[Chimera-users] Show molecular surface for one chain only

Elaine Meng meng at cgl.ucsf.edu
Mon Oct 22 09:10:40 PDT 2012

Hi Darrell!
By default, a model's biopolymer chains are grouped together for purposes of surfacing, but you can either define your own groups with "surfcat,"  or use "split" to make the chains separate models.

(a) "surfcat" example:

surfcat myprot :.a&protein
surfcat mypep :.b&protein
surface myprot
surface mypep

The "&protein" part intersects the chain ID with protein... there might be waters with the same chain IDs, but you wouldn't want them enclosed in the surfaces.

(b) "split" example:

split #0

... if #0 has chains A and B, that would generate model #0.1 containing A and #0.2 containing B. Splitting may be easier if there are many chains, and in this case less error-prone since Chimera will still apply the usual rules to separate peptides from water, ions, ligands etc.

Automatic surface categories:

Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 22, 2012, at 8:23 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:

> Hi Chimera folks,
> I have a peptide bound to a protein. They are two separate chains in single PDB. I want to show the molecular surface for the protein, but not the peptide (to see the surface where the peptide binds to the protein). This is easy (the default, actually) for small molecules. But when I select the chain of the protein and display its surface, the surface is "broken" around the peptide and I cannot see what I want. The rest of the surface is OK, but in the area of interest, I cannot see the surface.
> I tried the "Intersurf" command and it sort of works, but I want an MSMS molecular surface of the protein with the peptide sitting in it. Is there some trick for this other than separating the peptide from the protein and putting it into a separate model?
> Thanks,
> Darrell

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