By default, current versions of PyMOL excludes PDB HETATMs from surface
calculations. The idea behind this is to enable you to easily surface
the protein away from solvent and ligands.  To change this:

set surface_mode=1

which will cause all atoms to be included.

Cheers,
Warren

PS. surface_mode=2 will exclude all atoms but hydrogens.

-- 
mailto:war...@sunesis.com 
Warren L. DeLano, Ph.D. 
Informatics Manager 
Sunesis Pharmaceuticals, Inc. 
341 Oyster Point Blvd. 
S. San Francisco, CA 94080 
(650)-266-3606  FAX:(650)-266-3501 

From: Sutton, Roger B.

Warren,
I'm trying to surface a ligand independently from the protein in which
it's embedded to show the binding pocket more clearly.
For some reason, pymol will not draw a surface around this particular
molecule.  It will surface amino acids, but not this retinal.
Is there an obvious reason for this?  If I type pymol> show surface,
(resn ret).. nothing happens... 
If I abstract the ligand into a separate PDB file, it still doesn't do
anything...
I'm using v0.78
I'll include the pdb file in question.
Bryan

Reply via email to