VMD-L Mailing List

From: Dan Strahs (dstrahs_at_pace.edu)
Date: Tue Sep 20 2005 - 16:40:09 CDT

Well, I think I have the direct rendering working. Thank you John and
Axel: your suggestions over the past 24 hours have been invaluable. As a
result, DRI is working. I have uploaded both the XF86Config and the output
from glxinfo at these links:

http://storage.pace.edu/DStrahs/Research/XF86Config?uniq=-o8h7f3

http://storage.pace.edu/DStrahs/Research/glxinfo?uniq=-o8h7f8

VMD also is happier:
        Info) Multithreading available, 1 CPU detected.
        Info) OpenGL renderer: Mesa DRI Intel(R) 865G 20021115
        Info) Features: STENCIL RN CVA MTX
        Info) GLSL rendering mode is NOT available.
        Info) Textures: 2-D (1024x1024), 3-D (128x128x1), Multitexture (2)

However, the "Color Surface by Volume" function is still on the fritz. It
looks wrong. The protein is mostly colored a mottled darkred/white using
the RWB color scale model, even though the region of the protein is
positively charged. Altering the min/max/midpoint of the scale has little
effect. In comparison, isocontours are displaying the correct potential.

If you're curious, I could generate some lowres JPEGs so you could see the
effect. It doesn't look like a standard 2D "checkerboard", so I don't
believe that I'm dealing with a memory issue.

Any other ideas? If I can't get this to work soon, then I'll finish
developing that script I outlined in a previous post.

Dan Strahs

On Tue, 20 Sep 2005, John Stone wrote:

> Axel,
> I'm planning to add some code that'll automatically downsample the
> texture map to fit into the available texture memory. If Dan can get
> his video driver working correctly, I should be able to give you guys a
> binary that will cope with the small 3-D texture memory on those cards.
>
> John
>
> On Tue, Sep 20, 2005 at 09:17:54PM +0200, Axel Kohlmeyer wrote:
> > 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.
>
>