VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed May 09 2007 - 19:21:40 CDT

On Wed, 9 May 2007, John Stone wrote:

JS> Axel,
JS> I'm not so sure about that.... Please see Reena's first email.
JS> Reena's original email described using the GUI "load" button to load
JS> the PDB files, not the command line. It should not be possible

sorry,

my mistake. i have overlooked that.
i was irritated by seeing the wrong use of load again.

axel.

JS> for the load button to cause the program to terminate, and that is the
JS> reason why I am suspicious of the video driver. The fact that the video
JS> driver is a VESA software renderer increases the probability further,
JS> as I know of several versions that had bugs that would cause fatal
JS> crashes when processing vertex arrays akin to what Reena experienced.
JS>
JS> Reena, can you please test this by loading the PDB file using the
JS> graphical interface only? If it crashes again, please try running VMD
JS> with: vmd -debug and follow the steps described here, (5th bullet point):
JS> http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/linuxrelnotes.html
JS>
JS> Thanks,
JS> John
JS>
JS> On Wed, May 09, 2007 at 06:43:45PM -0400, Axel Kohlmeyer wrote:
JS> > reena,
JS> >
JS> > as pointed out by mario and me,
JS> > your problem has nothing to do with your video
JS> > driver or the fact that you have little experience with
JS> > linux, but you should read the VMD documentation instead
JS> > and find, that you have to use 'mol new' (or the GUI) to load
JS> > a file and not plain load.
JS> >
JS> > cheers,
JS> > axel.
JS> >
JS> > On 5/9/07, ren <rsainiren_at_gmail.com> wrote:
JS> > >Sir,
JS> > > I am new to the field of computational biology. I have just started being
JS> > >familiar with the Linux OS. After searching I have found the following.
JS> > >Hope
JS> > >this is the info required.
JS> > > videosrc: v4lsrc; Driver : "vesa"
JS> > > "Device"
JS> > > Identifier "Videocard0"
JS> > > Driver "vesa"
JS> > > VendorName "Videocard vendor"
JS> > > BoardName "VESA driver (generic)"
JS> > >
JS> > > The VMD startup messages printed to the VMD text console:
JS> > >
JS> > > Info) VMD for LINUX, version 1.8.6 (April 6, 2007)
JS> > > Info) http://www.ks.uiuc.edu/Research/vmd/
JS> > >
JS> > > Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
JS> > > Info) Please include this reference in published work using VMD:
JS> > > Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
JS> > > Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
JS> > > Info)
JS> > >-------------------------------------------------------------
JS> > > Info) Multithreading available, 2 CPUs detected.
JS> > > Info) Free system memory: 1561MB (77%)
JS> > > Info) OpenGL renderer: Mesa GLX Indirect
JS> > > Info) Features: STENCIL MDE MTX PP PS
JS> > > Info) GLSL rendering mode is NOT available.
JS> > > Info) Textures: 2-D (2048x2048), Multitexture (8)
JS> > > vmd > /usr/ren1/tutorial/TC5b_linear.pdb
JS> > > invalid command name "/usr/ren1/tutorial/TC5b_linear.pdb"
JS> > > vmd > load /usr/ren1/tutorial/TC5b_linear.pdb
JS> > > couldn't load file "/usr/ren1/tutorial/TC5b_linear.pdb":
JS> > >/usr/ren1/tutorial/TC5b
JS> > > _linear.pdb: invalid ELF header
JS> > > vmd > load /usr/ren1/tutorial/TC5b_linear.pdb
JS> > > couldn't load file "/usr/ren1/tutorial/TC5b_linear.pdb":
JS> > >/usr/ren1/tutorial/TC5b
JS> > > _linear.pdb: invalid ELF header
JS> > > vmd >
JS> > >
JS> > > regards
JS> > > Reena (rsaini)
JS> > >
JS> > >On 5/9/07, ren <rsainiren_at_gmail.com> wrote:
JS> > >> Sir,
JS> > >> I am new to the field of computational biology. I have just started being
JS> > >familiar with the Linux OS. After searching I have found the following.
JS> > >Hope
JS> > >this is the info required.
JS> > >> videosrc: v4lsrc; Driver : "vesa"
JS> > >> The VMD startup messages printed to the VMD text console:
