[Chimera-users] output data from findclash

[Eric Pettersen]

Hi Sunghoon,
	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>

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

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.
>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
>
> (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.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>
>
> I hope this helps,
> Elaine
> -----
> 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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