[Chimera-users] change of atom colors

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 27 09:29:45 PDT 2010

Hi Atila,
I'm guessing you are talking about the default colors when you first open one structure file.  In that case, the structure is  mostly all white (with shading it may look light gray) except non-carbon atoms are shown in element colors: red for oxygen, blue for nitrogen, etc.  If you opened a second structure, it would be mostly magenta, with non-carbon atoms shown in element colors, a third structure, mostly cyan, with non-carbon atoms shown in element colors, etc.

If you want to color all atoms including the carbons by element colors, one way is to use menu item "Actions... Color... byelement".  However, the default element color for carbon is dark gray, not green.

Here are the default element colors:

You could just change all carbons to green with these menu items:
Select... Chemistry... element... C
Actions... Color... atoms/bonds
Actions... Color... green

(then the following menu items just for cleanup)
Actions... Color... all of the above
Select... Clear Selection

or more efficiently, with this command:
color green,a C

To change your default element colors, see these previous messages:

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 Sep 27, 2010, at 7:18 AM, atila petrosian wrote:

> Hi chemera users
> I am beginner in chemira. I opened a pdb file containing protein by chimera, in my chimera both of carbon and hydrogen atoms have same color (light gray). I want to have carbon as green and hydrogen gray.how can I do that?

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