RE: [PyMOL] Question about surface calculation

[Warren DeLano]

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
 
 
 
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Re: [PyMOL] Question about surface calculation

[Lieven Buts]

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