[Chimera-users] Selection of a CASTp/Surfnet cavity from command line

Elaine Meng meng at cgl.ucsf.edu
Fri Mar 4 09:30:48 PST 2016


Hi,
Sorry, there is no way to select the sets of atoms lining the individual pockets from the command line.   For CASTp, each pocket is defined by a set of atoms, but you would click into the Chimera dialog on the row for that pocket to select that set of atoms.  For SURFNET, as far as I know it does not keep record of which atoms were next to which “blob,” so it is even less likely.

However, for CASTp you already have all the information about which atoms go with which pocket, in the files from CASTp.   So the direct approach is to simply look in those files, leaving Chimera out of the process.  It depends where your “Fetch” directory is, but on my mac, the CASTp fetch files go into ~/Downloads/Chimera/CASTp/

As mentioned briefly in the Chimera-CASTp documentation
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/castp.html>
the files have filename suffixes .poc, .pocInfo, .mouth, and .mouthInfo

… just looking at the files, I can guess that the poc file lists the pockets and their summary information, and that the pocInfo file is like a PDB file except it has some different columns at the end, and the next-to-the-last column appears to be the pocket ID number.  We did not create this format, I just figured it out by looking at the text of the file.  For example, this single line from a pocInfo file says that atom O in ASP residue 2 is next to pocket 13:

ATOM      9  O   ASP     2      49.292  16.362  24.807  1.00 47.01  13  POC 

Fetch directory location is set in the Preferences (open from Favorites menu), category: Fetch
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Fetch>

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 Mar 3, 2016, at 7:09 PM, Felipe Vasquez <anfelvas at gmail.com> wrote:

> Hi,
> I was trying to automatize the selection of those residues members of a certain cavity predicted by CASTp, starting from the opening of the file to the writing of the residues list (all from command line). However, I do not know how to select a cavity with an specific ID so I have not to do it manually. There is a strategy to achieve this goal from the command line? How could I do the same for Surfnet cavities?
> Thanks in advance for your help.
> Best regards,




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