VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 07 2005 - 11:56:58 CST

Oliver,
  I'd have guessed that the value range was the issue, but if you're
using the Red White Blue color scale, there shouldn't be any pixel
values that are black at all, so that points to some other issue
causing this difficulty. Can you send me a copy of the DX file in
question so I can have a look at it?

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Feb 07, 2005 at 04:58:50PM +0000, Oliver Beckstein wrote:
> John,
>
> > I assume you've got the latest NVidia drivers installed for your
> > video board?
>
> Yes, 1.0-6629 is the latest one.
>
> > What resolution is the potential map you're trying to load?
>
> 129x129x129
>
> Info) Analyzing Volume...
> Info) Grid size: 129x129x129 (32 MB)
> Info) Total voxels: 2146689
> Info) Min: -747.528870 Max: 633.049377 Range: 1380.578247
> Info) Computing volume gradient map for smooth shading
> Info) Added volume data, name=pot.dx : regular positions regular
> connections
>
> Hmm---is it perhaps a problem with the range of values?
>
> Any help is appreciated,
> Oliver
>
> > On Mon, Feb 07, 2005 at 04:03:34PM +0000, Oliver Beckstein wrote:
> > > Hi,
> > >
> > > I would like to create grasp-like electrostatic maps. I produced a pot.dx
> > > potential map with apbs and tried to colour a 'surf' or 'msms' surface
> > > using the new volume colouring feature. However, the surface stays
> > > uniformly black although I would expect some variation along
> > > red-white-blue (I think this is set with the colour scale.)
> > >
> > > Also, volume slice gives me a black surface. The iso contour
> > > representation works as expected, though.
> > >
> > > Do I need OpenGL shading for this to work?
> > >
> > > When I try Display>Render Mode>GLSL I get "Warning) OpenGL Programmable
> > > Shading not available."
> > >
> > > (I have
> > >
> > > VMD 1.8.3b1
> > >
> > > Info) OpenGL renderer: Quadro4 900 XGL/AGP/SSE
> > > Info) Features: STENCIL MSAA(4) RN MDE CVA MTX TCM PP PS GLSL SHO SHV
> > > Info) OpenGL Programmable shading is NOT available.
> > > Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (4)
> > >
> > > Fedora Core 3, xorg (nothing special in xorg.conf),
> > > NVIDIA-Linux-x86-1.0-6629 )
> > >
> > > Thanks,
> > > Oliver
> > >
> > > --
> > > Oliver Beckstein * oliver_at_biop.ox.ac.uk
> > > http://sansom.biop.ox.ac.uk/oliver/
> >
> > --
> > 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
> >
> >
>
> --
> Oliver Beckstein * oliver_at_biop.ox.ac.uk
> http://sansom.biop.ox.ac.uk/oliver/ 

-- 
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