Dear Roger,
I probably have a very simple solution for you. First create two
objects of your protein with a distinct names. Then show a
non-transparent surface for one of the objects. Hide the surface for
the residues you'd like to see under the transparent surface with a
comand:
"hide surface, (resi ......)"
Show the transparent surface for the second object of your protein.
This way you'll have the transparent surface under the solid one, and a
hole in a solid surface for the residues under the transparency.
Good luck,
Boris.
