From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 09 2007 - 17:56:18 CDT

Axel,
  I'm not so sure about that.... Please see Reena's first email.
Reena's original email described using the GUI "load" button to load
the PDB files, not the command line. It should not be possible
for the load button to cause the program to terminate, and that is the
reason why I am suspicious of the video driver. The fact that the video
driver is a VESA software renderer increases the probability further,
as I know of several versions that had bugs that would cause fatal
crashes when processing vertex arrays akin to what Reena experienced.

Reena, can you please test this by loading the PDB file using the
graphical interface only? If it crashes again, please try running VMD
with: vmd -debug and follow the steps described here, (5th bullet point):
   http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/linuxrelnotes.html

Thanks,
  John

On Wed, May 09, 2007 at 06:43:45PM -0400, Axel Kohlmeyer wrote:
> reena,
>
> as pointed out by mario and me,
> your problem has nothing to do with your video
> driver or the fact that you have little experience with
> linux, but you should read the VMD documentation instead
> and find, that you have to use 'mol new' (or the GUI) to load
> a file and not plain load.
>
> cheers,
> axel.
>
> On 5/9/07, ren <rsainiren_at_gmail.com> wrote:
> >Sir,
> > I am new to the field of computational biology. I have just started being
> >familiar with the Linux OS. After searching I have found the following.
> >Hope
> >this is the info required.
> > videosrc: v4lsrc; Driver : "vesa"
> > "Device"
> > Identifier "Videocard0"
> > Driver "vesa"
> > VendorName "Videocard vendor"
> > BoardName "VESA driver (generic)"
> >
> > The VMD startup messages printed to the VMD text console:
> >
> > Info) VMD for LINUX, version 1.8.6 (April 6, 2007)
> > 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, 2 CPUs detected.
> > Info) Free system memory: 1561MB (77%)
> > Info) OpenGL renderer: Mesa GLX Indirect
> > Info) Features: STENCIL MDE MTX PP PS
> > Info) GLSL rendering mode is NOT available.
> > Info) Textures: 2-D (2048x2048), Multitexture (8)
> > vmd > /usr/ren1/tutorial/TC5b_linear.pdb
> > invalid command name "/usr/ren1/tutorial/TC5b_linear.pdb"
> > vmd > load /usr/ren1/tutorial/TC5b_linear.pdb
> > couldn't load file "/usr/ren1/tutorial/TC5b_linear.pdb":
> >/usr/ren1/tutorial/TC5b
> > _linear.pdb: invalid ELF header
> > vmd > load /usr/ren1/tutorial/TC5b_linear.pdb
> > couldn't load file "/usr/ren1/tutorial/TC5b_linear.pdb":
> >/usr/ren1/tutorial/TC5b
> > _linear.pdb: invalid ELF header
> > vmd >
> >
> > regards
> > Reena (rsaini)
> >
> >On 5/9/07, ren <rsainiren_at_gmail.com> wrote:
> >> Sir,
> >> I am new to the field of computational biology. I have just started being
> >familiar with the Linux OS. After searching I have found the following.
> >Hope
> >this is the info required.
> >> videosrc: v4lsrc; Driver : "vesa"
> >> The VMD startup messages printed to the VMD text console:
> >>
> >> Info) VMD for LINUX, version 1.8.6 (April 6, 2007)
> >> 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, 2 CPUs detected.
> >> Info) Free system memory: 1561MB (77%)
> >> Info) OpenGL renderer: Mesa GLX Indirect
> >> Info) Features: STENCIL MDE MTX PP PS
> >> Info) GLSL rendering mode is NOT available.
> >> Info) Textures: 2-D (2048x2048), Multitexture (8)
> >> vmd > /usr/ren1/tutorial/TC5b_linear.pdb
> >> invalid command name "/usr/ren1/tutorial/TC5b_linear.pdb"
> >> vmd > load /usr/ren1/tutorial/TC5b_linear.pdb
> >> couldn't load file "/usr/ren1/tutorial/TC5b_linear.pdb":
> >/usr/ren1/tutorial/TC5b
> >> _linear.pdb: invalid ELF header
> >> vmd > load /usr/ren1/tutorial/TC5b_linear.pdb
> >> couldn't load file "/usr/ren1/tutorial/TC5b_linear.pdb":
> >/usr/ren1/tutorial/TC5b
> >> _linear.pdb: invalid ELF header
> >> vmd >
> >>
> >> regards
> >> Reena (rsaini)
> >>
> >>
> >>
> >>
> >> On 5/9/07, John Stone < johns_at_ks.uiuc.edu> wrote:
> >> >
> >> > Hi,
> >> > What video card and driver are you using? There's a
> >> > high probability that your video driver is the source of
> >> > this problem, so any information you have would be useful.
> >> > In particular, if you can send the VMD startup messages
> >> > printed to the VMD text console, that would be quite
> >> > helpful.
> >> >
> >> > Thanks,
> >> > John Stone
> >> > vmd_at_ks.uiuc.edu
> >> >
> >> > On Wed, May 09, 2007 at 12:40:48PM +0530, ren wrote:
> >> > > Sir,
> >> > > I am using VMD 1.8.6 for Linux (32-bit x86) using OpenGL, downloaded
> >via
> >> > > your site: http://www.ks.uiuc.edu/Research/vmd/
> >> > > Though i am able to visualise the trajectory files from MD
> >simulations, I am
> >> > > unable to load any pdb file. As soon as I hit the load button to open
> >such
> >> > > file, the VMD window closes.
> >> > > I have even tried opening pdb file downloaded from www.rcsb.org but
> >> > > unsuccessful.
> >> > > when trying to open via command window it displays:
> >> > > vmd > load /usr/ren1/tutorial/TC5b_linear.pdb
> >> > > couldn't load file
> >"/usr/ren1/tutorial/TC5b_linear.pdb":
> >> > > /usr/ren1/tutorial/TC5b_linear.pdb: invalid ELF
> >header
> >> > > vmd >
> >> > > Need your help
> >> > > regards
> >> > > Reena( rsaini)
> >> >
> >> > --
> >> > 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
> >> >
> >>
> >>
> >
> >
>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.

-- 
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