[Chimera-users] surfnet - separating clefts from cavities

Irene Newhouse einew at hotmail.com
Fri Aug 6 13:18:18 PDT 2010

I've been random-walking my way with surfnet, starting from the stand-alone version. I haven't been able to get the output file I need for displaying via RasMol, & while I was googling for cures to that, I discovered the surfnet plugin to Chimera, hurray. I have a protein with several internal cavities, plus many more surface clefts. Has someone worked out an efficient way to display only the internal cavities?  From my previous mucking about with the stand-alone, I already had a 'cavity atoms' pdb-format file which I loaded as model 1 & used that. However, generating the cavity atoms file involved considerable work by hand. At the moment, I can picture splitting the surfaces [using directions in the chimera user archive] & deleting all the surface ones. This is also a fair amount of manual labor - 50 blobs are generated & only 9 are internal. I have other proteins in this family to analyze, & they're probably similar.
Thanks for any advice!
Irene Newhouse 		 	   		  
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