[PyMOL] Interaction surfaces

[Becker, Joseph W]

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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RE: [PyMOL] Interaction surfaces

[Warren L. DeLano]

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
 
 
 
 
 


--
 
 Notice: This e-mail message, together with any attachments, contains
 information of Merck  Co., Inc. (Whitehouse Station, New Jersey,
 USA) that may be confidential, proprietary copyrighted and/or legally
 privileged, and is intended solely for the use of the individual or
entity
 named on this message. If you are not the intended recipient, and
 have received this message in error, please immediately return this by
 e-mail and then delete it.


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