[Chimera-users] output data from findclash
meng at cgl.ucsf.edu
Fri May 7 15:21:59 PDT 2010
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 ?
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