pymol-users

[PyMOL] mesh question

[Soisson, S. M. <ste...@me...>]

Hi everyone-

I have two interacting monomers, and have selected the contacting resides
between them and drawn a solid surface around these selected residues on one
monomer.  This worked fine and I had no problem.

I would now like to draw a mesh surface around the remaining residues in the
monomer, that is, everything but the contacting residues.  No matter what
selection scheme I try to use, the mesh is always drawn around the entire
molecule.  

For instance:

select contacts=(byres monA and (monB around 4))
show surface, contacts

show mesh, (monA and (!contacts)) ****mesh is still drawn around whole
molecule

However, the following command does work to color just the mesh surface that
is not in contact with the other monomer:

color grey70, (monA and (!contacts))

which leads me to believe that my syntax is correct for the selection.

What am I missing?  Is there a way to just show the mesh over a certain
portion of a molecule?

Many thanks in advance-

Steve

----------------------------------------------------------------------------
--
Stephen M. Soisson, Ph.D.
Senior Research Biochemist
X-ray Crystallography / Dept. of Medicinal Chemistry
Merck Research Laboratories
P.O. Box 2000, RY50-105
Rahway, NJ  07065
Phone: 	(732) 594-4349
Fax:	(732) 594-5042
ste...@me...

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RE: [PyMOL] mesh question

[Warren L. D. <wa...@de...>]

Stephen,

	Sorry, the mesh representation right now is limited to rendering
a Cartesian box.  The selection controls the size of the box, but all
atoms within the box are currently always shown.  I will look into
changing this so that the mesh performs more like the other
representations.

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users- 
> ad...@li...] On Behalf Of Soisson, Stephen Michael
> Sent: Friday, July 18, 2003 3:27 AM
> To: 'pym...@li...'
> Subject: [PyMOL] mesh question
> 
> Hi everyone-
> 
> I have two interacting monomers, and have selected the contacting 
> resides between them and drawn a solid surface around these selected 
> residues on one monomer.  This worked fine and I had no problem.
> 
> I would now like to draw a mesh surface around the remaining residues 
> in the monomer, that is, everything but the contacting residues.  No 
> matter what selection scheme I try to use, the mesh is always drawn 
> around the entire molecule.
> 
> For instance:
> 
> select contacts=(byres monA and (monB around 4))
> show surface, contacts
> 
> show mesh, (monA and (!contacts)) ****mesh is still drawn around whole

> molecule
> 
> However, the following command does work to color just the mesh 
> surface that is not in contact with the other monomer:
> 
> color grey70, (monA and (!contacts))
> 
> which leads me to believe that my syntax is correct for the selection.
> 
> What am I missing?  Is there a way to just show the mesh over a 
> certain portion of a molecule?
> 
> Many thanks in advance-
> 
> Steve
> 
> ----------------------------------------------------------------------
> ----
> --
> --
> Stephen M. Soisson, Ph.D.
> Senior Research Biochemist
> X-ray Crystallography / Dept. of Medicinal Chemistry
> Merck Research Laboratories
> P.O. Box 2000, RY50-105
> Rahway, NJ  07065
> Phone: 	(732) 594-4349
> Fax:	(732) 594-5042
> ste...@me...
> 
> ----------------------------------------------------------------------
> ----
> ----
> 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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