VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 19 2010 - 13:50:55 CST

Irene,
  What graphics card and driver version are you using?
(what does VMD print to the console when it starts up?)
To do visualizations of high resolution electrostatic maps using
the "Color by Volume" feature of VMD, you'll need a GPU that
has a good amount of video memory, ideally 512MB or more.
I have a simple electrostatics visualization mini-tutorial
for VMD available here:
  http://www.ks.uiuc.edu/Research/vmd/minitutorials/colorbypot/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 19, 2010 at 09:31:08AM -1000, Irene Newhouse wrote:
> I've been running APBS locally. When I have the results displayed with the
> top molecule, I see nothing. Displaying in a new window works. I've been
> trying to follow
> http://apbs.wustl.edu/MediaWiki/index.php/How_do_I_visualize_the_electrostatic_potential_around_my_biomolecule%3F#Isocontour_visualization?
> to map the potential to the molecular surface, and I can't get it to work.
> I can see isosurfaces w/out difficulty, as well as field lines, but I
> can't display the surface & color by volume. That website dates from an
> earlier version of VMD. Is there something slightly different in 1.8.7
> that I'm not aware of?
>
> Thanks!
>
> Irene Newhouse
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078