[Chimera-users] chimera and hydrophobic potentials

Thomas Goddard goddard at cgl.ucsf.edu
Mon Apr 12 17:07:15 PDT 2004

Hi Miguel,

  If GRID computes the hydrophobic potential on a surface, it seems like
a bad strategy to save it in a volume format.  If you interpolate onto
a slightly different surface, you will get values interpolated with zeros
in the volume because the hydrophobicity wasn't computed at most grid
vertices.  It seems it would be better to render the hydrophobicity values
with exactly the GRID surface.  Can GRID output the triangulated surface
with hydrophobicity values?

  I looked at the MSMS library.  It does not look like it provides a
triangulated version of the solvent accessible service needed by Chimera.
It can give you the surface area contributed by each atom to the solvent
accessible surface.


> Date: Sun, 11 Apr 2004 22:39:40 +0100
> From: Miguel Ortiz <mol at ysbl.york.ac.uk>
> To: Thomas Goddard <goddard at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] chimera and hydrophobic potentials
> Dear Tom,
> I've tested your cns2delphi script and, as expected, it works wonderful-
> ly. The problem with colouring the surface using these maps actually
> comes from the fact that for the hydrophobic probe, grid only calculates
> the potential on what it's called the "solvent accessible surface" and
> not on the whole volume (as delphi does for electrostatics and grid for
> other probes). Being this the case, the best solution would be to 
> render in chimera this surface (at present, msms renders the "solvent
> excluded surface" defined as you said in your email)
> I will try to find out how msms renders its surfaces, because the only
> difference between "solvent accessible " and "solvent excluded" is that
> the first is the "surface" defined by the center of the probe, while
> the second (msms one) is the contact surface between the surface of the
> probe and that of the protein (as defined by the Van der Waals radii of 
> its atoms). And it seems to me that it shouldn't be difficult to convert 
> from one to the other. Or perhaps I'm wrong and it's more tricky...
> Thank you again for all your help. It has been not only useful but 
> also instructive.
> Best regards,
> Miguel

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