[Apbs-users] Visualizing charge densities

[Nathan B. <ba...@bi...>]

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 electrostati=
c potentials I'm calculating with APBS. Now I'm running some calculations t=
o find the condensation of negative charges around a given protein. In summ=
ary, I have two questions: first, I saw the example of charge condensation =
around DNA, but DNA possesses many negative charges, while my protein posse=
sses many positive ones. I would like to know if the DNA input file is a go=
od 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 i=
ssue.
>
> 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/