[Chimera-users] Surface rendering

Tom Goddard goddard at sonic.net
Fri Jul 6 09:41:24 PDT 2012

Hi George,

   You might want to use the "molmap" command to create a Gaussian 
surface instead of a solvent excluded surface.  For example if 
_clusters.pdb is model #2 and you want a 5 Angstrom resolution surface use:

     molmap #2 5

This never fails.  It sums a Gaussian centered at each atom and computes 
a contour surface.


> Hi everybody,
> I'm using SiteComp to detect differences in binding affinities between two similar structures. The _clusters.pdb file produced by SiteComp is a standard PDB file in which the grid points corresponding to the difference clusters are represented by hydrogen atoms. They can be treated as any molecule in Chimera.
> Usually I find it useful to represent them as a mesh surface. Usually, I load in Chimera the protein.pdb, the ligand.pdb and the _clusters.pdb. After this, I select the _clusters.pdb and show it as mesh or solid using Actions-> Surface. In some cases, I fail to render the surface, or to be precise only one part of the clusters is rendered.
> I understand that this is a frequent problem with this type of discontinuous pdb. I'm attaching one such file and I would be grateful for any help
> Best regards
> George
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