Hi Daniel, If you don't HAVE to use Pymol, something like fPocket, HOLE or PocketDepth from this list might do what you want:
http://www.vls3d.com/links/bioinformatics/binding-pockets You might find this list interesting too: http://www.vls3d.com/links/bioinformatics/peptides-antibodies-epitopes cheers, Doug Quoting Andreas Warnecke <4ndreas.warne...@gmail.com> on Wed, 20 Jul 2016 00:57:39 +0200: > I haven't used it before, but I there is a PyMOL plugin called KVfinder > that detects cavities. Potentially this offers an approach for you. > On Jul 20, 2016 12:05 AM, "Daniel James" <daniel.jjam...@gmail.com> wrote: > >> Hi all, >> >> I haven't used this list before but can't find an answer to my question >> elsewhere. I am selecting the antibody binding site automatically to >> calculate the surface area of the binding sites. >> >> However, some of the binding sites have holes/cavities in the surface - I >> would like to be able to detect if a surface has a hole in it on PyMol (to >> make a note that it needs to be looked at manually). >> >> I create an object of the antigen binding site, show surface and then use >> get_area to get SASA. >> >> Any help will be appreciated. >> >> Thanks, >> Daniel >> >> >> ------------------------------------------------------------------------------ >> What NetFlow Analyzer can do for you? Monitors network bandwidth and >> traffic >> patterns at an interface-level. Reveals which users, apps, and protocols >> are >> consuming the most bandwidth. Provides multi-vendor support for NetFlow, >> J-Flow, sFlow and other flows. Make informed decisions using capacity >> planning >> reports.http://sdm.link/zohodev2dev >> _______________________________________________ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> > _________________________________________________________________ Dr. Douglas R. Houston Senior Lecturer in Computational Biochemistry Institute of Quantitative Biology, Biochemistry and Biotechnology Room 3.23, Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ------------------------------------------------------------------------------ What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
