VMD-L Mailing List

From: l.spitzer_at_fr.fournierpharma.com
Date: Thu Oct 27 2005 - 03:22:04 CDT

Hi John,

It is possible that the video driver is a source of problem...

I use the Linux version through VNC (I am connecting to the linux machine
with a graphic display) so I think it uses the same graphic card as
windows...
Here is the message I got with the Linux version :

Info) VMD for LINUX, version 1.8.3 (February 15, 2005)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 1 CPU detected.
Info) OpenGL renderer: Mesa GLX Indirect
Info) Features: STENCIL RN MTX
Info) GLSL rendering mode is NOT available.
Info) Textures: 2-D (2048x2048), Multitexture (6)
Found 4 plugins or data handlers in directory
        '/usr/local/lib/vmd/plugins/LINUX/molfile'.
vmd > Info) Using plugin pdb for structure file /home/spitzl/VMD/test.pdb
Info) Using plugin pdb for coordinates from file /home/spitzl/VMD/test.pdb
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 2221
Info) Residues: 272
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 1 Protein: 1 Nucleic: 0
Info) Finished with coordinate file /home/spitzl/VMD/test.pdb.
Warning) Unable to ascertain filetype from filename
'/home/spitzl/VMD/pme_test';
 assuming pdb.
Info) Analyzing Volume...
Info) Grid size: 72x80x64 (5 MB)
Info) Total voxels: 368640
Info) Min: -156.697998 Max: 159.477005 Range: 316.175003
Info) Computing volume gradient map for smooth shading
Info) Added volume data, name=pme_test : PME potential (kT/e, T=300K)
Type 'user add key Control-8 {my VMD commands...}' to use this key
Reading 2221 atoms..done
Probe radius = 1.400
Constructing solvent-accessible surface ..
Max edge length = 1.200
Malloc of zero or illegal length!!
length = 0
Malloc of zero or illegal length!!
length = 0
.......................
Total Triangles 114163 Total constraints 77110
Max Neighbors per atom 62 Average Neighbors per atom 34.7186
Surface construction + writing time 2.95 seconds
done
Info) This surface is made with SURF from UNC-Chapel Hill. The reference
is:
Info) A. Varshney, F. P. Brooks, W. V. Wright, Linearly Scalable
Computation
Info) of Smooth Molecular Surfaces, IEEE Comp. Graphics and Applications,
Info) v. 14 (1994) pp. 19-25.
Info) Reading Surf geometry output file...
Info) Read Surf output file, processing geometry...
Info) Done.

Thanks for helping...I am negociating with my boss for having a new graphic
card (not a single chipset on the motherboard!!)...

Luc SPITZER

                                                                                                                                       
                      John Stone
                      <johns_at_ks.uiuc.ed Pour : l.spitzer_at_fr.fournierpharma.com
                      u> cc : vmd-l_at_ks.uiuc.edu
                                               Objet : Re: vmd-l: Réf. : Re: vmd-l: visualization of DX map
                      27/10/2005 00:37
                                                                                                                                       
                                                                                                                                       

