VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Aug 18 2006 - 11:42:34 CDT

Dan,
  Yes, I've been testing stereo on a loaner Mac G5 with NVidia Quadro 4500
and VMD displays in stereo just fine on that machine so far.

That's interesting news about the non-G5 Mac seemingly able to display
in stereo, despite the emitter not lighting up. It sounds likely to me
that your stereoenabler or emitter output aren't active, even though VMD
and PyMol are able to acquire and draw into stereo-capable windows without
trouble. You might check the display settings and see if you have to enable
anything there? When you tested this setup before using MacPyMol, did you
see the emitter light up?

You mentioned you're having trouble with the emitter flashing
at a different rate than the CRT is flipping on Linux...
One thing to check when that sort of thing happens is that you
have the video driver set to turn on vertical retrace synchronization.
Most PC video cards have vertical retrace synchronization turned off
by default as it gives higher frames-per-second rates in games,
at the cost of having a little "screen tearing" which is often
unnoticable at very high frame rates.
For stereoscopic display, having vertical retrace synchronization
disabled can create problems similar to what you've described. In any
case, I'd double check your stereo driver settings on the Linux machine.
Some of the older emitters and shutter glasses have trouble at very high
refresh rates in the 120Hz range, they often do much better down around 112Hz.
(less flicker, less inter-eye ghosting, and more stable sync in general...)

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Aug 18, 2006 at 05:15:23PM +0300, Dan White wrote:
> >
> >Hi John,
> >
> >good news and bad news.
> >
> >OpenGL is doing the stereo business for crystal eyes stereo
> >with your new VMD alpha and also with Warrens MacPyMol
> >In both I select crystal eyes and i see the right kind of double
> >image on the CRT.
> >
> >However, for some reason, the E-2 emitter box led is not lighting
> >up...
> >i think the emitter box is working, as i use it on an adjacent
> >linux machine,,
> >although i have had problems recently with that, where the emitter
> >led is flashing
> >at a different frequency than the CRT screen is flipping.... which
> >is very odd...
> >cant seem to work that one out..... any ideas?
> >
> >I have an old SGI next to the G5 mac with the GeForce 5200 card,
> >and that has an ESGI emitter running at 96 Hz,
> >and with that on , I can see the stereo images in VMD and pymol
> >with the shutter glasses on,
> >if i by luck get the left and right in synch and the crossover at
> >the top or bottom of the screen.
> >
> >So it at least is partly working....
> >I cant really tell if it is my stereo enabler cable not working, or
> >something up with the emitter box,
> >of if Apple have broken the functionality I had a while back in
> >system updates....
> >
> >I dont see a blue line at the bottom of the display on the mac....
> >which I should right?
> >THats what the stereo enable cable is looking for for the synch
> >signal right?
> >My lnux machin has a quadro card with a port for the emitter box,
> >so that has no blue line... right?
> >
> >I wonder If i can turn on the blue line somehow?
> >
> >Have you tested it on a G5 or Mac Pro with the Quadro graphics card?
> >That should work nicely?
> >
> >cheers
> >
> >Dan
> >
> >
> >On Aug 17, 2006, at 12:21 AM, John Stone wrote:
> >
> >>
> >>Dan,
> >> I've posted a new MacOS X 10.4-based build of VMD that has stereo
> >>support compiled in. I'd be curious to know if it works with
> >>your stereoenabler device or not, when you get a chance to try it:
> >> http://www.ks.uiuc.edu/Research/vmd/alpha/
> >>
> >>The MacOS X stereo support is compiled into all of the 10.4 builds
> >>of VMD
> >>from here on out. In order to advise VMD that you want stereo
> >>ahead of
> >>other graphics features, you'll need to set an environment
> >>variable in your
> >>/bin/sh .profile (Mac builds now use /bin/sh startp scripts rather
> >>than csh):
> >> VMDPREFERSTEREO=1
> >> export VMDPREFERSTEREO
> >>
> >> John Stone
> >> vmd_at_ks.uiuc.edu
> >>
> >>On Fri, Mar 31, 2006 at 12:08:21PM +0300, Dan White wrote:
> >>>Hi,
> >>>
> >>>Yes mine looks just like that, i would have to check the part number
> >>>though.
> >>>Im not there right now
> >>>
> >>>Dan
> >>>
> >>>
> >>>>
> >>>>Probably this?
> >>>>
> >>>>http://www.stereographics.com/products/stereoenabler/
> >>>>body_stereoenabler.
> >>>>html
> >>>
> >>>Dr. Daniel James White BSc. (Hons.) PhD
> >>>Bioimaging Coordinator
> >>>Nanoscience Centre and Department of Biological and Environmental
> >>>Sciences
> >>>Division of Molecular Recognition
> >>>Ambiotica C242
> >>>PO Box 35
> >>>University of Jyväskylä
> >>>Jyväskylä
> >>>FIN 40014
> >>>Finland
> >>>
> >>>+358 14 260 4183 (work)
> >>>+358 468102840 (mobile)
> >>>http://www.bioimagexd.org
> >>>http://www.chalkie.org.uk
> >>>dan_at_chalkie.org.uk
> >>>white_at_cc.jyu.fi
> >>>
> >>>
> >>
> >>--
> >>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
> >
> >Dr. Daniel James White BSc. (Hons.) PhD
> >Bioimaging Coordinator
> >Nanoscience Centre and Department of Biological and Environmental
> >Sciences
> >Division of Molecular Recognition
> >Ambiotica C242
> >PO Box 35
> >University of Jyväskylä
> >Jyväskylä
> >FIN 40014
> >Finland
> >
> >+358 14 260 4183 (work)
> >+358 468102840 (mobile)
> >http://www.bioimagexd.org
> >http://www.chalkie.org.uk
> >dan_at_chalkie.org.uk
> >white_at_cc.jyu.fi
> >
> >
>
> Dr. Daniel James White BSc. (Hons.) PhD
> Bioimaging Coordinator
> Nanoscience Centre and Department of Biological and Environmental
> Sciences
> Division of Molecular Recognition
> Ambiotica C242
> PO Box 35
> University of Jyväskylä
> Jyväskylä
> FIN 40014
> Finland
>
> +358 14 260 4183 (work)
> +358 468102840 (mobile)
> http://www.bioimagexd.org
> http://www.chalkie.org.uk
> dan_at_chalkie.org.uk
> white_at_cc.jyu.fi
>
> 

-- 
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