[Chimera-users] FindClashes: iterative input feeding

Eric Pettersen pett at cgl.ucsf.edu
Mon Jul 27 13:48:47 PDT 2009

Hi Anna,
	One possibility if you know shell scripting is to use PROCHECK (http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html 
) on your PDB files.
	Otherwise it depends on whether you know Python scripting or a  
programming language of any kind.  If you know a non-Python  
programming language you would use that language to generate a script  
that does the following for your 10000 files:

open blah1.pdb
findclash :LIG saveFile out1.txt
close all
...repeat for file 2, 3, etc.

where LIG is the residue type of your ligand.  If the residue type  
varies for each file then using 'ligand' instead of ':LIG' might be  
	If you know Python you can do it somewhat more directly with a script  
with an embedded loop, something along the lines of:

import os
from chimera import runCommand as rc
rc("cd /dir_with_pdb_files")
for fname in os.listdir("."):
	if not fname.endswith(".pdb"):
	rc("open " + fname)
	rc("findclash :LIG saveFile " + fname[:-4] + ".out")
	rc("close all")

which basically does the same functions as the first script file but  
uses a loop instead of writing out all 10000 iterations explicitly.
	Let me know if you have more questions.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Jul 27, 2009, at 1:30 AM, Anna Feldman-Salit wrote:

> Dear Users and Developers,
> I'm interested in using a FindClashes option for a large set of files.
> It is about finding clashes between a small ligand and enzyme which  
> are
> found at different conformational stages (more than 10000 each).
> How can one do it iteratively? I understand this is a scripting or  
> could
> it be that such an application already exists?
> Thanks in advance.
> Regards,
> Anna
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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