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.


Lieven Buts
Department of Ultrastructure
Vrije Universiteit Brussel

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