]]]<br />
||[[File:Bb-solutions_thumb.png|frame|centre|text-bottom|Final solution shown in the GUI '''Top solution''' tab with possible further steps. [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Beta-blip-solutions.png Large]]]<br />
|}<br />
== Lysozyme ==<br />
<br />
As a frequently used test protein, there are good models for lysozyme. This tutorial demonstrates how to solve lysozyme starting from a homology search.<br />
<br />
=== Input ===<br />
{|<br />
|[[File:Lyso-basic-options_thumb.png|frame|centre|text-bottom|Basic options dialog. Note that the space group is enantiomorphic, but we pretend we know the correct space group P4₃2₁2 to save time [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-basic-options.png Large]]]<br />
||[[File:Lyso-composition_thumb.png|frame|centre|text-bottom|Setting up composition. It would be possible to tick the '''NCBI Blast''' option and run, but we want to avoid overloading the NCBI and provide a saved homology search file [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-composition.png Large]]]<br />
||[[File:Lyso-homology-searches_thumb.png|frame|centre|text-bottom|Specifying the homology search file. There are many hits, and the GUI by default selects the first three. Selecting any larger number, however, makes no difference! [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-homology-searches.png Large]]]<br />
|}<br />
;Running from the command line<br />
<br />
'''Input file''' (lysozyme.eff)<br />
<br />
hklin = lyso.mtz<br />
labin = "F_New,SIGF_New,DANO_New,SIGDANO_New,ISYM_New"<br />
<br />
composition<br />
{<br />
component<br />
{<br />
sequence = hewl.seq<br />
homology<br />
{<br />
file_name = hewl_ebi_wu_blast.xml<br />
max_hits = 3<br />
}<br />
}<br />
}<br />
<br />
'''Command line'''<br />
phaser.MRage --verbosity=VERBOSE lysozyme.eff<br />
<br />
=== Output ===<br />
{|<br />
|[[File:Lyso-fetch-1lsg_thumb.png|frame|centre|text-bottom|The program fetches the first homologue... [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-fetch-1lsg.png Large]]]<br />
||[[File:Lyso-sculptor-1lsg_thumb.png|frame|centre|text-bottom|...then processes it with sculptor. Note that although all 13 protocols in sculptor are active, it only creates 7 models, because remaining protocols create models that are identical to the ones used. [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-sculptor-1lsg.png Large]]]<br />
||[[File:Lyso-finish_thumb.png|frame|centre|text-bottom|This model gives a clear solution, and processing stops. Although 3 hits were specified, the second and the third was never downloaded, because the first gave a clear solution [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-finish.png Large]]]<br />
|}</div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Molecular_replacement_with_MRage&diff=1830Molecular replacement with MRage2013-07-19T10:41:19Z<p>Gaborb: </p>
<hr />
<div>This tutorial explains how to use to run phaser.MRage from the [http://www.phenix-online.org Phenix GUI] (input files to run the same through the command line examples are also available).<br />
<br />
<br />
== Beta/blip ==<br />
<br />
This is a complex between beta lactamase (''beta'') and beta lactamase inhibitor (''blip''). There are good models available, but the space group is ambiguous. This tutorial shows basic MRage functionality with a two-component system.<br />
<br />
Experimental data for this tutorial is distributed with [http://www.phenix-online.org Phenix GUI] and is also available from the [http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials Tutorials] page.<br />
<br />
=== Input ===<br />
<br />
The MRage GUI is available from the main Phenix window under the '''Molecular replacement''' tab (select the ''Enable alpha features'' options under ''File/Preferences'' dialog for it to show up). On startup, the GUI presents the '''Basic options''' dialog.<br />
<br />
The following screenshot shows the this required settings to run the tutorial. Note, that almost everything is filled in automatically once the reflection file has been selected, or default. The only additional change one needs to make is to switch the '''space group exploration''' box to ''enantiomorph'' from its default value ''dataset'', as the space group is enantiomorphic, and it is not possible to know without solving the structure, which hand is the correct one. In this tutorial, only a single CPU is used, but feel free to use more if available! Note that the '''Overall count''' box has been left blank. This tells the program to determine the number of copies automatically.<br />
{|<br />
|[[File:Bb-basic-options_thumb.png|frame|center|text-bottom|The '''Basic options''' dialog [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Basic-options.png Large]]]<br />
|}<br />
Next, we need to tell the program about the composition of the asymmetric unit and the available search models.<br />
<br />
First, the ''beta'' component is described with its sequence, and the only search model. Since there is no modification needed to this model (it is 100% identical), it is input through the '''Ensemble''' tab. This tells the program that there is one alternative model for the ''beta'' component.<br />
<br />
{|<br />
|[[File:Bb-beta-composition_thumb.png|frame|centre|text-bottom|The '''Basic info''' dialog of '''Component1''' (''beta'') [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/bb-beta-composition.png Large]]]<br />
||[[File:Bb-beta-ensembles_thumb.png|frame|centre|text-bottom|The '''Ensembles''' dialog of '''Component1''' (''beta'') [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/bb-beta-ensembles.png Large]]]<br />
|}<br />
Then, a new component is created for ''blip'' (using the '''Add component''' button on the '''Basic info''' tab). This is filled out accordingly.<br />
{|<br />
|[[File:Bb-blip-composition_thumb.png|frame|centre|text-bottom|The '''Basic info''' dialog of '''Component2''' (''blip'') [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/bb-blip-composition.png Large]]]<br />
||[[File:Bb-blip-ensembles_thumb.png|frame|centre|text-bottom|The '''Ensembles''' dialog of '''Component2''' (''blip'') [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/bb-blip-ensembles.png Large]]]<br />
|}<br />
The job is ready to run!<br />
<br />
;Running from the command line<br />
<br />
'''Input file''' (betablip.eff)<br />
<br />
hklin = beta_blip.mtz<br />
labin = Fobs,Sigma<br />
symmetry_exploration = enantiomorph<br />
<br />
composition<br />
{<br />
<br />
component<br />
{<br />
sequence = beta.seq<br />
ensemble<br />
{<br />
coordinates<br />
{<br />
pdb = beta.pdb<br />
identity = 1.00<br />
}<br />
}<br />
}<br />
<br />
component<br />
{<br />
sequence = blip.seq<br />
ensemble<br />
{<br />
coordinates<br />
{<br />
pdb = blip.pdb<br />
identity = 1.00<br />
}<br />
}<br />
}<br />
<br />
}<br />
<br />
'''Command line'''<br />
phaser.MRage --verbosity=VERBOSE betablip.eff<br />
<br />
<br />
=== Output ===<br />
<br />
The GUI displays the program output in the logfile window. First, the program starts searching in both possible space groups.<br />
{|[[File:Bb-log-first-round-start_thumb.png|frame|centre|text-bottom|Initially, search starts in both P3₁21 and P3₂21 [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Beta-blip-log-first-round-start.png Large]]]<br />
||[[File:Bb-log-space-group-evaluation_thumb.png|frame|centre|text-bottom|After finding the first component, the search in P3₁21 is dropped... [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Beta-blip-log-space-group-evaluation.png Large]]]<br />
||[[File:Bb-log-second-round-start_thumb.png|frame|centre|text-bottom|...and only P3₂21 is propagated with the partial solutions found. [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Beta-blip-log-second-round-start.png Large]]]<br />