Hi Luc,
  The Windows "Zebra" image you emailed makes me think that the problem is
rooted with the video driver and not with VMD itself, as that doesn't
look anything like what I'd expect, particularly from the 1.8.4a22 test
version you ran. On Linux the problem could be as simple as
using a video card that doesn't support 3-D texturing, that's my first
guess for why you got the solid white surface. Can you tell me what video
card the Linux machine is using? Please send me the startup messages from
the Linux machine as well, that may completely answer the reason why you're
getting the plain white surface on the Linux machine.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Oct 25, 2005 at 09:28:43AM +0200, l.spitzer_at_fr.fournierpharma.com
wrote:
>
>
>
>
> Dear John,
>
> Thanks for answering so fast.
>
> The driver version seems to be the most recent (see joined
snapshot...sorry
> it is in french!). Anyway, I cannot change it because it's used by our
> informatic team for distant help on our computer.
>
> Here is the message I got when I loaded the DX card :
>
> Info) VMD for WIN32, version 1.8.4a22 (October 11, 2005)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) OpenGL renderer: Intel 915G
> Info) Features: STENCIL MDE CVA MTX PP
> Info) GLSL rendering mode is NOT available.
> Info) Textures: 2-D (2048x2048), 3-D (128x128x128), Multitexture (8)
> Info) Spaceball driver not installed. Spaceball interface disabled.
> Info) No joysticks found. Joystick interface disabled.
> Found 50 plugins or data handlers in directory
> 'C:/Program Files/University of
> Illinois/VMD/plugins/WIN32/molfile'.
> Info) File loading in progress, please wait.
> Info) Using plugin pdb for structure file C:\Documents and
> Settings\spitzl\Mes d
> ocuments\DIVERS PDB\test.pdb
> Info) Using plugin pdb for coordinates from file C:\Documents and
> Settings\spitz
> l\Mes documents\DIVERS PDB\test.pdb
> Info) Determining bond structure from distance search ...
> Info) Finished with coordinate file C:\Documents and Settings\spitzl\Mes
> documen
> ts\DIVERS PDB\test.pdb.
> Info) Analyzing structure ...
> Info) Atoms: 2221
> Info) Bonds: 2284
> Info) Residues: 272
> Info) Waters: 0
> Info) Segments: 1
> Info) Fragments: 1 Protein: 1 Nucleic: 0
> The autopsf package could not be loaded:
>
> vmd > Info) Can't show volumetric data; no filename selected yet
> Info) Analyzing Volume...
> Info) Grid size: 72x80x64 (5 MB)
> Info) Total voxels: 368640
> Info) Min: -156.697998 Max: 159.477005 Range: 316.175003
> Info) Computing volume gradient map for smooth shading
> Info) Added volume data, name=C:/Documents and Settings/spitzl/Mes
> documents/DIV
> ERS PDB/pme_test : PME potential (kT/e, T=300K)
>
> The DX file is 3.10 Mo. (is it the information you wanted?)
>
> Joined I add (only to you, not to the list!) two screenshots of what
> appears on VMD, one on windows (admire the nice zebra!!!) and the other
one
> on Linux through VNC (it is 1.8.3 version on linux).
>
> Thanks in advance for help!
>
> Luc SPITZER
>
>
>
>
>

> John Stone

> <johns_at_ks.uiuc.ed Pour :
l.spitzer_at_fr.fournierpharma.com

> u> cc :
vmd-l_at_ks.uiuc.edu

> Objet : Re: vmd-l:
visualization of DX map
> 24/10/2005 20:15

>

>

>
>
>
>
>
> Hi,
> It sounds to me like there's something amiss with your video driver.
> The startup messages VMD is printing indicate that you have at least got
> minimal 3-D texturing support, though the max texture dimension is small.
> That test version of VMD you're using has automatic texture downsampling
> code so it should be attempting to squeeze the texture into the 128^3
limit
> of your video card, even if your DX map is much larger. GLSL doesn't
play
> a factor in the specific problem you're having. Can you verify that
you've
> got the most recent video driver for your machine? Please double check
> that and get back to me. How big is the DX map you're loading? Can you
> email me the messages that VMD prints in the console when you load it?
>
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Mon, Oct 24, 2005 at 05:38:40PM +0200, l.spitzer_at_fr.fournierpharma.com
> wrote:
> >
> >
> >
> >
> > Dear all,
> >
> > I have a problem with VMD (original, isn't it?)...
> > I am currently using VMD 1.8.4 on windows2000 pro and I tried to
> visualize
> > a potential map generated with this same VMD but it didn't work...the
> > surface stays definitely white, even as I try to modify the color range
> in
> > the graphics > color interface.
> > When I tried the map I generated directly on my colleague's Linux
version
> > (1.8.3) I could visualize it. So I tried to visualize it through VNC
on
> my
> > PC but it is desperately white...
> > So do you have any solution for me...
> >
> > When I launch VMD, I have the following messages :
> >
> > Info) VMD for WIN32, version 1.8.4a22 (October 11, 2005)
> > Info) http://www.ks.uiuc.edu/Research/vmd/
> > Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> > Info) Please include this reference in published work using VMD:
> > Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> > Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> > Info) -------------------------------------------------------------
> > Info) OpenGL renderer: Intel 915G
> > Info) Features: STENCIL MDE CVA MTX PP
> > Info) GLSL rendering mode is NOT available.
> > Info) Textures: 2-D (2048x2048), 3-D (128x128x128), Multitexture (8)
> >
> > Can my problem be linked to the fact that GLSL rendering is not
> available?
> > (what is GLSL? :-s)
> >
> > I am sorry if this problem has already been resolved within the mailing
> > list, but I am new and I don't have much time to read all the previous
> > messages of the list...
> >
> > Thanks in advance for any answer,
> >
> > Luc SPITZER
>
> --
> 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
>
>
> 

--
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