[Chimera-users] FindClashes: iterative input feeding
pett at cgl.ucsf.edu
Mon Jul 27 13:52:47 PDT 2009
I guess I should have mentioned that you would run the Python script
by opening it in Chimera, either with File..Open or with the "open"
command. The script should have a ".py" suffix in order for Chimera
to recognize it as a Python script.
On Jul 27, 2009, at 1:48 PM, Eric Pettersen wrote:
> 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
>> It is about finding clashes between a small ligand and enzyme which
>> found at different conformational stages (more than 10000 each).
>> How can one do it iteratively? I understand this is a scripting or
>> it be that such an application already exists?
>> Thanks in advance.
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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