[Apbs-users] RE: Visualizing charge densities

[Michel Espinoza-F. <me...@dd...>]

Hi all,

I've posted the above email few weeks ago... I found that CHIMERA can
also do a good job at visualizing dx files. I would like to know if any
of you have tried to visualize change densities, elec. Potential maps,
etc using chimera... It'll be nice to have some feedback.

Thanks!

Michel

-----Original Message-----
From: sob...@gm... [mailto:sob...@gm...] On Behalf Of
Nathan Baker
Sent: Tuesday, November 15, 2005 6:26 AM
To: Michel Espinoza-Fonseca
Cc: apb...@li...; John Stone; Eamon Caddigan
Subject: Visualizing charge densities

Hi Michel --

I think the DNA charge density is probably a good example to start
from.  I realize isosurfaces aren't the most intuitive for this (they
aren't for potentials either, really) but they're what we have to work
with.  They can be useful to ask questions like:  "where around my
molecule is the the charge density equal to X times the bulk
concentration?"

I'd love to see some sort of volume rendering capabilities in VMD like
those in PMV (see http://nbcr.net/software/doc/apbs/APBS_QuikFacts.pdf
for an example) but I'm not sure if there's any plan for this or not.

Hope this helps,

Nathan

On 11/14/05, Michel Espinoza-Fonseca <me...@dd...> wrote:
> Hi all,
>
> I have a tiny question. I've been using VMD to visualize the
electrostatic potentials I'm calculating with APBS. Now I'm running some
calculations to find the condensation of negative charges around a given
protein. In summary, I have two questions: first, I saw the example of
charge condensation around DNA, but DNA possesses many negative charges,
while my protein possesses many positive ones. I would like to know if
the DNA input file is a good starting for my calculations (e.g., if I
must modify something). Second, I've been trying to visualize the
isosurfaces with VMD, but I really don't know what the "isosurface"
value means when I analyze the charge density. I know you're not VMD
developers, but I guess you have experience on this issue.
>
> Thank you very much!
>
> Cheers,
> Michel
>
>
>


--
Assistant Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/