Fred, I think Lieven answered the second part, so I'll answer the first:
PyMOL's surfaces are discrete approximations of the solvent contact surface (the surface of waters in contact with the protein at all possible positions). I generally think of the "solvent accessible surface" as being the surface carved out by the center of those same waters. PyMOL doesn't currently provide a solid representation of this surface, but you can show it using dots: set dot_solvent,1 set dot_density,3 show dots In theory, mesh_solvent should do the same thing for mesh surfaces, but I just found a major bug in that code -- so don't use "mesh_solvent" until after the next release... Cheers, Warren > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Fred Berkovitch > Sent: Saturday, March 13, 2004 9:28 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Question about surface calculation > > Hi All, > > When I type "show surface", how is that surface calculated? > Is it a true solvent-accessible surface? Does PyMol take > into account heteroatoms (e.g., a metal or an Fe-S cluster) > in the calculation? > > -Fred > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IBM Linux Tutorials Free > Linux tutorial presented by Daniel Robbins, President and CEO > of GenToo technologies. Learn everything from fundamentals to > system > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
