RE: [PyMOL] Surface triangulation of isopotential surfaces

[Warren DeLano]

Nuno,

For a couple of reasons, I curently believe that electrostatic calculations 
based on point charge models are not valid near or within the protein surface 
-- you need to be at least one atom radius beyond the molecular envelope in 
order to draw physically meaningful interpretations.  

Why? 

1) Real atoms aren't point charges.

2) Atomic point charges are parameterized by fitting electrostatic potentials 
over a series of shells outside the molecular envelope.

In other words, despite the fact that this is commonly done, I question whether 
or not it is valid to display or interpret electrostatic potentials directly at 
the protein vdw surface.  That is why I now encourage the use of space-filling 
representations and solvent accessible surfaces, such as dots with dot_solvent 
= 1, when viewing electrostatic potentials.  

PyMOL could probably do more to make this easy, such as projecting the ESP on 
the solvent accessible surface back onto a molecular surfaces...

Do others agree with this analysis, or am I just a lone heretic?

Cheers,
Wraren

> -----Original Message-----
> From: pymol-users-ad...@lists.sourceforge.net 
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
> Nuno Micaelo
> Sent: Wednesday, February 04, 2004 1:49 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Surface triangulation of isopotential surfaces
> 
> 
> How do i improve the surface triangulation of isopotential 
> surfaces? The isosurface triangulation near the protein is 
> very poor and is independent of the grid size chosen in MEAD.
> 
> Thanks for your attention.
> 
> -- 
> 
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>       Nuno Miguel da Silva Micaelo
> 
> Instituto de Tecnologia Química e Biológica
> 
>    ITQB - Protein Modeling Group
> 
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