[Chimera-users] molecular surface isolated to chain

[Elaine Meng]

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.
<http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html>

One way is to use the "split" command to put each chain in a separate model.
<http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/split.html>

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.
<http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/msms.html>

For example, commands:

~surf
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
-----
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