[Chimera-users] molecular surface isolated to chain

Elaine Meng meng at cgl.ucsf.edu
Wed Aug 24 11:58:42 PDT 2011

Hi Jeffrey,
You can definitely control this, there are a couple of ways.   By default, a model gets divided up into categories named solvent, ions, ligand, and main.  What you are seeing is the "main" surface that includes both protein and DNA.

One way is to use the "split" command to put each chain in a separate model.

The other way is to use "surfcat" to create your own categories with the desired content, then "surface" to show the molecular surface of the category.

For example, commands:

surfcat myprot protein
surfcat mydna nucleic acid
surf myprot
surf mydna

The commands take any kind of command-line specification, not just "protein" and "nucleic acid" like above.  For example,

surfcat achain :.a
(all of chain A)
surfcat achain :.a & ~ solvent
(all of chain A except solvent)

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

On Aug 24, 2011, at 11:47 AM, Jeffrey Kentner wrote:

> Hello, 
> I am trying to create a nice aesthetic model of a protein binding to DNA. When I show molecular surface, the program doesn't seem to be able to differentiate between the DNA chain and the protein chain. I either end up with a surface on the DNA which is not fully closed, or if I extend the surface via the 'surface zone' it simply begins to cover the protein as well... I have consulted the documentation and can not find any description of how one would isolate the molecular surface to a particular chain. Is this not possible in Chimera?
> Cheerio, 
> Jeffrey 

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