Sarma,
I am trying to create a surface representation of a protein with mutations that abolish activity in one color (say yellow) and the ones that don't change activity in another (say green). The rest of the residues colored gray.
I can change the color of the surface to gray or a rainbow gradient using the options but can't find a way to specify the residues that need to be colored differently in a surface representation.

One easy way to go about coloring residues differently based on some property like a residue number is to create atom selections for the various sets of residues in which you're interested and then color those selections using the PyMOL menu commands... Look in the "Command Syntax and Atom Selections" section of the PyMOL User's Manual (http://pymol.sourceforge.net/newman/user/toc.html) in order to learn about atom selections.  You can enter a command like "select mymuts, all and resi 23,32,45" to create a selection consisting of all atoms in residues 23, 32, and 45, and then something like "color green, mymuts" to color these residues green.  So something like this might be what you want:
select mymut, (resi 23,32,45)
select mywt, (resi 1,2,3,4,5)
color grey, all
color yellow, mymut
color green, mywt
If you don't foresee needing the atom selections for anything else, you could just combine the atom selection with the color command ("color yellow, (resi 23,32,45)"), but it's most often useful to create an independent atom selection. 

If you want to color even more precisely by a parameter such as the strength of the mutant's inactivity -- so multiple values instead of just 0/1 -- then you could try looking at the Sequence Conservation example on my PyMOL page (this is documented at http://mccammon.ucsd.edu/~cmura/PyMOL for now; I'll eventually migrate this stuff into PyMolWiki and post updates of new stuff at http://www.pymolwiki.org/index.php/Cmura).

Good luck,
Cameron


=== pymol-users-request@lists.sourceforge.net wrote (on 04/03/2005 08:19 PM): ===
Today's Topics:

   1. surface representation showing mutations (Ganapathy Sarma)
  

Subject:
[PyMOL] surface representation showing mutations
From:
Ganapathy Sarma <gnsarma@gmail.com>
Date:
Sun, 03 Apr 2005 18:13:49 -0700
To:
pymol-users@lists.sourceforge.net

Hello PYMOLers,

I am a very new entry to the world of Pymol after seeing the program in action at a recent conference.

I am trying to create a surface representation of a protein with mutations that abolish activity in one color (say yellow) and the ones that don't change activity in another (say green). The rest of the residues colored gray.

I can change the color of the surface to gray or a rainbow gradient using the options but can't find a way to specify the residues that need to be colored differently in a surface representation.

Any help is appreciated.

Thanks,
Sarma