SCEDS using CCP4i - Revision history

Airlie: /* Glutamine Binding Protein */

2013-07-22T13:25:00Z

‎Glutamine Binding Protein

Airlie at 13:14, 22 July 2013

2013-07-22T13:14:39Z

Airlie at 12:36, 22 July 2013

2013-07-22T12:36:55Z

Airlie: Created page with '===Pyruvate Phosphate dikinase=== Data for this tutorial are found [http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials here] Coordinates: 2r82.pdb This tutorial demonstrate…'

2013-07-22T11:51:34Z

Created page with '===Pyruvate Phosphate dikinase=== Data for this tutorial are found [http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials here] Coordinates: 2r82.pdb This tutorial demonstrate…'

New page

===Pyruvate Phosphate dikinase===

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

Coordinates: 2r82.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. 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.
# In the section "Define parameters for SCEDS" set '''"Split the protein into 5 domains"''' from "Split the protein into 2 domains"
# 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 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 default "SCEDS".
 # All the yellow boxes need to be filled in.
 #* It is also a good idea to fill in the TITLE.

@@ Line 8: / Line 8: @@
 # 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. 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.
+# Make a new project called "phaser_tute" using the Directories&ProjectDir button on the RHS of the GUI.
 # 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).

@@ Line 1: / Line 1: @@
-===Pyruvate Phosphate dikinase===
+===Glutamine Binding Protein===
 Data for this tutorial are found [http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials here]
-  Coordinates: 2r82.pdb
+  Coordinates: 1GGG_A.pdb
 This tutorial demonstrates SCEDS domain division using the CCP4 interface
@@ Line 14: / Line 14: @@
 # 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