[Chimera-users] Chimera surfaces

[Tom Goddard]

Hi Vijay,

   The MSMS molecular surface calculation (Actions / Surface / show) 
fails on some molecular models.  The mailing list describes some tricks 
that might make surface calculation work:

     
http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-January/004713.html

An alternative is to use a Gaussian surface instead of the MSMS solvent 
excluded surface, using the command (Favorites / Command-Line)

     molmap #0 3 gridSpacing 0.5

to make a 3 Angstrom surface for molecular model #0.  Then use the Color 
Zone dialog (menu Tools / Volume Data / Color Zone) to color the surface 
to match selected atoms within a specified distance from the atoms.  You 
can select all the atoms with menu Select / Select All or use command 
"select #0".  The Gaussian surface doesn't look much like a solvent 
excluded surface -- it puts a Gaussian at each atom position to compute 
a density map.  If you prefer the solvent excluded surface then look at 
the above mailing list message for suggestions.

     Tom


> Hi Tom, Greetings, Hope all is well
>
> I have a question about generating surfaces. When I load a simple PDB 
> and try to display surfaces... by selecting a molecule,
>
> Actions/Surface/Show
>
> I get the error Surface calculation failed, mscalc returned code 2
>
> I could always generate a surface using multiscale models in HIgher 
> order structure... But how can I can color the surface corresponding 
> to different region of the protein surface (corresponding to few 
> residues) in selected colors.
>
> Many thanks,
>
> Kind regards
> Vijay
>
> ========================================
> Vijay S. Reddy, Ph.D.
> Associate Professor
> Department of Molecular Biology, TPC6
> The Scripps Research Institute,
> 10550 North Torrey Pines Road,
> La Jolla, CA 92037
>
> ========================================
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