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: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortables.html#byelement> 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: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003683.html> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003689.html> 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 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?