[Chimera-users] FindClashes: iterative input feeding
pett at cgl.ucsf.edu
Mon Jul 27 13:48:47 PDT 2009
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:
findclash :LIG saveFile out1.txt
...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:
from chimera import runCommand as rc
for fname in os.listdir("."):
if not fname.endswith(".pdb"):
rc("open " + fname)
rc("findclash :LIG saveFile " + fname[:-4] + ".out")
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.
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
> 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
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