JS> > >>
JS> > >> Info) VMD for LINUX, version 1.8.6 (April 6, 2007)
JS> > >> Info) http://www.ks.uiuc.edu/Research/vmd/
JS> > >
JS> > >> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
JS> > >> Info) Please include this reference in published work using VMD:
JS> > >> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
JS> > >> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
JS> > >> Info)
JS> > >-------------------------------------------------------------
JS> > >> Info) Multithreading available, 2 CPUs detected.
JS> > >> Info) Free system memory: 1561MB (77%)
JS> > >> Info) OpenGL renderer: Mesa GLX Indirect
JS> > >> Info) Features: STENCIL MDE MTX PP PS
JS> > >> Info) GLSL rendering mode is NOT available.
JS> > >> Info) Textures: 2-D (2048x2048), Multitexture (8)
JS> > >> vmd > /usr/ren1/tutorial/TC5b_linear.pdb
JS> > >> invalid command name "/usr/ren1/tutorial/TC5b_linear.pdb"
JS> > >> vmd > load /usr/ren1/tutorial/TC5b_linear.pdb
JS> > >> couldn't load file "/usr/ren1/tutorial/TC5b_linear.pdb":
JS> > >/usr/ren1/tutorial/TC5b
JS> > >> _linear.pdb: invalid ELF header
JS> > >> vmd > load /usr/ren1/tutorial/TC5b_linear.pdb
JS> > >> couldn't load file "/usr/ren1/tutorial/TC5b_linear.pdb":
JS> > >/usr/ren1/tutorial/TC5b
JS> > >> _linear.pdb: invalid ELF header
JS> > >> vmd >
JS> > >>
JS> > >> regards
JS> > >> Reena (rsaini)
JS> > >>
JS> > >>
JS> > >>
JS> > >>
JS> > >> On 5/9/07, John Stone < johns_at_ks.uiuc.edu> wrote:
JS> > >> >
JS> > >> > Hi,
JS> > >> > What video card and driver are you using? There's a
JS> > >> > high probability that your video driver is the source of
JS> > >> > this problem, so any information you have would be useful.
JS> > >> > In particular, if you can send the VMD startup messages
JS> > >> > printed to the VMD text console, that would be quite
JS> > >> > helpful.
JS> > >> >
JS> > >> > Thanks,
JS> > >> > John Stone
JS> > >> > vmd_at_ks.uiuc.edu
JS> > >> >
JS> > >> > On Wed, May 09, 2007 at 12:40:48PM +0530, ren wrote:
JS> > >> > > Sir,
JS> > >> > > I am using VMD 1.8.6 for Linux (32-bit x86) using OpenGL, downloaded
JS> > >via
JS> > >> > > your site: http://www.ks.uiuc.edu/Research/vmd/
JS> > >> > > Though i am able to visualise the trajectory files from MD
JS> > >simulations, I am
JS> > >> > > unable to load any pdb file. As soon as I hit the load button to open
JS> > >such
JS> > >> > > file, the VMD window closes.
JS> > >> > > I have even tried opening pdb file downloaded from www.rcsb.org but
JS> > >> > > unsuccessful.
JS> > >> > > when trying to open via command window it displays:
JS> > >> > > vmd > load /usr/ren1/tutorial/TC5b_linear.pdb
JS> > >> > > couldn't load file
JS> > >"/usr/ren1/tutorial/TC5b_linear.pdb":
JS> > >> > > /usr/ren1/tutorial/TC5b_linear.pdb: invalid ELF
JS> > >header
JS> > >> > > vmd >
JS> > >> > > Need your help
JS> > >> > > regards
JS> > >> > > Reena( rsaini)
JS> > >> >
JS> > >> > --
JS> > >> > NIH Resource for Macromolecular Modeling and Bioinformatics
JS> > >> > Beckman Institute for Advanced Science and Technology
JS> > >> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
JS> > >> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
JS> > >> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
JS> > >> >
JS> > >>
JS> > >>
JS> > >
JS> > >
JS> >
JS> >
JS> > --
JS> > =======================================================================
JS> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
JS> > Center for Molecular Modeling -- University of Pennsylvania
JS> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
JS> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
JS> > =======================================================================
JS> > If you make something idiot-proof, the universe creates a better idiot.
JS>
JS> 

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