[PyMOL] Interaction surfaces

[Becker, J. W <jos...@me...>]

I have a problem representing the contact surface between, e.g., a protein
and its ligand.  The surface is displayed, but it is full of holes,
apparently at the points of contact.  The script:

load protein.pdb, protein
load ligand.pdb, ligand
hide everything
show surface, (protein and (ligand around 4))

gives something like one wants, but full of holes.

With that object displayed, if one says "show surface, protein" one gets the
full surface, without the holes.  Any ideas on how to get the *partial*
surface *without* the holes?

Joe Becker
Merck Research Labs

P.S.

load protein.pdb, protein
load ligand.pdb, ligand
hide everything
create junk, (protein and (ligand around 4))
show surface, junk

gives a similar (holey) result





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