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
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
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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participants (3)
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Elaine Meng -
Eric Pettersen -
Kim, Sunghoon