[Chimera-users] FindClashes: iterative input feeding

[Eric Pettersen]

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
>>
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>
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