||[[File:Bb-log-final_thumb.png|frame|centre|text-bottom|The final solution: evaluation shows a high probability for it to be correct. [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Beta-blip-log-finish.png Large]]]<br />
||[[File:Bb-solutions_thumb.png|frame|centre|text-bottom|Final solution shown in the GUI '''Top solution''' tab with possible further steps. [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Beta-blip-solutions.png Large]]]<br />
|}<br />
== Lysozyme ==<br />
<br />
As a frequently used test protein, there are good models for lysozyme. This tutorial demonstrates how to solve lysozyme starting from a homology search.<br />
<br />
=== Input ===<br />
{|<br />
|[[File:Lyso-basic-options_thumb.png|frame|centre|text-bottom|Basic options dialog. Note that the space group is enantiomorphic, but we pretend we know the correct space group P4₃2₁2 to save time]]<br />
||[[File:Lyso-composition_thumb.png|frame|centre|text-bottom|Setting up composition. It would be possible to tick the '''NCBI Blast''' option and run, but we want to avoid overloading the NCBI and provide a saved homology search file]]<br />
||[[File:Lyso-homology-searches_thumb.png|frame|centre|text-bottom|Specifying the homology search file. There are many hits, and the GUI by default selects the first three. Selecting any larger number, however, makes no difference!]]<br />
|}<br />
;Running from the command line<br />
<br />
'''Input file''' (lysozyme.eff)<br />
<br />
hklin = lyso.mtz<br />
labin = "F_New,SIGF_New,DANO_New,SIGDANO_New,ISYM_New"<br />
<br />
composition<br />
{<br />
component<br />
{<br />
sequence = hewl.seq<br />
homology<br />
{<br />
file_name = hewl_ebi_wu_blast.xml<br />
max_hits = 3<br />
}<br />
}<br />
}<br />
<br />
'''Command line'''<br />
phaser.MRage --verbosity=VERBOSE lysozyme.eff<br />
<br />
=== Output ===<br />
{|<br />
|[[File:Lyso-fetch-1lsg_thumb.png|frame|centre|text-bottom|The program fetches the first homologue...]]<br />
||[[File:Lyso-sculptor-1lsg_thumb.png|frame|centre|text-bottom|...then processes it with sculptor. Note that although all 13 protocols in sculptor are active, it only creates 7 models, because remaining protocols create models that are identical to the ones used.]]<br />
||[[File:Lyso-finish_thumb.png|frame|centre|text-bottom|This model gives a clear solution, and processing stops. Although 3 hits were specified, the second and the third was never downloaded, because the first gave a clear solution]]<br />
|}</div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Molecular_replacement_with_MRage&diff=1829Molecular replacement with MRage2013-07-19T09:45:46Z<p>Gaborb: </p>
<hr />
<div>This tutorial explains how to use to run phaser.MRage from the [http://www.phenix-online.org Phenix GUI] (input files to run the same through the command line examples are also available).<br />
<br />
<br />
== Beta/blip ==<br />
<br />
This is a complex between beta lactamase (''beta'') and beta lactamase inhibitor (''blip''). There are good models available, but the space group is ambiguous. This tutorial shows basic MRage functionality with a two-component system.<br />
<br />
Experimental data for this tutorial is distributed with [http://www.phenix-online.org Phenix GUI] and is also available from the [http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials Tutorials] page.<br />
<br />
=== Input ===<br />
<br />
The MRage GUI is available from the main Phenix window under the '''Molecular replacement''' tab (select the ''Enable alpha features'' options under ''File/Preferences'' dialog for it to show up). On startup, the GUI presents the '''Basic options''' dialog.<br />
<br />
The following screenshot shows the this required settings to run the tutorial. Note, that almost everything is filled in automatically once the reflection file has been selected, or default. The only additional change one needs to make is to switch the '''space group exploration''' box to ''enantiomorph'' from its default value ''dataset'', as the space group is enantiomorphic, and it is not possible to know without solving the structure, which hand is the correct one. In this tutorial, only a single CPU is used, but feel free to use more if available! Note that the '''Overall count''' box has been left blank. This tells the program to determine the number of copies automatically.<br />
{|<br />
|[[File:Bb-basic-options_thumb.png|frame|center|text-bottom|The '''Basic options''' dialog]]<br />
|}<br />
Next, we need to tell the program about the composition of the asymmetric unit and the available search models.<br />
<br />
First, the ''beta'' component is described with its sequence, and the only search model. Since there is no modification needed to this model (it is 100% identical), it is input through the '''Ensemble''' tab. This tells the program that there is one alternative model for the ''beta'' component.<br />
<br />
{|<br />
|[[File:Bb-beta-composition_thumb.png|frame|centre|text-bottom|The '''Basic info''' dialog of '''Component1''' (''beta'')]]<br />
||[[File:Bb-beta-ensembles_thumb.png|frame|centre|text-bottom|The '''Ensembles''' dialog of '''Component1''' (''beta'')]]<br />
|}<br />
Then, a new component is created for ''blip'' (using the '''Add component''' button on the '''Basic info''' tab). This is filled out accordingly.<br />
{|<br />
|[[File:Bb-blip-composition_thumb.png|frame|centre|text-bottom|The '''Basic info''' dialog of '''Component2''' (''blip'')]]<br />
||[[File:Bb-blip-ensembles_thumb.png|frame|centre|text-bottom|The '''Ensembles''' dialog of '''Component2''' (''blip'')]]<br />
|}<br />
The job is ready to run!<br />
<br />
;Running from the command line<br />
<br />
'''Input file''' (betablip.eff)<br />
<br />
hklin = beta_blip.mtz<br />
labin = Fobs,Sigma<br />
symmetry_exploration = enantiomorph<br />
<br />
composition<br />
{<br />
<br />
component<br />
{<br />
sequence = beta.seq<br />
ensemble<br />
{<br />
coordinates<br />
{<br />
pdb = beta.pdb<br />
identity = 1.00<br />
}<br />
}<br />
}<br />
<br />
component<br />
{<br />
sequence = blip.seq<br />
ensemble<br />
{<br />
coordinates<br />
{<br />
pdb = blip.pdb<br />
identity = 1.00<br />
}<br />
}<br />
}<br />
<br />
}<br />
<br />
'''Command line'''<br />
phaser.MRage --verbosity=VERBOSE betablip.eff<br />
<br />
<br />
=== Output ===<br />
<br />
The GUI displays the program output in the logfile window. First, the program starts searching in both possible space groups.<br />
{|[[File:Bb-log-first-round-start_thumb.png|frame|centre|text-bottom|Initially, search starts in both P3₁21 and P3₂21]]<br />
||[[File:Bb-log-space-group-evaluation_thumb.png|frame|centre|text-bottom|After finding the first component, the search in P3₁21 is dropped...]]<br />
||[[File:Bb-log-second-round-start_thumb.png|frame|centre|text-bottom|...and only P3₂21 is propagated with the partial solutions found.]]<br />
||[[File:Bb-log-final_thumb.png|frame|centre|text-bottom|The final solution: evaluation shows a high probability for it to be correct.]]<br />
||[[File:Bb-solutions_thumb.png|frame|centre|text-bottom|Final solution shown in the GUI '''Top solution''' tab with possible further steps.]]<br />
|}<br />
== Lysozyme ==<br />
<br />
As a frequently used test protein, there are good models for lysozyme. This tutorial demonstrates how to solve lysozyme starting from a homology search.<br />
<br />
=== Input ===<br />
{|<br />
|[[File:Lyso-basic-options_thumb.png|frame|centre|text-bottom|Basic options dialog. Note that the space group is enantiomorphic, but we pretend we know the correct space group P4₃2₁2 to save time]]<br />
