I use this a lot - I simply duplicate the object and show one object as sticks in the desired color, and the other as spheres in other colors. The size of the spheres can be controlled with 
 
set sphere_scale, 0.3, myobject  
 
where 0.3 is the scaling relative to the default van der Waals radii.
 
 
cheers
 
Esben
 
 
 
 
 -----Original Message-----
From: pymol-users-admin@lists.sourceforge.net [mailto:pymol-users-admin@lists.sourceforge.net] On Behalf Of Tim Mack
Sent: 21. maj 2006 18:55
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Atom Color

Hello,

Is it possible, with PyMol,  to depict the atoms within a residue as a sphere of one color and the bonds as sticks of a different color? I want, for example, to color only the spheres black and the region between the spheres gray. I realize that this is not an accurate representation of the electronic environment of an atom but I would like to see how it looks.

Tim