VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 01 2005 - 17:26:20 CST

Hi,
  The coloring of the map has to do with the color method you've got selected
in the Graphical Representations window. If you want to color by potential,
you'll need to use the "Color by volume" coloring method, and you'll need a
video board that does 3-D texture mapping. You'll also want to check the
color scale data range values in the Trajectory tab and make sure that the
potential value range makes sense for the color scheme you want. I got it
to work on my machine here, so let me know if you need help getting this
loaded on your machines. You should check the VMD startup messages and make
sure that you see a message like this:
Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (4)

The "3-D" item is the important one.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Dec 01, 2005 at 03:10:03PM -0800, Mengjuei Hsieh wrote:
> Hi
> I was testing the Grd plugin and trying to see if it works on delphibinary map. My VMD was able to read the file and show the correctdimension. However when I was using the volume as coloring method, itgives me gray color in my linux, partial green in my Mac, dark gray ina windows machine.
> The PDB I was testing is thishttp://pdbbeta.rcsb.org/pdb/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1HVRand my phi map is in http://apple.sysbio.info/~mjhsieh/files/1hvr_emap.phi
> It works correctly with pymol so maybe that can prove my binary map isnot bogus.
> Any idea?
> --Mengjuei 

-- 
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