||[[File:Lyso-composition_thumb.png|frame|centre|text-bottom|Setting up composition. It would be possible to tick the '''NCBI Blast''' option and run, but we want to avoid overloading the NCBI and provide a saved homology search file]]<br />
||[[File:Lyso-homology-searches_thumb.png|frame|centre|text-bottom|Specifying the homology search file. There are many hits, and the GUI by default selects the first three. Selecting any larger number, however, makes no difference!]]<br />
|}<br />
;Running from the command line<br />
<br />
'''Input file''' (lysozyme.eff)<br />
<br />
hklin = lyso.mtz<br />
labin = "F_New,SIGF_New,DANO_New,SIGDANO_New,ISYM_New"<br />
<br />
composition<br />
{<br />
component<br />
{<br />
sequence = hewl.seq<br />
homology<br />
{<br />
file_name = hewl_ebi_wu_blast.xml<br />
max_hits = 3<br />
}<br />
}<br />
}<br />
<br />
'''Command line'''<br />
phaser.MRage --verbosity=VERBOSE lysozyme.eff<br />
<br />
=== Output ===<br />
{|<br />
|[[File:Lyso-fetch-1lsg_thumb.png|frame|centre|text-bottom|The program fetches the first homologue...]]<br />
||[[File:Lyso-sculptor-1lsg_thumb.png|frame|centre|text-bottom|...then processes it with sculptor. Note that although all 13 protocols in sculptor are active, it only creates 7 models, because remaining protocols create models that are identical to the ones used.]]<br />
||[[File:Lyso-finish_thumb.png|frame|centre|text-bottom|This model gives a clear solution, and processing stops. Although 3 hits were specified, the second and the third was never downloaded, because the first gave a clear solution]]<br />
|}</div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Molecular_replacement_with_MRage&diff=1828Molecular replacement with MRage2013-07-19T09:44:54Z<p>Gaborb: </p>
<hr />
<div>This tutorial explains how to use to run phaser.MRage from the [http://www.phenix-online.org Phenix GUI] (input files to run the same through the command line examples are also available).<br />
<br />
<br />
== Beta/blip ==<br />
<br />
This is a complex between beta lactamase (''beta'') and beta lactamase inhibitor (''blip''). There are good models available, but the space group is ambiguous. This tutorial shows basic MRage functionality with a two-component system.<br />
<br />
Experimental data for this tutorial is distributed with [http://www.phenix-online.org Phenix GUI] and is also available from the [http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials Tutorials] page.<br />
<br />
=== Input ===<br />
<br />
The MRage GUI is available from the main Phenix window under the '''Molecular replacement''' tab (select the ''Enable alpha features'' options under ''File/Preferences'' dialog for it to show up). On startup, the GUI presents the '''Basic options''' dialog.<br />
<br />
The following screenshot shows the this required settings to run the tutorial. Note, that almost everything is filled in automatically once the reflection file has been selected, or default. The only additional change one needs to make is to switch the '''space group exploration''' box to ''enantiomorph'' from its default value ''dataset'', as the space group is enantiomorphic, and it is not possible to know without solving the structure, which hand is the correct one. In this tutorial, only a single CPU is used, but feel free to use more if available! Note that the '''Overall count''' box has been left blank. This tells the program to determine the number of copies automatically.<br />
{|<br />
|[[File:Bb-basic-options_thumb.png|frame|center|text-bottom|The '''Basic options''' dialog]]<br />
|}<br />
Next, we need to tell the program about the composition of the asymmetric unit and the available search models.<br />
<br />
First, the ''beta'' component is described with its sequence, and the only search model. Since there is no modification needed to this model (it is 100% identical), it is input through the '''Ensemble''' tab. This tells the program that there is one alternative model for the ''beta'' component.<br />
<br />
{|<br />
|[[File:Bb-beta-composition_thumb.png|frame|centre|text-bottom|The '''Basic info''' dialog of '''Component1''' (''beta'')]]<br />
||[[File:Bb-beta-ensembles_thumb.png|frame|centre|text-bottom|The '''Ensembles''' dialog of '''Component1''' (''beta'')]]<br />
|}<br />
Then, a new component is created for ''blip'' (using the '''Add component''' button on the '''Basic info''' tab). This is filled out accordingly.<br />
{|<br />
|[[File:Bb-blip-composition_thumb.png|frame|centre|text-bottom|The '''Basic info''' dialog of '''Component2''' (''blip'')]]<br />
||[[File:Bb-blip-ensembles_thumb.png|frame|centre|text-bottom|The '''Ensembles''' dialog of '''Component2''' (''blip'')]]<br />
|}<br />
The job is ready to run!<br />
<br />
;Running from the command line<br />
<br />
'''Input file''' (betablip.eff)<br />
<br />
hklin = beta_blip.mtz<br />
labin = Fobs,Sigma<br />
symmetry_exploration = enantiomorph<br />
<br />
composition<br />
{<br />
<br />
component<br />
{<br />
sequence = beta.seq<br />
ensemble<br />
{<br />
coordinates<br />
{<br />
pdb = beta.pdb<br />
identity = 1.00<br />
}<br />
}<br />
}<br />
<br />
component<br />
{<br />
sequence = blip.seq<br />
ensemble<br />
{<br />
coordinates<br />
{<br />
pdb = blip.pdb<br />
identity = 1.00<br />
}<br />
}<br />
}<br />
<br />
}<br />
<br />
'''Command line'''<br />
phaser.MRage --verbosity=VERBOSE betablip.eff<br />
<br />
<br />
=== Output ===<br />
<br />
The GUI displays the program output in the logfile window. First, the program starts searching in both possible space groups.<br />
{|[[File:Bb-log-first-round-start_thumb.png|frame|centre|text-bottom|Initially, search starts in both P3₁21 and P3₂21]]<br />
||[[File:Bb-log-space-group-evaluation_thumb.png|frame|centre|text-bottom|After finding the first component, the search in P3₁21 is dropped...]]<br />
||[[File:Bb-log-second-round-start_thumb.png|frame|centre|text-bottom|...and only P3₂21 is propagated with the partial solutions found.]]<br />
||[[File:Bb-log-finish_thumb.png|frame|centre|text-bottom|The final solution: evaluation shows a high probability for it to be correct.]]<br />
||[[File:Bb-solutions_thumb.png|frame|centre|text-bottom|Final solution shown in the GUI '''Top solution''' tab with possible further steps.]]<br />
|}<br />
== Lysozyme ==<br />
<br />
As a frequently used test protein, there are good models for lysozyme. This tutorial demonstrates how to solve lysozyme starting from a homology search.<br />
<br />
=== Input ===<br />
{|<br />
|[[File:Lyso-basic-options_thumb.png|frame|centre|text-bottom|Basic options dialog. Note that the space group is enantiomorphic, but we pretend we know the correct space group P4₃2₁2 to save time]]<br />
||[[File:Lyso-composition_thumb.png|frame|centre|text-bottom|Setting up composition. It would be possible to tick the '''NCBI Blast''' option and run, but we want to avoid overloading the NCBI and provide a saved homology search file]]<br />
||[[File:Lyso-homology-searches_thumb.png|frame|centre|text-bottom|Specifying the homology search file. There are many hits, and the GUI by default selects the first three. Selecting any larger number, however, makes no difference!]]<br />
|}<br />
;Running from the command line<br />
<br />
'''Input file''' (lysozyme.eff)<br />
<br />
hklin = lyso.mtz<br />
labin = "F_New,SIGF_New,DANO_New,SIGDANO_New,ISYM_New"<br />
<br />
composition<br />
{<br />
component<br />
{<br />
sequence = hewl.seq<br />
homology<br />
{<br />
file_name = hewl_ebi_wu_blast.xml<br />
max_hits = 3<br />
}<br />
}<br />
}<br />
<br />
'''Command line'''<br />
phaser.MRage --verbosity=VERBOSE lysozyme.eff<br />
<br />
=== Output ===<br />
{|<br />
|[[File:Lyso-fetch-1lsg_thumb.png|frame|centre|text-bottom|The program fetches the first homologue...]]<br />
