VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Mon Feb 07 2005 - 14:27:53 CST

On Mon, 7 Feb 2005, Oliver Beckstein wrote:

oliver,

please check whether the coordinates of your
potential map agree with the volume you want
to colorize.

plese see the attached image for an example,
where i mapped a file containing only zeros
on top of a density. the isosurface is black
wherever there is no data to be mapped onto
the isosurface.

this is done with a GeForce4 Ti 4400, btw.

regards,
        axel.

OB> John,
OB>
OB> > I assume you've got the latest NVidia drivers installed for your
OB> > video board?
OB>
OB> Yes, 1.0-6629 is the latest one.
OB>
OB> > What resolution is the potential map you're trying to load?
OB>
OB> 129x129x129
OB>
OB> Info) Analyzing Volume...
OB> Info) Grid size: 129x129x129 (32 MB)
OB> Info) Total voxels: 2146689
OB> Info) Min: -747.528870 Max: 633.049377 Range: 1380.578247
OB> Info) Computing volume gradient map for smooth shading
OB> Info) Added volume data, name=pot.dx : regular positions regular
OB> connections
OB>
OB> Hmm---is it perhaps a problem with the range of values?
OB>
OB> Any help is appreciated,
OB> Oliver
OB>
OB> > On Mon, Feb 07, 2005 at 04:03:34PM +0000, Oliver Beckstein wrote:
OB> > > Hi,
OB> > >
OB> > > I would like to create grasp-like electrostatic maps. I produced a pot.dx
OB> > > potential map with apbs and tried to colour a 'surf' or 'msms' surface
OB> > > using the new volume colouring feature. However, the surface stays
OB> > > uniformly black although I would expect some variation along
OB> > > red-white-blue (I think this is set with the colour scale.)
OB> > >
OB> > > Also, volume slice gives me a black surface. The iso contour
OB> > > representation works as expected, though.
OB> > >
OB> > > Do I need OpenGL shading for this to work?
OB> > >
OB> > > When I try Display>Render Mode>GLSL I get "Warning) OpenGL Programmable
OB> > > Shading not available."
OB> > >
OB> > > (I have
OB> > >
OB> > > VMD 1.8.3b1
OB> > >
OB> > > Info) OpenGL renderer: Quadro4 900 XGL/AGP/SSE
OB> > > Info) Features: STENCIL MSAA(4) RN MDE CVA MTX TCM PP PS GLSL SHO SHV
OB> > > Info) OpenGL Programmable shading is NOT available.
OB> > > Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (4)
OB> > >
OB> > > Fedora Core 3, xorg (nothing special in xorg.conf),
OB> > > NVIDIA-Linux-x86-1.0-6629 )
OB> > >
OB> > > Thanks,
OB> > > Oliver
OB> > >
OB> > > --
OB> > > Oliver Beckstein * oliver_at_biop.ox.ac.uk
OB> > > http://sansom.biop.ox.ac.uk/oliver/
OB> >
OB> > --
OB> > NIH Resource for Macromolecular Modeling and Bioinformatics
OB> > Beckman Institute for Advanced Science and Technology
OB> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
OB> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
OB> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
OB> >
OB> >
OB>
OB> 

-- 
=======================================================================
Dr. Axel Kohlmeyer   e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

snap.jpg