[Chimera-users] color side chain only

Elaine Meng meng at cgl.ucsf.edu
Tue May 10 14:52:03 PDT 2011

Hi Ming!
If you are using the color command, you would include ",a" right after the color name, no spaces, to color the atoms but not ribbons, surfaces, labels, etc..  For example:

color hot pink,a :45.a,55.a,13.b

.... would color the atoms only of residues 45 and 55 in chain A and 13 in chain B

If you are using the Actions menu, you would open the Color Actions dialog (Actions... Color... all options...) and in the right-hand side set Coloring applies to "atoms/bonds" instead of "all of the above."  Clicking to choose a color will then color only the atoms/bonds of the selected residues.

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 May 10, 2011, at 12:18 PM, Zhou, Ming (NIH/NCI) [C] wrote:

> Hello, this is Ming Zhou at NCI-Frederick, Maryland. I am trying to use Chimera to make some ribbon structure figures. I am wondering how I can display only side chain (without backbone) for a specific residue.
> Usually, if I display the residue, select the residue at the Atom specifier and color it. The color would be partially on the ribbon structure too since the backbone of that residue is on the ribbon. How do I avoid coloring backbone, only color the side chain?
> Thank you very much.
> Ming

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