NMA Coordinate Perturbation using CCP4i - Revision history

Airlie: /* Glutamine Binding Protein */

2013-07-22T13:26:22Z

‎Glutamine Binding Protein

Airlie: /* Glutamine Binding Protein */

2013-07-22T13:24:25Z

‎Glutamine Binding Protein

Airlie: Created page with '===Glutamine Binding Protein=== Data for this tutorial are found [http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials here] Coordinates: 1GGG_A.pdb This tutorial demonstrate…'

2013-07-22T13:14:08Z

Created page with '===Glutamine Binding Protein=== Data for this tutorial are found [http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials here] Coordinates: 1GGG_A.pdb This tutorial demonstrate…'

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===Glutamine Binding Protein===

Data for this tutorial are found [http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials here]

Coordinates: 1GGG_A.pdb

This tutorial demonstrates SCEDS domain division using the CCP4 interface

# Start the ccp4 GUI by typing ccp4i at the command line.
# Make a new project called "phaser_tute" using the Directories&ProjectDir button on the RHS of the GUI.
#* Or use a previously defined "phaser_tute" ProjectDir
# Set the "Project" to "phaser_tute" and "uses directory" to the directory where the files for this tutorial are located, and make this the "Project for this session of the CCP4Interface". You will then be able to go directly to this directory in the GUI using the pull-down menu that appears before every file selection.
# Go to the Molecular Replacement module, in the yellow pull-down on the LHS of the GUI
# Open the Model Generation tab, then bring up the GUI for Phaser Model Generation (NMA).
# You can choose (near the top) whether to use SCEDS or Coordinate Perturbation. Select the default, SCEDS.
# All the yellow boxes need to be filled in.
#* It is also a good idea to fill in the TITLE.
# When you have entered all the information, run Phaser.
# Look at the logfile
#* What are the residues included in each of the 5 SCEDS domains produced?
#* Find the normal modes used for the perturbation that generated the SCEDS domains.
#* Find the number of residues not included in any of the top 5 domains.
# Look at the pdb files containing the domains with Coot

[[Category:Tutorial]]

@@ Line 19: / Line 19: @@
 #* Use modes 7 and 8. Mode 5 selects the first 5 non-trivial normal modes (7 8 9 10 11). Replace the default "5" with "7". Use the "add mode for perturbation" button to enter Mode "8".
 # Changes from the defaults should be made in the Define Perturbations section
-#* Enter the RMS step size as 1.0A
+#* Enter the RMS step size as 0,5A and the maximum step size as 1.0A. This makes the perturbations more visible than the default of 0.2A RMS.
 # When you have entered all the information, run Phaser.
 # Look at the logfile.

@@ Line 13: / Line 13: @@
 # Go to the Molecular Replacement module, in the yellow pull-down on the LHS of the GUI
 # Open the Model Generation tab, then bring up the GUI for Phaser Model Generation (NMA).
-# You can choose (near the top) whether to use SCEDS or Coordinate Perturbation. Select the default, SCEDS.
+# You can choose (near the top) whether to use "SCEDS" or "Perturb Coordinates". Select the option "Perturb Coordinates"
 # All the yellow boxes need to be filled in.
 #* It is also a good idea to fill in the TITLE.
 # When you have entered all the information, run Phaser.
-# Look at the logfile
+# Look at the logfile.
-#* What are the residues included in each of the 5 SCEDS domains produced?
+#* How many pdb files were generated?
-#* Find the normal modes used for the perturbation that generated the SCEDS domains.
+# Look at the perturbed coordinates with Coot
 [[Category:Tutorial]]