[Chimera-users] output data from findclash
pett at cgl.ucsf.edu
Mon May 10 16:27:53 PDT 2010
The other small tidbit to know is that the "echo" command will put
any text you want into the reply log. So you could do something like:
echo Setting residue 14 chi 1 to 25
setattr r chi1 25 :14.a
findclash <your options>
UCSF Computer Graphics Lab
On May 7, 2010, at 3:21 PM, Elaine Meng wrote:
> 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 Chimera)
> 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 ?
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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