Hi Anna, 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 sufficient.
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"):
continue
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
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@cgl.ucsf.eduhttp://www.cgl.ucsf.edu/mailman/listinfo/chimera-users