LC, PyMOL's surfacing algorithm current only works well for standard atomic geometries...radii in the 1 - 3 A range, and solvent radii of 1-3 A. Perhaps you can simply scale the problem to fit within that range?
Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of co1 > Sent: Monday, June 06, 2005 3:26 AM > To: pymol-users > Subject: [PyMOL] surface with vdw > 6 > > > Hello, > I would like to represent the surface of a model made of > dummy C atoms, but they should have a van der Waals diameter > bigger than 6 A. When I increase their vdw above 5.9 (for > ex.: alter elem c, vdw=6; rebuild), the surface just disappear. > > Do I need to change some other parameters? > Is it -actually- impossible for pymol to calculate a surface > for a vdw > 6A? > > I would appreciate any help and advice. > Best regards. > LC > > > Accédez au courrier électronique de La Poste : www.laposte.net ; > 3615 LAPOSTENET (0,34€/mn) ; tél : 08 92 68 13 50 (0,34€/mn) > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: NEC IT Guy Games. How far > can you shotput > a projector? How fast can you ride your desk chair down the > office luge track? > If you want to score the big prize, get to know the little guy. > Play to win an NEC 61" plasma display: http://www.necitguy.com/?r > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
