On Sunday 14 March 2004 06:27, Fred Berkovitch wrote: > 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?
As for the latter question, this is determined by the "surface_mode" setting. After "set surface_mode,0" (the default) heteroatoms are ignored and the surface is generated only for the protein atoms, leaving water molecules and ligands alone. After "set surface_mode,1", all atoms are included for surface generation. You can also create separate objects to generate exactly the surfaces you want. Cheers, -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel
