NMA Coordinate Perturbation using CCP4i

Glutamine Binding Protein

Data for this tutorial are found here

Coordinates: 1GGG_A.pdb

This tutorial demonstrates SCEDS domain division using the CCP4 interface

1. Start the ccp4 GUI by typing ccp4i at the command line.
2. 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
3. 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.
4. Go to the Molecular Replacement module, in the yellow pull-down on the LHS of the GUI
5. Open the Model Generation tab, then bring up the GUI for Phaser Model Generation (NMA).
6. You can choose (near the top) whether to use "SCEDS" or "Perturb Coordinates". Select the option "Perturb Coordinates"
7. All the yellow boxes need to be filled in.
   • It is also a good idea to fill in the TITLE.
8. The defaults are set for SCEDS. For coordinate perturbation the defaults need to be changed.
   • 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".
9. Changes from the defaults should be made in the Define Perturbations section
   • 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.
10. When you have entered all the information, run Phaser.
11. Look at the logfile.
    • How many pdb files were generated?
12. Look at the perturbed coordinates with Coot