User:Wayne Decatur/3kg2 Morph Methods

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Revision as of 16:52, 10 July 2010

First split all chains A, B, C, and D into single files and then used PyMol to change all chains to A for chains:
 
for example:
<source lang="python"> alter (chain B),chain='A' sort </source>

Used Beta server - mainly because it allows turning off fitting so I can show relationship of identical conformations, left fitting on for showing difference between chain A and chain B.

Next I was trying to get the subunit A to B morph to load already close to the familiar arrangement, so I tried in PyMol to orient it like I wanted it and then save all states (just fyi...found I could show all states at same time on screen with 'set all_states,1' from - PyMol reference card). From http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg02004.html found this series of commands (ENTERED ONE LINE AT A TIME) helped make a file with all models from PyMOL:
 
<source lang="python"> split_states 3kg2atob delete 3kg2atob alter all, segi = model[-4:] rewind save test.pdb, all </source>

However, this didn't save the orientation I had moved it to at the start. Seems I could use get_view and set_view commands to get back to what I wanted after reload but I need it to open in Jmol the way I wanted so that doesn't help. A little more searching turned up on the Modeling and Editing Structures page of the PyMol Wiki that I could save with transformed coordinates using a simple Python script:
<source lang="python">

1. Adds the command save_transformed
2. Usage: save_transformed object, file

def save_transformed(object,file):

   m = cmd.get_view(0)
   ttt = [m[0], m[1], m[2], 0.0,
          m[3], m[4], m[5], 0.0,
          m[6], m[7], m[8], 0.0,
          0.0,   0.0,  0.0, 1.0]
   cmd.transform_object(object,ttt)
   cmd.save(file,object)

cmd.extend('save_transformed',save_transformed) </source>