Hi Hena - 

You can type the following commands in the command line of the pymol graphics window, one at a time.

color red, ss h
color yellow, ss s
color white, ss l+''

If you don't mind the loops being green, you could also use the first preset under the Color menu for your object.

[C] > by ss > helix sheet loop (choose the colors you want)

Hope that helps,

Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Ave MSB 398
New York, NY 10016

On Jul 10, 2012, at 1:39 PM, Hena Dutta wrote:


Sorry, I forgot to mention that, I have only C-alpha coordinates of 60 chains in one pdb file.

I have 60 identical chains. Each chain is about 140 residues. Residues from 10-36 is helix and residues from 50-56 is beta sheet. I want to prepare a cartoon diagram displaying helix and sheet in red and yellow color respectively and the rest part(loop) in white. I need to do this for all 60 chains in diagram. Can someone help me? what commands I can use for this?
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