VMD-L Mailing List

From: Samuel Coulbourn Flores 花山 (scflores_at_stanford.edu)
Date: Thu Mar 12 2009 - 16:54:11 CDT

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 è~J±å±± 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

花山
科学者
生物工学部
スタンフォ一ド大学
スタンフォ一ド、カリフォルニア、米国