Have you tried the "select resi" function? This allows you to specify the identification numbers of the amino-acids you want to select (and color). Have a look here for the complete description: http://pymol.sourceforge.net/newman/user/S0220commands.html
Regards, Grégori Gerebtzoff Division of Biophysical Chemistry Biozentrum, University of Basel Klingelbergstrasse 70 CH-4056 Basel / Switzerland
