User:Wayne Decatur/3kg2 Morph Methods

From Proteopedia

Revision as of 17:46, 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:

alter (chain B),chain='A'
sort

Used Beta server - mainly because it allows turning off fitting so I can show relationship (symmetry operations until the SYMOP functions within Jmol work within Proteopedia when newer version added) 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 - 'set all_states,0' turns it back to one frame only shown). 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:
 

split_states 3kg2atob 
delete 3kg2atob 
alter all, segi = model[-4:] 
rewind 
save test.pdb, all 

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:

# Adds the command save_transformed
# 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)

And so I again loaded the 3kg2 a to b morph (assigned secondary structure so cartoon look matched what I was used to looking at) and oriented like I wanted, then split them all and deleted original using commands above up until 'rewind' command, then ran the script I had saved on my drive, and then typed 'save_transformed all, test.pdb'