||[[File:Lyso-sculptor-1lsg_thumb.png|frame|centre|text-bottom|...then processes it with sculptor. Note that although all 13 protocols in sculptor are active, it only creates 7 models, because remaining protocols create models that are identical to the ones used.]]<br />
||[[File:Lyso-finish_thumb.png|frame|centre|text-bottom|This model gives a clear solution, and processing stops. Although 3 hits were specified, the second and the third was never downloaded, because the first gave a clear solution]]<br />
|}</div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=File:Bb-solutions_thumb.png&diff=1827File:Bb-solutions thumb.png2013-07-19T09:35:55Z<p>Gaborb: </p>
<hr />
<div></div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=File:Bb-log-space-group-evaluation_thumb.png&diff=1826File:Bb-log-space-group-evaluation thumb.png2013-07-19T09:35:45Z<p>Gaborb: </p>
<hr />
<div></div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=File:Bb-log-second-round-start_thumb.png&diff=1825File:Bb-log-second-round-start thumb.png2013-07-19T09:35:35Z<p>Gaborb: </p>
<hr />
<div></div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=File:Bb-log-first-round-start_thumb.png&diff=1824File:Bb-log-first-round-start thumb.png2013-07-19T09:35:20Z<p>Gaborb: </p>
<hr />
<div></div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=File:Bb-log-final_thumb.png&diff=1823File:Bb-log-final thumb.png2013-07-19T09:35:09Z<p>Gaborb: </p>
<hr />
<div></div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=File:Bb-blip-ensembles_thumb.png&diff=1822File:Bb-blip-ensembles thumb.png2013-07-19T09:35:00Z<p>Gaborb: </p>
<hr />
<div></div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=File:Bb-blip-composition_thumb.png&diff=1821File:Bb-blip-composition thumb.png2013-07-19T09:34:50Z<p>Gaborb: </p>
<hr />
<div></div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=File:Bb-beta-ensembles_thumb.png&diff=1820File:Bb-beta-ensembles thumb.png2013-07-19T09:34:42Z<p>Gaborb: </p>
<hr />
<div></div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=File:Bb-beta-composition_thumb.png&diff=1819File:Bb-beta-composition thumb.png2013-07-19T09:34:32Z<p>Gaborb: </p>
<hr />
<div></div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=File:Bb-basic-options_thumb.png&diff=1818File:Bb-basic-options thumb.png2013-07-19T09:34:23Z<p>Gaborb: </p>
<hr />
<div></div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Molecular_replacement_with_MRage&diff=1817Molecular replacement with MRage2013-07-19T09:33:44Z<p>Gaborb: </p>
<hr />
<div>This tutorial explains how to use to run phaser.MRage from the [http://www.phenix-online.org Phenix GUI] (input files to run the same through the command line examples are also available).<br />
<br />
<br />
== Beta/blip ==<br />
<br />
This is a complex between beta lactamase (''beta'') and beta lactamase inhibitor (''blip''). There are good models available, but the space group is ambiguous. This tutorial shows basic MRage functionality with a two-component system.<br />
<br />
Experimental data for this tutorial is distributed with [http://www.phenix-online.org Phenix GUI] and is also available from the [http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials Tutorials] page.<br />
<br />
=== Input ===<br />
<br />
The MRage GUI is available from the main Phenix window under the '''Molecular replacement''' tab (select the ''Enable alpha features'' options under ''File/Preferences'' dialog for it to show up). On startup, the GUI presents the '''Basic options''' dialog.<br />
<br />
The following screenshot shows the this required settings to run the tutorial. Note, that almost everything is filled in automatically once the reflection file has been selected, or default. The only additional change one needs to make is to switch the '''space group exploration''' box to ''enantiomorph'' from its default value ''dataset'', as the space group is enantiomorphic, and it is not possible to know without solving the structure, which hand is the correct one. In this tutorial, only a single CPU is used, but feel free to use more if available! Note that the '''Overall count''' box has been left blank. This tells the program to determine the number of copies automatically.<br />
{|<br />
|[[File:Basic-options.png|thumb|center|text-bottom|The '''Basic options''' dialog]]<br />
|}<br />
Next, we need to tell the program about the composition of the asymmetric unit and the available search models.<br />
<br />
First, the ''beta'' component is described with its sequence, and the only search model. Since there is no modification needed to this model (it is 100% identical), it is input through the '''Ensemble''' tab. This tells the program that there is one alternative model for the ''beta'' component.<br />
<br />
{|<br />
|[[File:Beta-composition.png|thumb|centre|text-bottom|The '''Basic info''' dialog of '''Component1''' (''beta'')]]<br />
||[[File:Beta-ensembles.png|thumb|centre|text-bottom|The '''Ensembles''' dialog of '''Component1''' (''beta'')]]<br />
|}<br />
Then, a new component is created for ''blip'' (using the '''Add component''' button on the '''Basic info''' tab). This is filled out accordingly.<br />
{|<br />
|[[File:Blip-composition.png|thumb|centre|text-bottom|The '''Basic info''' dialog of '''Component2''' (''blip'')]]<br />
||[[File:Blip-ensembles.png|thumb|centre|text-bottom|The '''Ensembles''' dialog of '''Component2''' (''blip'')]]<br />
|}<br />
The job is ready to run!<br />
<br />
;Running from the command line<br />
<br />
'''Input file''' (betablip.eff)<br />
<br />
hklin = beta_blip.mtz<br />
labin = Fobs,Sigma<br />
symmetry_exploration = enantiomorph<br />
<br />
composition<br />
{<br />
<br />
component<br />
{<br />
sequence = beta.seq<br />
ensemble<br />
{<br />
coordinates<br />
{<br />
pdb = beta.pdb<br />
identity = 1.00<br />
}<br />
}<br />
}<br />
<br />
component<br />
{<br />
sequence = blip.seq<br />
ensemble<br />
{<br />
coordinates<br />
{<br />
pdb = blip.pdb<br />
identity = 1.00<br />
}<br />
}<br />
}<br />
<br />
}<br />
<br />
'''Command line'''<br />
phaser.MRage --verbosity=VERBOSE betablip.eff<br />
<br />
<br />
=== Output ===<br />
<br />
The GUI displays the program output in the logfile window. First, the program starts searching in both possible space groups.<br />
{|[[File:Beta-blip-log-first-round-start.png|thumb|centre|text-bottom|Initially, search starts in both P3₁21 and P3₂21]]<br />
||[[File:Beta-blip-log-space-group-evaluation.png|thumb|centre|text-bottom|After finding the first component, the search in P3₁21 is dropped...]]<br />
||[[File:Beta-blip-log-second-round-start.png|thumb|centre|text-bottom|...and only P3₂21 is propagated with the partial solutions found.]]<br />
||[[File:Beta-blip-log-finish.png|thumb|centre|text-bottom|The final solution: evaluation shows a high probability for it to be correct.]]<br />
||[[File:Beta-blip-solutions.png|thumb|centre|text-bottom|Final solution shown in the GUI '''Top solution''' tab with possible further steps.]]<br />
|}<br />
== Lysozyme ==<br />
<br />
As a frequently used test protein, there are good models for lysozyme. This tutorial demonstrates how to solve lysozyme starting from a homology search.<br />
<br />
=== Input ===<br />
{|<br />
|[[File:Lyso-basic-options_thumb.png|frame|centre|text-bottom|Basic options dialog. Note that the space group is enantiomorphic, but we pretend we know the correct space group P4₃2₁2 to save time]]<br />
||[[File:Lyso-composition_thumb.png|frame|centre|text-bottom|Setting up composition. It would be possible to tick the '''NCBI Blast''' option and run, but we want to avoid overloading the NCBI and provide a saved homology search file]]<br />
