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
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 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 Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu 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.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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. --Eric 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 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
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
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.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Anna Feldman-Salit -
Eric Pettersen