This is probably not the slickest way to do this but generally I think it is one surface one object, so in a simple case of a peptide bound to a protein, I would select the peptide chain (right click in the viewer) and extract that selection to a new object and then you can generate two separate surfaces.
Hope this helps
From: Robert Hanson [mailto:hansonr@...]
Sent: Friday, 31 May 2013 6:26 a.m.
Subject: [PyMOL] surfaces involving more than one object
PyMOL questions about surfaces:
Simple enough to create a surface for one object. What about for only a portion of the object? How to do each of these?
-- closed surface ignoring a selected set of atoms
-- open surface not ignoring any atoms, but also not displaying their part
Is the rule, "One surface, one object"? That is, all atoms involved in a surface must originate from a single object?
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900