||[[File:Lyso-homology-searches_thumb.png|frame|centre|text-bottom|Specifying the homology search file. There are many hits, and the GUI by default selects the first three. Selecting any larger number, however, makes no difference!]]<br />
|}<br />
;Running from the command line<br />
<br />
'''Input file''' (lysozyme.eff)<br />
<br />
hklin = lyso.mtz<br />
labin = "F_New,SIGF_New,DANO_New,SIGDANO_New,ISYM_New"<br />
<br />
composition<br />
{<br />
component<br />
{<br />
sequence = hewl.seq<br />
homology<br />
{<br />
file_name = hewl_ebi_wu_blast.xml<br />
max_hits = 3<br />
}<br />
}<br />
}<br />
<br />
'''Command line'''<br />
phaser.MRage --verbosity=VERBOSE lysozyme.eff<br />
<br />
=== Output ===<br />
{|<br />
|[[File:Lyso-fetch-1lsg_thumb.png|frame|centre|text-bottom|The program fetches the first homologue...]]<br />
||[[File:Lyso-sculptor-1lsg_thumb.png|frame|centre|text-bottom|...then processes it with sculptor. Note that although all 13 protocols in sculptor are active, it only creates 7 models, because remaining protocols create models that are identical to the ones used.]]<br />
||[[File:Lyso-finish_thumb.png|frame|centre|text-bottom|This model gives a clear solution, and processing stops. Although 3 hits were specified, the second and the third was never downloaded, because the first gave a clear solution]]<br />
|}</div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=File:Lyso-sculptor-1lsg_thumb.png&diff=1816File:Lyso-sculptor-1lsg thumb.png2013-07-19T09:27:42Z<p>Gaborb: </p>
<hr />
<div></div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=File:Lyso-homology-searches_thumb.png&diff=1815File:Lyso-homology-searches thumb.png2013-07-19T09:27:34Z<p>Gaborb: </p>
<hr />
<div></div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=File:Lyso-finish_thumb.png&diff=1814File:Lyso-finish thumb.png2013-07-19T09:27:21Z<p>Gaborb: </p>
<hr />
<div></div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=File:Lyso-fetch-1lsg_thumb.png&diff=1813File:Lyso-fetch-1lsg thumb.png2013-07-19T09:27:08Z<p>Gaborb: </p>
<hr />
<div></div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=File:Lyso-composition_thumb.png&diff=1812File:Lyso-composition thumb.png2013-07-19T09:26:56Z<p>Gaborb: </p>
<hr />
<div></div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=File:Lyso-basic-options_thumb.png&diff=1811File:Lyso-basic-options thumb.png2013-07-19T09:26:44Z<p>Gaborb: </p>
<hr />
<div></div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Molecular_replacement_with_MRage&diff=1766Molecular replacement with MRage2013-07-05T16:31:18Z<p>Gaborb: </p>
<hr />
<div>This tutorial explains how to use to run phaser.MRage from the [http://www.phenix-online.org Phenix GUI] (input files to run the same through the command line examples are also available).<br />
<br />
<br />
== Beta/blip ==<br />
<br />
This is a complex between beta lactamase (''beta'') and beta lactamase inhibitor (''blip''). There are good models available, but the space group is ambiguous. This tutorial shows basic MRage functionality with a two-component system.<br />
<br />
Experimental data for this tutorial is distributed with [http://www.phenix-online.org Phenix GUI] and is also available from the [http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials Tutorials] page.<br />
<br />
=== Input ===<br />
<br />
The MRage GUI is available from the main Phenix window under the '''Molecular replacement''' tab (select the ''Enable alpha features'' options under ''File/Preferences'' dialog for it to show up). On startup, the GUI presents the '''Basic options''' dialog.<br />
<br />
The following screenshot shows the this required settings to run the tutorial. Note, that almost everything is filled in automatically once the reflection file has been selected, or default. The only additional change one needs to make is to switch the '''space group exploration''' box to ''enantiomorph'' from its default value ''dataset'', as the space group is enantiomorphic, and it is not possible to know without solving the structure, which hand is the correct one. In this tutorial, only a single CPU is used, but feel free to use more if available! Note that the '''Overall count''' box has been left blank. This tells the program to determine the number of copies automatically.<br />
<br />
[[File:Basic-options.png|frame|center|The '''Basic options''' dialog]]<br />
<br />
Next, we need to tell the program about the composition of the asymmetric unit and the available search models.<br />
<br />
First, the ''beta'' component is described with its sequence, and the only search model. Since there is no modification needed to this model (it is 100% identical), it is input through the '''Ensemble''' tab. This tells the program that there is one alternative model for the ''beta'' component.<br />
<br />
[[File:Beta-composition.png|frame|center|The '''Basic info''' dialog of '''Component1''' (''beta'')]]<br />
[[File:Beta-ensembles.png|frame|center|The '''Ensembles''' dialog of '''Component1''' (''beta'')]]<br />
<br />
Then, a new component is created for ''blip'' (using the '''Add component''' button on the '''Basic info''' tab). This is filled out accordingly.<br />
<br />
[[File:Blip-composition.png|frame|center|The '''Basic info''' dialog of '''Component2''' (''blip'')]]<br />
[[File:Blip-ensembles.png|frame|center|The '''Ensembles''' dialog of '''Component2''' (''blip'')]]<br />
<br />
The job is ready to run!<br />
<br />
;Running from the command line<br />
<br />
'''Input file''' (betablip.eff)<br />
<br />
hklin = beta_blip.mtz<br />
labin = Fobs,Sigma<br />
symmetry_exploration = enantiomorph<br />
<br />
composition<br />
{<br />
<br />
component<br />
{<br />
sequence = beta.seq<br />
ensemble<br />
{<br />
coordinates<br />
{<br />
pdb = beta.pdb<br />
identity = 1.00<br />
}<br />
}<br />
}<br />
<br />
component<br />
{<br />
sequence = blip.seq<br />
ensemble<br />
{<br />
coordinates<br />
{<br />
pdb = blip.pdb<br />
identity = 1.00<br />
}<br />
}<br />
}<br />
<br />
}<br />
<br />
'''Command line'''<br />
phaser.MRage --verbosity=VERBOSE betablip.eff<br />
<br />
<br />
=== Output ===<br />
<br />
The GUI displays the program output in the logfile window. First, the program starts searching in both possible space groups.<br />
[[File:Beta-blip-log-first-round-start.png|frame|center|Initially, search starts in both P3₁21 and P3₂21]]<br />
[[File:Beta-blip-log-space-group-evaluation.png|frame|center|After finding the first component, the search in P3₁21 is dropped...]]<br />
[[File:Beta-blip-log-second-round-start.png|frame|center|...and only P3₂21 is propagated with the partial solutions found.]]<br />
[[File:Beta-blip-log-finish.png|frame|center|The final solution: evaluation shows a high probability for it to be correct.]]<br />
[[File:Beta-blip-solutions.png|frame|center|Final solution shown in the GUI '''Top solution''' tab with possible further steps.]]<br />
<br />
== Lysozyme ==<br />
<br />
As a frequently used test protein, there are good models for lysozyme. This tutorial demonstrates how to solve lysozyme starting from a homology search.<br />
<br />
=== Input ===<br />
<br />
[[File:Lysozyme-basic-options.png|frame|center|Basic options dialog. Note that the space group is enantiomorphic, but we pretend we know the correct space group P4₃2₁2 to save time]]<br />
[[File:Lysozyme-composition.png|frame|center|Setting up composition. It would be possible to tick the '''NCBI Blast''' option and run, but we want to avoid overloading the NCBI and provide a saved homology search file]]<br />
[[File:Lysozyme-homology-searches.png|frame|center|Specifying the homology search file. There are many hits, and the GUI by default selects the first three. Selecting any larger number, however, makes no difference!]]<br />
