On Tue, 13 Sep 2005, surendra negi wrote:
check this link!
http://www.csb.yale.edu/userguides/graphics/pymol/electro.html
That page is actually quite out of date. I emailed them about it a few
months ago, but didn't get a response.
You don't need to go through any of that hassle to use the APBS plugin
these days .. it comes included with PyMOL. Yay for open source! :)
-michael
--
www.umich.edu/~mlerner | _ |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan
it's a cheer-ocracy. | - against HTML email X | Biophysics
-Torrence, Bring It On| / \ | mler...@umich
Hope it wud help.
best sn
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Today's Topics:
1. Displaying an electrostatic potential on msms
(Anna Feldman-Salit)
2. Re: Displaying an electrostatic potential on
msms (Peter Adrian Meyer)
--__--__--
Message: 1
Date: Mon, 12 Sep 2005 11:25:39 +0200
From: Anna Feldman-Salit
<anna.feldman-sa...@eml-r.villa-bosch.de>
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Displaying an electrostatic
potential on msms
Dear All,
I have a 0.98 PyMol version with APBS and
Iso_Sliders plugins. However,
my aim is not just visualize isosurfaces of
electrostatic potential at
certain values, but to display/map it on molecular
surface.
Would you be so kind to share your knowledge with me
on this subject?
I'd appreciate any help or advice of yours!
Thanks,
Anna.
--__--__--
Message: 2
Date: Mon, 12 Sep 2005 12:03:54 -0400 (EDT)
Subject: Re: [PyMOL] Displaying an electrostatic
potential on msms
From: "Peter Adrian Meyer" <pa...@cornell.edu>
To: "Anna Feldman-Salit"
<anna.feldman-sa...@eml-r.villa-bosch.de>
Cc: pymol-users@lists.sourceforge.net
Hi Anna,
I generally run apbs seperately (due to difficulties
with Alphas), but use
the plugin to display with pymol. apbs will
produce two output files,
acc.dx and pot.dx. acc.dx is the electrostatic
potential mapped to the
solvent accessible surface; pot.dx is the
electrostatic potential over the
grid. What I generally do is to load acc.dx into
pymol, and they use the
plugin->apbs->display to show the surface (not sure
of the exact sequence;
pymol's doing a ray-tracing job for me at the moment
so I can't check).
Hope this helps...I've never tried the iso_sliders
plugin. I believe the
author of the apbs plugin is on this list, and will
probably give you
clearer answers.
Pete
Dear All,
I have a 0.98 PyMol version with APBS and
Iso_Sliders plugins. However,
my aim is not just visualize isosurfaces of
electrostatic potential at
certain values, but to display/map it on molecular
surface.
Would you be so kind to share your knowledge with
me on this subject?
I'd appreciate any help or advice of yours!
Thanks,
Anna.
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Pete Meyer
Fu Lab
BMCB grad student
Cornell University
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