VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Oct 27 2005 - 11:27:13 CDT

Luc,
  The Linux machine is using Mesa, so it has no hardware acceleration and
since Mesa doesn't do 3-D texture mapping, this does indeed explain why
you get a plain white surface on that machine. VNC shouldn't have any
effect at all since it isn't involved in the OpenGL that VMD uses.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Oct 27, 2005 at 10:22:04AM +0200, l.spitzer_at_fr.fournierpharma.com wrote:
>
>
>
>
> 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
>
>
> 

-- 
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