Paul, PyMOL generally shows all sides of an exposed atom, but perhaps you could load both the GOLD output and the original structure.
You could then only show the surface on the atoms in the original structure with corresponding atoms in the gold output as follows: load orig.pdb load gold.pdb then show surface, orig in gold or show surface, orig like gold That might produce something close to what you want. Note that: "in" matches chains, segments, residue names, residue ids, and atom names. "like" just matches residue ids and atom names. You can use alter all, segi='' alter all, chain='' to clear out the segment and/or chain IDs before using "in" to selectively reduce its stringency. 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 > Paul Wilhelm Elsinghorst > Sent: Friday, January 20, 2006 11:33 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Surface of cavity > > Hi, > > > a little question regarding cavity surfaces :-) > > > I have a set of active atoms (GOLD output) that surround a > cavity. Now I want to dipslay the surface only for the cavity > wall, not on the outside. > > > Any ideas? > > > Paul >
