VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Nov 16 2006 - 17:18:24 CST

Mihaly,
  I wrote a shrot tutorial on how to do this for APBS, but the
same method works for Delphi, CHARMM PBEQ, and any other potential map
format that you can load into VMD:
  http://www.ks.uiuc.edu/Research/vmd/minitutorials/colorbypot/

If you're getting a black and white "leopard" surface when you follow the
instructions on that page, this indicates that there's some sort of problem
with the implementation of 3-D texture mapping on your video card.
The MSMS atom-based surface coloring is done using a much simpler per-vertex
coloring (no textures used) and so it's not a good test for whether you
have a working video driver for 3-D texturing. The "Volume" coloring method
uses 3-D textures exclusively, which makes it different from all of the
other coloring methods, and more dependent on a working video driver...

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Nov 16, 2006 at 06:06:06PM -0500, Mihaly Mezei wrote:
> I am trying to color surfaces by electrostatic potential. I saw in the archives a few items on this, but they all seem to refer to Linux or hardware problems - I am running under Windows VMD 1.8.4. An MSMS surface comes up, nicely colored with atom types, so the hardware is able to do it. When I take the tutorial example I get a leopard-like surface, black and white. I tried to change the scale in the Graphics/Trajectory menu but nothing changed. Same results if I try my own protein.
>
> Any help would be much appreciated.
>
> Mihaly Mezei
>
> Department of Molecular Physiology & Biophysics, Mount Sinai School of Medicine, NYU
> Voice: (212) 659-5475 Fax: (212) 849-2456
> WWW (MSSM home): http://directory.mssm.edu/faculty/mihaly.mezei
> WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei 

-- 
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