From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Dec 06 2005 - 17:08:10 CST

Hi,
  Try setting the color scale mode to RWB in the Graphics->Colors window,
by selecting the "Color Scale" tab, and then choosing the method "RWB"
from there. If you're getting a dark surface even after doing all of this
correctly, there's a possibility that you've got a buggy video driver.
I'd suggest that you double check and make sure your video driver is
current. I've got a Radeon 9600 card in a Windows box at home and I know
that VMD's 3-D texturing works fine on my card with the driver version that
my machine is running. If you aren't running an up-to-date driver, that'd
be the next thing to check if you're sure you're doing everything else
correctly.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Dec 05, 2005 at 05:59:12PM -0800, Mengjuei Hsieh wrote:
> Hi John,
> After setting it to -1 to 1 the surface is still staying dark. I ampretty sure that there is nothing fishy in the data since I candisplay correct color in pymol. Also I could not find where can I setthe color flavor to RWB because there seems no 'Volume' object in thecolor setting panel.
> Thanks for your help.--Mengjuei
> On 12/5/05, John Stone <johns_at_ks.uiuc.edu> wrote:> 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.

-- 
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
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