[chimera-dev] python for finding clashes

Dr. Jean-Didier Maréchal jeandidier.marechal at gmail.com
Tue Oct 28 10:09:33 PDT 2008

Hi Elaine,

Thanks a lot for the input. The thing is that I'd like to store the value in
an array if it is possible. 


-----Mensaje original-----
De: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Enviado el: martes, 28 de octubre de 2008 17:29
Para: JeanDidier.Marechal at uab.es
CC: chimera-dev at cgl.ucsf.edu
Asunto: Re: [chimera-dev] python for finding clashes

Hi JD,
Many (all?) options are available from the Chimera command "findclash"  


for example "log true" to send information to the Reply Log or  
"saveFile pathname" to write it to a text file with location/name  

Is that what you needed, or does the information need to be stored in  
an array or variable?
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 28, 2008, at 7:15 AM, Jean Didier Pie Marechal wrote:

> Hi everyone,
> I am writing a script for which I need the number of clashes for a  
> given selection for continuing.
> My first thought was to simply run in my script:
> runCommand("findclash selection ignoreIntraRes false")
> after having selected the region I was interested in.
> However, I realize that I come to the recurrent problem: having the  
> information I am interested in printed in the reply log. I don't  
> know how to have the info passed into an array or any kind of  
> variable in the  python environment. Could you tell me how to do so  
> please?
> On the other side, I would be pleased if you could tell me what is  
> the correct arguments I have to pass and syntax I have to use for  
> the functions  detectClash and/or cmdDetectClash (which I guess is  
> the basis of the same findclash).
> All the best,
> JD

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