I guess I have to answer this question since I asked it before but did
not manage to make the results publicly available (for some reasons both
times I tried mail bounced back).
Here is the summary for similar question asked before:
PyMol, a molecular graphics program, uses the program APBS to generate
electrostatic potential maps/surfaces. Both PyMol and APBS run on linux
machines.
What about SPOCK or VMD ?
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You can use molmol.
There is also SPOKE.
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I am aware of two alternatives:
a) dino, see http://www.dino3d.org
see tutorials -> advanced there
makes very nice pictures, btw.
b) pymol now can also calculate and display electrostatic potentials
you can use mead for example to calculate your potential, msms to
calculate a surface and visualize everything in Dino
Here's how you can do it:
www.dino3d.org
http://www.dino3d.org/tutorials/?p=esp
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One that was left off you list is
Grasp2 -- windows version is in beta release and
the system requirements page says there is a version
for linux comming.
http://trantor.bioc.columbia.edu/grasp2/
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Also look at mead..Mead calculates potentials which can them be
combined with surfaces calculated with msms and then displayed using
dino..
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Try the APBS plug-in for PyMol:
http://www-personal.umich.edu/~mlerner/PyMOL/
Easy to use and very nice results. Works under Linux just fine.
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Two programs that come to mind for electrostatic calculations on graphical
surface renditions suitable for Linux OS include:
PYMOL : < http://pymol.sourceforge.net/ > After installation there is a
menu
button "Plugin" > APBS Tools... for the calculations. See <
http://www.csb.yale.edu/userguides/graphics/pymol/electro.html > for some
details as to how APBS program was installed in Pymol.
SPOCK : < http://mackerel.tamu.edu/spock/ >
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What about GRASP2 that runs under Windows!? They are working on a Linux
version to my understanding.
That was the news one year ago......
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The CCP4MG graphics offers a GRASP alternative and certainly runs on
Linux OS
Go to the CCP4 main page
http://www.ccp4.ac.uk/main.html
nd click CCP4MG from the top tool bar
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One more: chimera from ucsf which runs on both linux and windows. You
have to run delphi first though to generate the potential map but you
may be doing this already anyway.
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MSMS in combination with MEAD and DINO can replace grasp.
DINO can read in msms surfaces and map electrostatic potentials
calculated by
MEAD ( see
http://www.scripps.edu/pub/olson-web/people/sanner/html/msms_home.html
and also
http://www.dino3d.org/tutorials/?p=esp )
And these all run on linux.
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The SwissPDBviewer can calculate potentials with a uniform dielectric,
and can read in maps from Grasp, MSMS, and Delphi
(http://www.expasy.org/spdbv/text/epot.htm).
Here is a link to a movie made with the SPDBviewer, povray, and
quicktime, showing the electrostatic potential of a binding site.
(http://arjournals.annualreviews.org/doi/suppl/10.1146/annurev.physiol.66.032802.154710?file=ph.67.nettles.mov)
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Lots of options nowadays! Just to clarify what you can or can't do with
PyMOL, here are the choices:
1) PyMOL has an automated menu action that generates a "local protein
contact potential" with a constant dielectric screening function. If all
you want is a GRASP-like surface image to get a qualitative idea of what
regions of your protein surface are relatively positive, neutral, or
negative, this is a trivially easy way to access that information. However,
as Nathan Baker correctly points out, it is best to simply think of this as
a "charge-smoothed" surface representation rather than a true electrostatic
potential.
To generate this view of any protein object consisting of ONLY the standard
20 amino acids, follow the "A" (action) pop-up menu to "generate", "vacuum
electrostatics", and "protein contact potential (local)".
You might want the latest beta for this. Builds for Win & Mac can be found
at: http://delsci.com/beta and http://delsci.com/macbeta. Recent additions:
sequence viewer, easier mouse actions, perspective rendering, right-click
menu, animated scenes & transitions, and more. As usual, beta cautions
apply...
2) PyMOL comes with an APBS Tools plugin written by Michael Lerner that can
call upon an external copy of Nathan's APBS to calculate true
Possion-Boltzmann electrostatic potentials. This can require a little bit
more manual intervention, but the resulting potential is much more correct
and can be used for quantitative analysis.
3) You can use MEAD, GRASP, or ZAP to calculate potentials externally and
then read them into PyMOL for realtime visualization and photorealistic
rendering.
As with any volumetric data in PyMOL, the resulting 3D field can be used to
color molecular objects, to create solid or mesh isosurfaces, or to color a
slice-plane or height-map that intersects the grid.
http://www.pymol.org
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