From: John Stone (
Date: Thu Jul 14 2016 - 09:43:52 CDT

  This issue is very likely a bug in the particular display driver
version that you're running or in the X11 composite extension implementation.

I have seen further discussions of various bugs with composite causing
problems in complex display setups. There are known problems that are as yet
not yet fixed last time I looked at their bug tracking lists. That being said,
it is true that the latest KDE/GNOME are more dependent on the composite
extension. Last I checked it was not easy to disable in the same way
that it used to be. Of course one could always use Xfce or something similar
that doesn't need composite at all. That might be an interesting test case.

I would expect Chimera or PyMol to experience the same issue you see when
you run VMD unless there is something uniquely broken with OpenGL
stencil buffers, which an OpenGL buffer that VMD uses that the other two
probably aren't using.

  John Stone

On Thu, Jul 14, 2016 at 10:04:49AM +0200, Vlad Cojocaru wrote:
> HI Matic,
> Thanks for answering ...
> Disabling Composite is not needed anymore, NVIDIA driver works well with
> Composite on and 3d (as I said I have no problem with the Samsung monitor)
> .. In fact neither latest KDE nor GNOME work properly with Composite
> disabled ....
> I'll try with a single monitor, did not think that there may be some
> interference from the second monitor ...
> NO, I haven't tried pymol or other software .. but will do so (I guess I
> will try chimera ...) ..
> Best
> Vlad
> On 07/14/2016 08:53 AM, Matic Kisovec wrote:
> Dear Vlad,
> did you also disable composite in xorg.conf?
> Section "Extensions"
> \001\001\001 Option\001\001\001\001\001\001\001\001 "Composite"
> "Disable"
> EndSection
> To evade any interference with the other monitor you could also test the
> setup with only the stereo monitor.
> Did you test stereo in any other programs (Pymol for example)?
> Kind regards,
> Matic
> On 13. 07. 2016 12:06, Vlad Cojocaru wrote:
> Dear VMDers,
> I am wondering if anybody had experienced the following problem when
> doing 3d viewing with Nvidia 3d vision. If yes, I'd appreciate any
> thoughts on whether it can be fixed. Here is the issue:
> I bought a new monitor (ASUS 27'' - model VG278HE) which is connected
> to a Quadro K4000 graphics card with a direct DVI-D cable. In addition
> I have a Samsung SyncMaster that is connected via a DVI-DP adapter. I
> have a stereo bracket connected to the graphics card.
> When I switch stereo on in VMD (using option Stereo 10 in xorg.conf),
> I get very good viewing on the Samsung with no problems whatsoever.
> However, on the new ASUS screen the VMD window turns black at defined
> intervals. It comes back but it then turns black again and it goes on
> like this. I tried reverting the connections for the 2 monitors, but
> the same issue.
> No issue under windows and I have not tested other applications than
> VMD under linux.
> Further details: I have VMD 1.9.2 (with Stereo-QuadBufferred on) on
> openSUSE 42, NVIDIA driver 367.27)
> Best wishes
> Vlad
> --
> Dr. Vlad Cojocaru
> Computational Structural Biology Laboratory
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> Roentgenstrasse 20, 48149 Muenster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]
> [1]
> References
> Visible links
> 1.

NIH Center for Macromolecular Modeling and Bioinformatics
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