[Chimera-users] output data from findclash

Elaine Meng meng at cgl.ucsf.edu
Fri May 7 15:21:59 PDT 2010

Hi Sunghoon,
The "findclash" command has keyword options to save info to a file  
("saveFile") and/or the Reply Log ("log").  If you only care about how  
many clashes there are and not the details, there is another keyword  
("summary") to send the count to the status line and Reply Log.  There  
are also keywords to change cutoff values if you want to make clash  
detection more or less permissive.


(or you can see that manual page using the command "help findclash" in  

By the way, if you use the "swapaa" command with default settings, it  
will automatically choose the rotamer with the fewest clashes.

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 7, 2010, at 3:09 PM, Kim, Sunghoon wrote:

> I'm trying to see clashes of a specific sidechain with its rotating  
> chi angles using 'findclash' command in python script.
> At this point, because I 'm just looking for a set of rotamers that  
> doesn't have any contacts or clashes, I just want to see the number  
> of contacts from a set of specific rotameric states, rather than a  
> detailed information. But I don't know how to print 'the number of  
> contacts' together with its corresponding chi angles. Is there any  
> way to write a output file from findclash calculation? Or can I  
> modify reply log as I want ?
>  Thanks,
> Sunghoon

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