Molecular replacement with MRage - Revision history

Airlie: /* Output */

2013-07-19T11:49:02Z

‎Output

Airlie: /* Input */

2013-07-19T11:48:51Z

‎Input

Airlie: /* Input */

2013-07-19T11:48:20Z

‎Input

Airlie: /* Output */

2013-07-19T11:47:46Z

‎Output

Gaborb at 11:18, 19 July 2013

2013-07-19T11:18:45Z

Gaborb at 11:13, 19 July 2013

2013-07-19T11:13:21Z

Gaborb at 10:45, 19 July 2013

2013-07-19T10:45:21Z

Gaborb at 10:41, 19 July 2013

2013-07-19T10:41:19Z

Gaborb at 09:45, 19 July 2013

2013-07-19T09:45:46Z

Gaborb at 09:44, 19 July 2013

2013-07-19T09:44:54Z

@@ Line 142: / Line 142: @@
 === Output ===
-{|class="wikitable"
+{|class="wikitable"  width=10%
 |[[File:Lyso-fetch-1lsg_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-fetch-1lsg.png|centre]]
 ||[[File:Lyso-sculptor-1lsg_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-sculptor-1lsg.png|centre]]

@@ Line 13: / Line 13: @@
 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.
-{| class="wikitable"
+{| class="wikitable" width=10%
 |[[File:Bb-basic-options_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Basic-options.png]]
 |-
@@ Line 22: / Line 22: @@
 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.
-{|class="wikitable"
+{|class="wikitable" width=10%
 |[[File:Bb-beta-composition_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/bb-beta-composition.png|centre]]
 ||[[File:Bb-beta-ensembles_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/bb-beta-ensembles.png|centre]]
@@ Line 30: / Line 30: @@
 |}
 Then, a new component is created for ''blip'' (using the '''Add component''' button on the '''Basic info''' tab). This is filled out accordingly.
-{|class="wikitable"
+{|class="wikitable"  width=10%
 |[[File:Bb-blip-composition_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/bb-blip-composition.png|centre]]
 ||[[File:Bb-blip-ensembles_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/bb-blip-ensembles.png|centre]]
@@ Line 80: / Line 80: @@
 '''Command line'''
   phaser.MRage --verbosity=VERBOSE betablip.eff
 === Output ===

@@ Line 110: / Line 110: @@
 === Input ===
-{|class="wikitable"
+{|class="wikitable" width=10%
 |[[File:Lyso-basic-options_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-basic-options.png|centre]]
 ||[[File:Lyso-composition_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-composition.png|centre]]

@@ Line 85: / Line 85: @@
 The GUI displays the program output in the logfile window. First, the program starts searching in both possible space groups.
 {|class="wikitable"
 |[[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]]
 ||[[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]]
 ||[[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]]
 |-
 |Initially, search starts in both P3₁21 and P3₂21
 |After finding the first component, the search in P3₁21 is dropped...
 |...and only P3₂21 is propagated with the partial solutions found.
 |The final solution: evaluation shows a high probability for it to be correct.
 |Final solution shown in the GUI '''Top solution''' tab with possible further steps.
 |}
 == Lysozyme ==

@@ Line 103: / Line 103: @@
 === Input ===
-{|
+{|class="wikitable"
-|[[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]]]
+|[[File:Lyso-basic-options_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-basic-options.png|centre]]
-||[[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]]]
+||[[File:Lyso-composition_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-composition.png|centre]]
-||[[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]]]
+||[[File:Lyso-homology-searches_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-homology-searches.png|centre]]
 |}
 ;Running from the command line
@@ Line 132: / Line 136: @@
 === Output ===
-{|
+{|class="wikitable"
-|[[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]]]
+|[[File:Lyso-fetch-1lsg_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-fetch-1lsg.png|centre]]
-||[[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]]]
+||[[File:Lyso-sculptor-1lsg_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-sculptor-1lsg.png|centre]]
-||[[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]]]
+||[[File:Lyso-finish_thumb.png|link=http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/Lysozyme-finish.png|centre]]
 |}

@@ Line 14: / Line 14: @@
 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.
 {|
-|[[File:Bb-basic-options_thumb.png|frame|center|text-bottom|The '''Basic options''' dialog]]
+|[[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]]]
 |}
 Next, we need to tell the program about the composition of the asymmetric unit and the available search models.
@@ Line 21: / Line 21: @@
 {|
-|[[File:Bb-beta-composition_thumb.png|frame|centre|text-bottom|The '''Basic info''' dialog of '''Component1''' (''beta'')]]
+|[[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]]]
-||[[File:Bb-beta-ensembles_thumb.png|frame|centre|text-bottom|The '''Ensembles''' dialog of '''Component1''' (''beta'')]]
+||[[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]]]
 |}
 Then, a new component is created for ''blip'' (using the '''Add component''' button on the '''Basic info''' tab). This is filled out accordingly.
 {|
-|[[File:Bb-blip-composition_thumb.png|frame|centre|text-bottom|The '''Basic info''' dialog of '''Component2''' (''blip'')]]
+|[[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]]]
-||[[File:Bb-blip-ensembles_thumb.png|frame|centre|text-bottom|The '''Ensembles''' dialog of '''Component2''' (''blip'')]]
+||[[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]]]
 |}
 The job is ready to run!
@@ Line 77: / Line 77: @@
 The GUI displays the program output in the logfile window. First, the program starts searching in both possible space groups.
-{|[[File:Bb-log-first-round-start_thumb.png|frame|centre|text-bottom|Initially, search starts in both P3₁21 and P3₂21]]
+{|[[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]]]
-||[[File:Bb-log-space-group-evaluation_thumb.png|frame|centre|text-bottom|After finding the first component, the search in P3₁21 is dropped...]]
+||[[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]]]
-||[[File:Bb-log-second-round-start_thumb.png|frame|centre|text-bottom|...and only P3₂21 is propagated with the partial solutions found.]]
+||[[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]]]
-||[[File:Bb-log-final_thumb.png|frame|centre|text-bottom|The final solution: evaluation shows a high probability for it to be correct.]]
+||[[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]]]
-||[[File:Bb-solutions_thumb.png|frame|centre|text-bottom|Final solution shown in the GUI '''Top solution''' tab with possible further steps.]]
+||[[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]]]
 |}
 == Lysozyme ==