<br />
;Running from the command line<br />
<br />
'''Input file''' (lysozyme.eff)<br />
<br />
hklin = lyso.mtz<br />
labin = "F_New,SIGF_New,DANO_New,SIGDANO_New,ISYM_New"<br />
<br />
composition<br />
{<br />
component<br />
{<br />
sequence = hewl.seq<br />
homology<br />
{<br />
file_name = hewl_ebi_wu_blast.xml<br />
max_hits = 3<br />
}<br />
}<br />
}<br />
<br />
'''Command line'''<br />
phaser.MRage --verbosity=VERBOSE lysozyme.eff<br />
<br />
=== Output ===<br />
[[File:Lysozyme-fetch-1lsg.png|frame|center|The program fetches the first homologue...]]<br />
[[File:Lysozyme-sculptor-1lsg.png|frame|center|...then processes it with sculptor. Note that although all 13 protocols in sculptor are active, it only creates 7 models, because remaining protocols create models that are identical to the ones used.]]<br />
[[File:Lysozyme-finish.png|frame|center|This model gives a clear solution, and processing stops. Although 3 hits were specified, the second and the third was never downloaded, because the first gave a clear solution]]</div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Molecular_replacement_with_MRage&diff=1759Molecular replacement with MRage2013-07-05T14:56:34Z<p>Gaborb: </p>
<hr />
<div>This tutorial explains how to use to run phaser.MRage from the [http://www.phenix-online.org Phenix GUI] (input files to run the same through the command line examples are also available).<br />
<br />
<br />
== Beta/blip ==<br />
<br />
=== Input ===<br />
<br />
Experimental data for this tutorial is distributed with [http://www.phenix-online.org Phenix GUI] and is also available from the [http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials Tutorials] page.<br />
<br />
The MRage GUI is available from the main Phenix window under the '''Molecular replacement''' tab (select the ''Enable alpha features'' options under ''File/Preferences'' dialog for it to show up). On startup, the GUI presents the '''Basic options''' dialog.<br />
<br />
The following screenshot shows the this required settings to run the tutorial. Note, that almost everything is filled in automatically once the reflection file has been selected, or default. The only additional change one needs to make is to switch the '''space group exploration''' box to ''enantiomorph'' from its default value ''dataset'', as the space group is enantiomorphic, and it is not possible to know without solving the structure, which hand is the correct one. In this tutorial, only a single CPU is used, but feel free to use more if available! Note that the '''Overall count''' box has been left blank. This tells the program to determine the number of copies automatically.<br />
<br />
[[File:Basic-options.png|frame|center|The '''Basic options''' dialog]]<br />
<br />
Next, we need to tell the program about the composition of the asymmetric unit and the available search models.<br />
<br />
First, the ''beta'' component is described with its sequence, and the only search model. Since there is no modification needed to this model (it is 100% identical), it is input through the '''Ensemble''' tab. This tells the program that there is one alternative model for the ''beta'' component.<br />
<br />
[[File:Beta-composition.png|frame|center|The '''Basic info''' dialog of '''Component1''' (''beta'')]]<br />
[[File:Beta-ensembles.png|frame|center|The '''Ensembles''' dialog of '''Component1''' (''beta'')]]<br />
<br />
Then, a new component is created for ''blip'' (using the '''Add component''' button on the '''Basic info''' tab). This is filled out accordingly.<br />
<br />
[[File:Blip-composition.png|frame|center|The '''Basic info''' dialog of '''Component2''' (''blip'')]]<br />
[[File:Blip-ensembles.png|frame|center|The '''Ensembles''' dialog of '''Component2''' (''blip'')]]<br />
<br />
The job is ready to run!<br />
<br />
;Running from the command line<br />
<br />
'''Input file''' (betablip.eff)<br />
<br />
hklin = beta_blip.mtz<br />
labin = Fobs,Sigma<br />
symmetry_exploration = enantiomorph<br />
<br />
composition<br />
{<br />
<br />
component<br />
{<br />
sequence = beta.seq<br />
ensemble<br />
{<br />
coordinates<br />
{<br />
pdb = beta.pdb<br />
identity = 1.00<br />
}<br />
}<br />
}<br />
<br />
component<br />
{<br />
sequence = blip.seq<br />
ensemble<br />
{<br />
coordinates<br />
{<br />
pdb = blip.pdb<br />
identity = 1.00<br />
}<br />
}<br />
}<br />
<br />
}<br />
<br />
'''Command line'''<br />
phaser.MRage --verbosity=VERBOSE betablip.eff<br />
<br />
<br />
=== Output ===<br />
<br />
The GUI displays the program output in the logfile window. First, the program starts searching in both possible space groups.<br />
[[File:Beta-blip-log-first-round-start.png|frame|center|Initially, search starts in both P3₁21 and P3₂21]]<br />
[[File:Beta-blip-log-space-group-evaluation.png|frame|center|After finding the first component, the search in P3₁21 is dropped...]]<br />
[[File:Beta-blip-log-second-round-start.png|frame|center|...and only P3₂21 is propagated with the partial solutions found.]]<br />
[[File:Beta-blip-log-finish.png|frame|center|The final solution: evaluation shows a high probability for it to be correct.]]<br />
[[File:Beta-blip-solutions.png|frame|center|Final solution shown in the GUI '''Top solution''' tab with possible further steps.]]</div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Molecular_replacement_with_MRage&diff=1753Molecular replacement with MRage2013-07-05T14:14:09Z<p>Gaborb: </p>
<hr />
<div>This tutorial explains how to use to run phaser.MRage from the [http://www.phenix-online.org Phenix GUI] (input files to run the same through the command line examples are also available).<br />
<br />
<br />
== Beta/blip ==<br />
<br />
;Input<br />
<br />
Experimental data for this tutorial is distributed with [http://www.phenix-online.org Phenix GUI] and is also available from the [http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials Tutorials] page.<br />
<br />
The MRage GUI is available from the main Phenix window under the '''Molecular replacement''' tab (select the ''Enable alpha features'' options under ''File/Preferences'' dialog for it to show up). On startup, the GUI presents the '''Basic options''' dialog.<br />
<br />
The following screenshot shows the this required settings to run the tutorial. Note, that almost everything is filled in automatically once the reflection file has been selected, or default. The only additional change one needs to make is to switch the '''space group exploration''' box to ''enantiomorph'' from its default value ''dataset'', as the space group is enantiomorphic, and it is not possible to know without solving the structure, which hand is the correct one. In this tutorial, only a single CPU is used, but feel free to use more if available! Note that the '''Overall count''' box has been left blank. This tells the program to determine the number of copies automatically.<br />
<br />
[[File:Basic-options.png]]<br />
<br />
Next, we need to tell the program about the composition of the asymmetric unit and the available search models.<br />
<br />
First, the ''beta'' component is described with its sequence, and the only search model. Since there is no modification needed to this model (it is 100% identical), it is input through the '''Ensemble''' tab. This tells the program that there is one alternative model for the ''beta'' component.<br />
<br />
[[File:Beta-composition.png]]<br />
[[File:Beta-ensembles.png]]<br />
<br />
Then, a new component is created for ''blip'' (using the '''Add component''' button on the '''Basic info''' tab). This is filled out accordingly.<br />
<br />
[[File:Blip-composition.png]]<br />
[[File:Blip-ensembles.png]]<br />
<br />
