Hi Thomas, PyMOL can detect cavities and voids on its own. From the upper control window, select Settings > Surface > Cavities and Pockets and then show your object or selection as surface, which will show the cavities as surface, not the outer molecular surface.
If you need a properly vetted and published system then I recommend using one of the other suggested algorithms. Cheers, -- Jason On Fri, Dec 3, 2010 at 12:15 PM, Thomas Evangelidis <[email protected]> wrote: > Dear Pymol users, > > I want to display clearly the volume of a buried cavity inside my protein. > Does anybody know how to do this? I've tried CastP and Caver plugins > already, but they do not produce exactly the volume I want to display. I > would greatly appreciate any advice. > > thanks, > Tom > > ------------------------------------------------------------------------------ > Increase Visibility of Your 3D Game App & Earn a Chance To Win $500! > Tap into the largest installed PC base & get more eyes on your game by > optimizing for Intel(R) Graphics Technology. Get started today with the > Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. > http://p.sf.net/sfu/intelisp-dev2dev > _______________________________________________ > PyMOL-users mailing list ([email protected]) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/[email protected] > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) [email protected] (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ What happens now with your Lotus Notes apps - do you make another costly upgrade, or settle for being marooned without product support? Time to move off Lotus Notes and onto the cloud with Force.com, apps are easier to build, use, and manage than apps on traditional platforms. Sign up for the Lotus Notes Migration Kit to learn more. http://p.sf.net/sfu/salesforce-d2d _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
