Joe,
Currently with PyMOL, you are selecting are atoms, not points on
the surface. Thus, you may need to increase the distance by 1-2 A or so
to get what you want. It's also possible that something else is going
on.
I would not expect to see whole at the points of contact, but
between them, where the contacts aren't so close. If the above advice
doesn't help, then perhaps you could send me an example PNG file which
illustrates the problem as an attachment?
Cheers,
Warren
(PS. Selection of individual surface points will likely come in a
future version...)
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----Original Message-----
> From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> ad...@lists.sourceforge.net] On Behalf Of Becker, Joseph W
> Sent: Friday, July 11, 2003 10:45 AM
> To: PyMOL (E-mail)
> Subject: [PyMOL] Interaction surfaces
>
> 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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