The job is ready to run!<br />
<br />
;Output<br />
<br />
The logfile</div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Molecular_replacement_with_MRage&diff=1748Molecular replacement with MRage2013-07-05T13:30:29Z<p>Gaborb: </p>
<hr />
<div>This tutorial explains how to use to run phaser.MRage from the [http://www.phenix-online.org Phenix GUI] (input files to run the same through the command line examples are also available).<br />
<br />
;Beta/Blip<br />
<br />
Experimental data for this tutorial is distributed with [http://www.phenix-online.org Phenix GUI] and is also avaiable from the [http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials Tutorials] page.<br />
<br />
The MRage GUI is available from the main Phenix window under the *Molecular replacement* tab (select the *Enable alpha features* options under File/Preferences for it to show up).<br />
<br />
[[File:Basic-options.png]]</div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Molecular_replacement_with_MRage&diff=1746Molecular replacement with MRage2013-07-05T13:22:18Z<p>Gaborb: Created page with 'This tutorial explains how to use to run phaser.MRage from the [http://www.phenix-online.org Phenix GUI] (input files to run the same through the command line examples are also a…'</p>
<hr />
<div>This tutorial explains how to use to run phaser.MRage from the [http://www.phenix-online.org Phenix GUI] (input files to run the same through the command line examples are also available).<br />
<br />
;Beta/Blip<br />
<br />
Experimental data for this tutorial is distributed with [http://www.phenix-online.org Phenix GUI] and is also avaiable from the [http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials Tutorials] page.</div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Tutorials&diff=1745Tutorials2013-07-05T10:52:33Z<p>Gaborb: </p>
<hr />
<div>;Tutorials<br />
:The tutorials are suitable for individual use or class teaching.<br />
:* [[MR using CCP4i:TOXD|MR using CCP4i:TOXD]]<br />
:* [[MR using CCP4i:BETA/BLIP|MR using CCP4i:BETA/BLIP]]<br />
:* [[MR using keyword input|MR using keyword input]]<br />
:* [[Finding a search model:TOXD|Finding a search model:TOXD]]<br />
:* [[Molecular replacement with MRage]]<br />
:* [[SAD using CCP4i|SAD using CCP4i]]<br />
:* [[Combined MR-SAD using CCP4i|Combined MR-SAD using CCP4i]]<br />
:* [[EP using Phenix|EP using Phenix]]<br />
<br />
;Data<br />
:The coordinate (pdb), sequence (fasta) and reflection (mtz) files required to run the tutorials are distributed with Phaser.<br />
:They can also be obtained from:<br />
:[[Image:Download.png|link=]] [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/phaser-mr-tutorial.tar.gz Data for Molecular Replacement Examples and Tutorials]<br />
:[[Image:Download.png|link=]] [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/phaser-ep-tutorial.tar.gz Data for Experimental Phasing Examples and Tutorials]<br />
<br />
;Phenix Tutorials<br />
:Movies of the phenix GUI in action<br />
:*[[beta-blip-mr | TEM-1 beta-blip (β-lactamase/β-lactamase inihibitor)]]<br />
:*[[b-CA-mr | b-CA-mr (β-carbonic anhydrase)]]<br />
<br />
;References<br />
: The crystal structure of a hetero-dimer of beta-lactamase (BETA) and beta-lactamase inhibitor protein (BLIP), both with molecular replacement models from crystal structures of the individual BETA and BLIP components. We thank Mike James and Natalie Strynadka for the diffraction data. Reference: Strynadka, N.C.J., Jensen, S.E., Alzari, P.M. &amp; James. M.N.G. (1996) ''Nat. Struct. Biol.'' '''3''' 290-297.<br />
: The crystal structure of insulin phased on intrinsic sulphurs. We thank Paul Adams for the diffraction data. Reference: Adams (2001) ''Acta Cryst'' D'''57'''. 990-995.</div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Gabor_Bunkoczi&diff=819Gabor Bunkoczi2011-01-18T09:10:38Z<p>Gaborb: </p>
<hr />
<div>'''Talks:'''<br />
<br />
CCP4 Study Weekend 2011: [http://www-structmed.cimr.cam.ac.uk/phaser/ccp4-sw2011.pdf What's new in: Phaser]</div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Gabor_Bunkoczi&diff=818Gabor Bunkoczi2011-01-18T09:10:08Z<p>Gaborb: </p>
<hr />
<div>'''Talks:'''<br />
<br />
CCP4 Study Weekend 2011: [http://http://www-structmed.cimr.cam.ac.uk/phaser/ccp4-sw2011.pdf What's new in: Phaser]</div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Gabor_Bunkoczi&diff=817Gabor Bunkoczi2011-01-18T09:02:16Z<p>Gaborb: </p>
<hr />
<div>'''Talks:'''<br />
<br />
CCP4 Study Weekend 2011:</div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Gabor_Bunkoczi&diff=816Gabor Bunkoczi2011-01-17T16:47:22Z<p>Gaborb: </p>
<hr />
<div>'''Talks:'''<br />
<br />
CCP4 Study Weekend 2011: [[What's new in: Phaser?]]</div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Gabor_Bunkoczi&diff=814Gabor Bunkoczi2011-01-17T11:43:31Z<p>Gaborb: Created page with ''''Bold text'''Talks: CCP4 Study Weekend 2011Media:Example.ogg'</p>
<hr />
<div>'''Bold text'''Talks:<br />
<br />
CCP4 Study Weekend 2011[[Media:Example.ogg]]</div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Developers&diff=812Developers2011-01-17T11:42:05Z<p>Gaborb: </p>
<hr />
<div>;Principal Investigator<br />
* [[Randy J. Read | Professor Randy J. Read]]<br />
<br />
<br />
;Group<br />
* [[ Gabor Bunkoczi | Dr Gabor Bunkoczi ]]<br />
* [[ Airlie J. McCoy | Dr Airlie McCoy ]]<br />
* Dr Robert Oeffner <br />
<br />
<br />
;Alumni<br />
* Dr Anne Baker<br />
* Dr Laurent Storoni<br />
* Dr Hamsapriye</div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Developers&diff=811Developers2011-01-17T11:41:50Z<p>Gaborb: </p>
<hr />
<div>;Principal Investigator<br />
* [[Randy J. Read | Professor Randy J. Read]]<br />
<br />
<br />
;Group<br />
* [ [ Gabor Bunkoczi | Dr Gabor Bunkoczi ] ]<br />
* [[ Airlie J. McCoy | Dr Airlie McCoy ]]<br />
* Dr Robert Oeffner <br />
<br />
<br />
;Alumni<br />
* Dr Anne Baker<br />
* Dr Laurent Storoni<br />
* Dr Hamsapriye</div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Events&diff=454Events2009-07-21T10:14:10Z<p>Gaborb: /* 2009 */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
New developments in Phaser are represented regularly at conferences. Please come and talk to us at these meetings if you have any queries, suggestions or comments.<br />
<br />
==Upcoming==<br />
<br />
==2009==<br />
<br />
;VII Regional School of Crystallography, 13-17 July 2009, Havana (Cuba)<br />
:Molecular replacement: Pattersons and likelihood and Experimental phasing<br />
:Gabor Bunkoczi<br />
<br />
;EMBO / MAX-INF2 Practical Course, 15-19 June 2009, Grenoble (France)<br />
:Density modification and Phaser for experimental phasing<br />
:Gabor Bunkoczi<br />
<br />
;Phenix Workshop, 12 March 2009, Durham, NC (USA)<br />
:Difficult MR made easy with Phaser<br />
:Gabor Bunkoczi<br />
<br />
;CCP4 Study Weekend, 3-4 Jan 2009, Nottingham (UK)<br />
:The First Map<br />
:Airlie J. McCoy<br />
<br />
==2008==<br />
;Biocrys2008, 4-11 October 2008, Oeiras (Portugal)<br />
:Molecular replacement: from Pattersons to likelihood<br />
:Gabor Bunkoczi<br />
<br />
;CCP4 Workshop, 1-5 September 2008, Tokyo (Japan)<br />
:Molecular replacement in Phaser and Experimental phasing in Phaser<br />
:Gabor Bunkoczi<br />
<br />
;CCP4 Workshop, 23-28 May 2008, Chicago, IL (USA)<br />
:Molecular replacement in Phaser and Experimental phasing in Phaser<br />
:Gabor Bunkoczi<br />
<br />
;Phenix Workshop, 26-27 March 2008, Berkeley, CA (USA)<br />
:Difficult MR made easy with Phaser<br />
:Gabor Bunkoczi<br />
<br />
==2007==<br />
;MAXLAB Annual User's Meeting, 30 October - 2 November 2007, Lund (Sweden)<br />
:SAD Phasing in Phenix<br />
:Gabor Bunkoczi<br />
<br />
==2006==<br />
<br />
;Gordon Research Conference, 16-21 July 2006, Lewiston (USA)<br />
