VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Tue Sep 20 2005 - 14:17:54 CDT

On Tue, 20 Sep 2005, Dan Strahs wrote:

dan,

DS> I am having a problem with coloring my MSMS-generated surface by
DS> electrostatic potential. I have APBS installed; in the potential file I've
DS> uploaded, I know that the maximum/minimum run from approx. -1500 to +1000.
DS> Yet my surface remains stubbornly white. I've loaded the potential as a DX

that usually means, that your setup does not provide the minimum
requirement for colormapped surfaces, that VMD requires.

DS> format, I've tried both the graphics trajectory tab and the "color
DS> scale method RWB" "color scale min -5.0" "color scale max 5.0": no change.
DS> Altering the range from -0.001/0.001 to -1500/1000 has no effect.
DS>
DS> I've enabled the 3d_accelerator: I have Dell GX270 with an Intel 82865G
DS> chipset on the motherboard. Since I'm running Linux (RH9), I'm using
DS> XFree86-4.3.0-2.90.55. I have DRI enabled with the i830 driver - the i830
DS> kernel module is loaded.

first off, if you update to a recent driver from intel, the
respective module should be named 'gdg'.

DS>
DS> VMD starts with:
DS> Info) Multithreading available, 1 CPU detected.
DS> Info) OpenGL renderer: Mesa GLX Indirect
DS> Info) Features: RN MTX

please check your X configuration. you do _not_ have DRI enabled.
if you had, you would see something like this:

Info) OpenGL renderer: Mesa DRI Intel(R) 852GM/855GM 20040331 x86/MMX/SSE2
Info) Features: STENCIL RN MDE CVA MTX

i have a centrino laptop with intel graphics here, also running RH9.
for that to work reasonably, i had to update the driver with newer
software from intel. but still that did not make color mapping work
for that machine. i _do_ get some colorization, but it is something
that is supposed to indicate that there is a problem with memory for
textures. for more details, please see:
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/4734.html

DS> Info) GLSL rendering mode is NOT available.
DS> Info) Textures: 2-D (2048x2048), Multitexture (6)
DS>
DS> Is there some clue here about what's happening? I've uploaded the makefile
DS> output from the VMD and plugins compile (with configure options LINUX
DS> OPENGL FLTK TK IMD TCL PTHREADS ACTC PYTHON NUMPY) at these links:
DS> http://storage.pace.edu/DStrahs/Research/make.log?uniq=-o8hxtn
DS> http://storage.pace.edu/DStrahs/Research/log.LINUX?uniq=-o8hxts
DS>
DS> I would be grateful for any help (other than recommending a different
DS> graphics card).

sorry, but if you look through the mailing list archives,
you'll learn that there are next to no alternatives for that
due to the way surface mapping is implemented in VMD.

axel.

DS>
DS> Dan Strahs
DS>
DS> 

-- 
=======================================================================
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.