From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 12 2009 - 17:02:21 CDT

Hi,
  What video card/chipset are you using? The problems you're experiencing
on that Linux machine sound like they are caused by a flaky video driver
or X server configuration. If you tell us more about your hardware
we may be able to give further suggestions.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 12, 2009 at 04:54:11PM -0500, Samuel Coulbourn Flores ?????? wrote:
> Hi Guys,
>
> Thanks for your help with the VMD display issue. In fact I needed a c+
> + compatibility library; that part is done now.
>
> However I'm having a different problem now. On both Windows and Linux
> when I render using NewCartoon, the results do not look right. The
> sticks for the bases are visible, but the backbone is not rendered at
> all. This happens even for perfect single-stranded helices, so it's
> not a problem with recognizing topology. My Mac installation renders
> these beautifully, but the Mac is not available to the person who
> needs to be making the movies. Any idea what might be wrong?
>
> As a separate issue, on the Linux installation once VMD is opened a
> "phantom" of the OpenGL display window is always in the foreground.
> Not the frame, just the black background, axes, molecule, etc. It
> does not respond to mouse clicks, instead the mouse clicks act on
> whatever application is behind the window. Some guidance on this
> would also be great, although the first issue is higher priority for us.
>
> Many thanks
>
> Sam
>
> On Mar 4, 2009, at 9:55 PM, Axel Kohlmeyer wrote:
>
> >On Wed, 4 Mar 2009, Samuel Coulbourn Flores 鑯J卞北 wrote:
> >
> >SCF> Hi Guys,
> >SCF>
> >SCF> I downloaded binaries to install VMD on Ubuntu and followed
> >instructions to
> >SCF> install. I don't have root privileges so I installed it in a
> >home
> >SCF> directory. I then changed two variables in the configure
> >script and ran
> >SCF> with no error messages, then did a make install. On running
> >VMD I got a
> >SCF> message like [1] 1234 or some such which would indicate the
> >process
> >SCF> started, but no XWindow pops up. I also don't see anything
> >like "vmd"
> >SCF> running when I query the scheduler. I found a thread in the
> >archives which
> >SCF> advises checking that the $DISPLAY variable is set correctly,
> >but it is not
> >
> >sam,
> >
> >this is most likely not the problem. you should have found
> >_many_ recommendations to check out the linux release notes.
> >
> >http://www.ks.uiuc.edu/Research/vmd/current/linuxrelnotes.html
> >
> >they contain a list of common problems and instructions how
> >to detect and work around them.
> >i suspect you are missing the c++ compatibility library.
> >
> >cheers,
> > axel.
> >
> >SCF> said what the correct value of this variable should be. On my
> >machine it's
> >SCF> :0.0. Can you help?
> >SCF>
> >SCF> Many thanks
> >SCF>
> >SCF> Sam
> >SCF>
> >
> >--
> >=
> >======================================================================
> >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.
>
> Samuel Coulbourn Flores, PhD
> Altman Lab
> Department of BioEngineering
> Stanford University
> samuel.flores_at_aya.yale.edu
> 650.644.8416
>
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-- 
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