Hi Andy,
There are lots of different ways to specify or select the atoms you  
want to color, far too many to list here, but here are a few ideas.

You can specify #model:residues.chain in commands, for example:

color violet red #0:355-486.A
   or even
color violet red #0:355-end.A

More details on command-line specification:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html

Color list:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortables.html>

Or, if you don't know what the numbers are, you can select the  
residues in the sequence window (Tools... Structure Analysis...  
Sequence) by dragging with the mouse, and then use the Actions...  
Color menu to color them.

Or, if it is just a few residues you want to color, you can Ctrl-click  
on an atom to select it, Shift-Ctrl-click on another atom to add it to  
the selection, press the keyboard up arrow key to "promote" the  
selection from atoms up to whole residues, and then use the Actions...  
Color menu.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng@cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                     http://www.cgl.ucsf.edu/home/meng/index.html



On Oct 6, 2008, at 3:09 PM, Anindito Sen wrote:

HI all

I was wondering how to color the c and n terminals of the crystal  

structure docked in the density map different.

Thanks

Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry  

and Molecular Genetics University of Virginia Box 800733  

Charlottesville, VA 22908

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