:Phasing with Phaser<br />
:Airlie J. McCoy<br />
<br />
;8th International School on the Crystallography of Biological Macromolecules, 21-25 May 2006, Como (Italy)<br />
:Likelihood in Phaser<br />
:Randy J. Read<br />
<br />
;CCP4 Study Weekend, 6-7 Jan 2006, Leeds (UK)<br />
:Solving Difficult Molecular Replacement Problems with Phaser<br />
:Airlie J. McCoy<br />
<br />
==2005==<br />
; ACA 2005 Annual Meeting, 28 May - 2 June 2005, Orlando (USA)<br />
:Maximum Likelihood Molecular Replacement in Phaser<br />
:Airlie J. McCoy<br />
<br />
; International School of Crystallography - 37th Course, 13 - 22 May 2005, Erice (Italy)<br />
:Likelihood-based molecular replacement in Phaser : view the talk<br />
:Randy J. Read<br />
<br />
; International School of Crystallography - 37th Course, 13 - 22 May 2005, Erice (Italy)<br />
:Likelihood-based experimental phasing in Phaser : view the talk<br />
:Airlie J. McCoy<br />
<br />
==2004==<br />
; BioCrys2004, Fundamentals of modern methods in biocrystallography, 19-26 Nov 2004, Oeiras (Portugal)<br />
:Liking Likelihood<br />
:Airlie J. McCoy<br />
<br />
; Gordon Research Conference, 11-16 July 2004, Lewiston (USA)<br />
:Phasing with maximum likelihood in Phaser<br />
:Randy J. Read<br />
<br />
; CCP4 Study Weekend, 4-5 Jan 2004, Leeds (UK)<br />
:Liking Likelihood<br />
:Airlie J. McCoy<br />
<br />
==2003==<br />
;ACA 2003 Annual Meeting, 26-31 July 2003, Covington (USA)<br />
:Fast Molecular Replacement by Maximum Likelihood in Phaser<br />
:Airlie J. McCoy<br />
<br />
;7th International School on Crystallography of Biological Macromolecules, 10 - 14 May 2003, Como (Italy)<br />
:Maximum Likelihood Molecular Replacement<br />
:Airlie J. McCoy</div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Events&diff=92Events2009-07-02T12:27:21Z<p>Gaborb: </p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
New developments in Phaser are represented regularly at conferences. Please come and talk to us at these meetings if you have any queries, suggestions or comments.<br />
<br />
==Upcoming==<br />
<br />
==2009==<br />
<br />
;EMBO / MAX-INF2 Practical Course, 15-19 June 2009, Grenoble (France)<br />
:Density modification and Phaser for experimental phasing<br />
:Gabor Bunkoczi<br />
<br />
;Phenix Workshop, 12 March 2009, Durham, NC (USA)<br />
:Difficult MR made easy with Phaser<br />
:Gabor Bunkoczi<br />
<br />
;CCP4 Study Weekend, 3-4 Jan 2009, Nottingham (UK)<br />
:The First Map<br />
:Airlie J. McCoy<br />
<br />
==2008==<br />
;Biocrys2008, 4-11 October 2008, Oeiras (Portugal)<br />
:Molecular replacement: from Pattersons to likelihood<br />
:Gabor Bunkoczi<br />
<br />
;CCP4 Workshop, 1-5 September 2008, Tokyo (Japan)<br />
:Molecular replacement in Phaser and Experimental phasing in Phaser<br />
:Gabor Bunkoczi<br />
<br />
;CCP4 Workshop, 23-28 May 2008, Chicago, IL (USA)<br />
:Molecular replacement in Phaser and Experimental phasing in Phaser<br />
:Gabor Bunkoczi<br />
<br />
;Phenix Workshop, 26-27 March 2008, Berkeley, CA (USA)<br />
:Difficult MR made easy with Phaser<br />
:Gabor Bunkoczi<br />
<br />
==2007==<br />
;MAXLAB Annual User's Meeting, 30 October - 2 November 2007, Lund (Sweden)<br />
:SAD Phasing in Phenix<br />
:Gabor Bunkoczi<br />
<br />
==2006==<br />
<br />
;Gordon Research Conference, 16-21 July 2006, Lewiston (USA)<br />
:Phasing with Phaser<br />
:Airlie J. McCoy<br />
<br />
;8th International School on the Crystallography of Biological Macromolecules, 21-25 May 2006, Como (Italy)<br />
:Likelihood in Phaser<br />
:Randy J. Read<br />
<br />
;CCP4 Study Weekend, 6-7 Jan 2006, Leeds (UK)<br />
:Solving Difficult Molecular Replacement Problems with Phaser<br />
:Airlie J. McCoy<br />
<br />
==2005==<br />
; ACA 2005 Annual Meeting, 28 May - 2 June 2005, Orlando (USA)<br />
:Maximum Likelihood Molecular Replacement in Phaser<br />
:Airlie J. McCoy<br />
<br />
; International School of Crystallography - 37th Course, 13 - 22 May 2005, Erice (Italy)<br />
:Likelihood-based molecular replacement in Phaser : view the talk<br />
:Randy J. Read<br />
<br />
; International School of Crystallography - 37th Course, 13 - 22 May 2005, Erice (Italy)<br />
:Likelihood-based experimental phasing in Phaser : view the talk<br />
:Airlie J. McCoy<br />
<br />
==2004==<br />
; BioCrys2004, Fundamentals of modern methods in biocrystallography, 19-26 Nov 2004, Oeiras (Portugal)<br />
:Liking Likelihood<br />
:Airlie J. McCoy<br />
<br />
; Gordon Research Conference, 11-16 July 2004, Lewiston (USA)<br />
:Phasing with maximum likelihood in Phaser<br />
:Randy J. Read<br />
<br />
; CCP4 Study Weekend, 4-5 Jan 2004, Leeds (UK)<br />
:Liking Likelihood<br />
:Airlie J. McCoy<br />
<br />
==2003==<br />
;ACA 2003 Annual Meeting, 26-31 July 2003, Covington (USA)<br />
:Fast Molecular Replacement by Maximum Likelihood in Phaser<br />
:Airlie J. McCoy<br />
<br />
;7th International School on Crystallography of Biological Macromolecules, 10 - 14 May 2003, Como (Italy)<br />
:Maximum Likelihood Molecular Replacement<br />
:Airlie J. McCoy</div>Gaborbhttps://www.phaser.cimr.cam.ac.uk/index.php?title=Events&diff=89Events2009-07-02T11:58:41Z<p>Gaborb: </p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
New developments in Phaser are represented regularly at conferences. Please come and talk to us at these meetings if you have any queries, suggestions or comments.<br />
<br />
==Upcoming==<br />
<br />
==2009==<br />
<br />
;EMBO / MAX-INF2 Practical Course, 15-19 June 2009, Grenoble (France)<br />
:Density modification and Phaser for experimental phasing<br />
:Gabor Bunkoczi<br />
<br />
;Phenix Workshop, 12 March 2009, Durham, NC (USA)<br />
:Difficult MR made easy with Phaser<br />
:Gabor Bunkoczi<br />
<br />
<br />
;CCP4 Study Weekend, 3-4 Jan 2009, Nottingham (UK)<br />
:The First Map<br />
:Airlie J. McCoy<br />
<br />
==2008==<br />
<br />
==2007==<br />
<br />
==2006==<br />
<br />
;Gordon Research Conference, 16-21 July 2006, Lewiston (USA)<br />
:Phasing with Phaser<br />
:Airlie J. McCoy<br />
<br />
;8th International School on the Crystallography of Biological Macromolecules, 21-25 May 2006, Como (Italy)<br />
:Likelihood in Phaser<br />
:Randy J. Read<br />
<br />
;CCP4 Study Weekend, 6-7 Jan 2006, Leeds (UK)<br />
:Solving Difficult Molecular Replacement Problems with Phaser<br />
:Airlie J. McCoy<br />
<br />
==2005==<br />
; ACA 2005 Annual Meeting, 28 May - 2 June 2005, Orlando (USA)<br />
:Maximum Likelihood Molecular Replacement in Phaser<br />
:Airlie J. McCoy<br />
<br />
; International School of Crystallography - 37th Course, 13 - 22 May 2005, Erice (Italy)<br />
:Likelihood-based molecular replacement in Phaser : view the talk<br />
:Randy J. Read<br />
<br />
; International School of Crystallography - 37th Course, 13 - 22 May 2005, Erice (Italy)<br />
:Likelihood-based experimental phasing in Phaser : view the talk<br />
:Airlie J. McCoy<br />
<br />
==2004==<br />
; BioCrys2004, Fundamentals of modern methods in biocrystallography, 19-26 Nov 2004, Oeiras (Portugal)<br />
:Liking Likelihood<br />
:Airlie J. McCoy<br />
<br />
; Gordon Research Conference, 11-16 July 2004, Lewiston (USA)<br />
:Phasing with maximum likelihood in Phaser<br />
:Randy J. Read<br />
<br />
; CCP4 Study Weekend, 4-5 Jan 2004, Leeds (UK)<br />
:Liking Likelihood<br />
:Airlie J. McCoy<br />
<br />
==2003==<br />
;ACA 2003 Annual Meeting, 26-31 July 2003, Covington (USA)<br />
:Fast Molecular Replacement by Maximum Likelihood in Phaser<br />
:Airlie J. McCoy<br />
<br />
;7th International School on Crystallography of Biological Macromolecules, 10 - 14 May 2003, Como (Italy)<br />
:Maximum Likelihood Molecular Replacement<br />
:Airlie J. McCoy</div>Gaborb