VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Dec 05 2005 - 16:22:46 CST

Hi,
  I'd try a color scale data range of -5 to 5 or something like that to start
with, and then adjust to match the actual range that's physically interesting
in your particular system. (you'll want to know what the physically meaningful
range of values output by Delphi/APBS/UHBD/etc is so that the colors mean
something to you when you see them within VMD. Making the color scale range
smaller (-1 to 1) increases the color contrast. You can also change the
color scale to something that's more appropriate for potential maps, say
the RWB color scale.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Dec 02, 2005 at 04:11:30PM -0800, Mengjuei Hsieh wrote:
> Hi,
> I guess that I need a little help about the color range, can anyonesuggest a range? It seems that the auto-ranging might not work for me.
> The windows shows dark grayInfo) VMD for WIN32, version 1.8.3 (February 15, 2005)Info) GLSL rendering mode is NOT available.Info) Textures: 2-D (2048x2048), 3-D (2048x2048x2048), Multitexture (8)
> The powerbook shows dark greenInfo) OpenGL renderer: ATI Radeon 9600 OpenGL EngineInfo) Features: STENCIL RN MTXInfo) Textures: 2-D (2048x2048), 3-D (128x128x128), Multitexture (8)
> The linux shows dark grayInfo) VMD for LINUX, version 1.8.4a22 (October 11, 2005)Info) OpenGL renderer: GeForce FX 5200/AGP/SSE2Info) Features: STENCIL MSAA(4) RN MDE CVA MTX PP PS GLSL(OVF)Info) Full GLSL rendering mode is available.Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (4)
> Non OpenGL version only shows bright grayInfo) VMD for LINUX, version 1.8.4a22 (October 11, 2005)Info) OpenGL renderer: ATI Radeon 9600 OpenGL EngineInfo) Features: STENCIL RN MDE MTX PP PSInfo) GLSL rendering mode is NOT available.Info) Textures: 2-D (2048x2048), Multitexture (8)
> --Mengjuei
>
> On 12/1/05, John Stone <johns_at_ks.uiuc.edu> wrote:> 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 

-- 
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