From: Jason V. <jas...@sc...> - 2010-12-04 03:25:37
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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 <te...@gm...> 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |