Hello, I would like to report an apparent bug in Pymol's surface rendering. I am using version 0.99rc1.
Pymol does not render a surface around SelenoMet residues. It leaves a large hole in the surface surrounding them. The residue is fully visible in this surface hole when turning on sticks with the surface. After mutating MSE to MET, the surface "hole" is filled in and the stick representation of the residue is now no longer visible (unless the surface is made transparent). Thanks, Eric