[chimera-dev] monitor suitable for stereo visualization in Chimera

Thu Jan 30 20:19:24 PST 2020

Wei,
There are also options available if you want to provide stereo viewing 
to an audience using a video projector. We are currently upgrading our 
projector at the RBVI to higher def and passive glasses, but haven't yet 
chosen a specific solution. Regardless, this approach will cost much 
more than a single monitor or VR headset solution.

--tom

On 1/30/20 7:42 PM, Tom Goddard wrote:
> Hi Wei,
> 
>    The computers can run different operating systems.  But almost all VR 
> is done on Windows 10.  It can be made to work on Linux and Mac but 
> there are many problems using VR on those operating systems.
> 
>    Tom
> 
>> On Jan 30, 2020, at 7:35 PM, Wei Zhang <zhangwei at umn.edu> wrote:
>>
>> 
>> Tom,
>>
>> This is terrific and so exciting!
>> The movie you attached in the previous email must be what the second 
>> person see during a "meeting" session.
>> About the meeting to sync the to sessions. All the computers have to 
>> run on the same type of operating system, ie.
>>  not mixed with PC-Mac-Linux, right?
>>
>> I am happy I reached out to the Chimera group about stereo display and 
>> now see this new opportunity.
>>
>> Thanks!
>>
>> Wei
>>
>>
>>
>>
>>
>>
>>
>> On Thu, Jan 30, 2020 at 8:34 PM Tom Goddard <goddard at sonic.net 
>> <mailto:goddard at sonic.net>> wrote:
>>
>>     Hi Wei,
>>
>>       We do routinely do 2 person VR sessions, and have sometimes done
>>     3 or 4.  Each VR headset has to be connected to a separate
>>     computer.  This is a limitation of the current VR driver
>>     technology where it only allows communicating with one attached
>>     headset.  So for two or more people, each start ChimeraX and VR on
>>     separate computers and use a command "meeting" to sync the to
>>     sessions.  Each person sees the other persons VR hand controller
>>     cones and an image of the other person's face and these track the
>>     person's movement so it is easy to point to parts of the
>>     structures, and each person can move the models and change them. 
>>     I should make a video showing multiperson VR like that opioids
>>     video.  Here is another VR video that shows some 2 person VR
>>
>>     https://www.youtube.com/watch?v=S4lDzUEUFL0&feature=youtu.be
>>
>>     More about VR for molecules and cells is at the UCSF VR web site
>>
>>     https://vr.ucsf.edu
>>
>>     I develop the ChimeraX VR capabilities and they have a long ways
>>     to go, but also a lot of potential.  The RTX 2080 Ti is the best
>>     graphics you can get for VR.
>>
>>       Tom
>>
>>
>>>     On Jan 30, 2020, at 6:14 PM, Wei Zhang <zhangwei at umn.edu
>>>     <mailto:zhangwei at umn.edu>> wrote:
>>>
>>>     Tom,
>>>
>>>     This movie itself is magic! You can merge the operator with the
>>>     molecule in the movie ---- VR world and the real world are merged
>>>     together, that is amazing!
>>>
>>>     It is so delightful to see this movie, making me want to go away
>>>     from the old system right now and embrace the new one.
>>>
>>>     With the VR system,  is it possible to have two people see the
>>>     same view of the object as we did with the old system? I guess it
>>>     takes two sets of VR system, but without a mouse cursor, how can
>>>     we see the same view and points to the same place?
>>>
>>>     Thanks so much for the detailed and professional description
>>>     about old and new stereo  systems. I guess when the old
>>>     technology is dying out, we have no choice but to keep up with
>>>     the trend. I have to read and learn more in order to make a wise
>>>     decision. Your email is a good start.
>>>
>>>     Thank you,
>>>
>>>     Wei
>>>
>>>
>>>     On Thu, Jan 30, 2020 at 6:49 PM Tom Goddard <goddard at sonic.net
>>>     <mailto:goddard at sonic.net>> wrote:
>>>
>>>         Hi Wei,
>>>
>>>           Unfortunately stereoscopic visualization is dying out,
>>>         hardware vendors are not supporting it.  Nvidia 3D Vision
>>>         which was LCD shutter glasses that worked with many gaming
>>>         displays (fast refresh displays, e.g. 120 Hz or 144 Hz) was
>>>         dropped by Nvidia last April, they removed support for it
>>>         from their graphics drivers.  The Zalman row interleaved
>>>         displays were discontinued long ago.  Here is old info about
>>>         Nvidia 3D for Chimera, and also old information about PyMol
>>>         stereo display
>>>
>>>         https://www.rbvi.ucsf.edu/Outreach/technotes/3dvision.html
>>>
>>>         https://pymolwiki.org/index.php/Stereo_3D_Display_Options
>>>
>>>           We still have a stereo projector system working with
>>>         Chimera and ChimeraX that uses RealD CE4S LCD shutter glasses
>>>         (http://www.colorlinkjapan.com/brand/product/ce4s.html) and
>>>         an old StereoGraphics EXXR IR emitter
>>>         (http://www.ultimate3dheaven.com/crst.html).  The emitter
>>>         connects to a 3-pin DIN connector available on some old
>>>         Nvidia Quadro graphics cards.  We use a P6000 which has a
>>>         daughter board to provide the 3-pin DIN signal that syncs the
>>>         glasses with the left and right eye displayed images.  I'm
>>>         not sure any of this is sold anymore, but maybe you could get
>>>         it and maybe it would work, but not with 2080Ti graphics.
>>>
>>>           We use virtual reality for stereoscopic display in ChimeraX
>>>         (https://www.rbvi.ucsf.edu/chimerax/docs/user/vr.html). 
>>>         Here's a YouTube video showing it being used
>>>         (https://www.youtube.com/watch?v=FCotNi6213w).  This isn't
>>>         very similar to the older stereo systems because it blocks
>>>         your view of everything and requires all new user interface
>>>         since you can't use the mouse and keyboard easily with VR. 
>>>         But it does provide even better stereoscopic depth perception
>>>         than the old systems.
>>>
>>>           In short, you can probably do old stereo with lcd or
>>>         polarized glasses if you are going to go to a great deal of
>>>         trouble working with unsupported hardware.  Since no one uses
>>>         this stuff, the graphics drivers also have lots of trouble
>>>         delivering the images -- we have problems every year keeping
>>>         our stereo projection system working in the face of updated
>>>         graphics drivers that no longer work with stereo and 2 displays.
>>>
>>>           If you still want to pursue the old stereo, Ken Satuyshur
>>>         at University of Wisconsin has a few systems working and you
>>>         could ask him for more info.
>>>
>>>         Tom
>>>
>>>
>>>>         On Jan 29, 2020, at 7:57 PM, Wei Zhang <zhangwei at umn.edu
>>>>         <mailto:zhangwei at umn.edu>> wrote:
>>>>
>>>>         Hi Elaine and Tom,
>>>>
>>>>         I am trying to build a GPU workstation that mostly focuses
>>>>         on computation, ie. I want to have 4 2080Ti GPU cards. But I
>>>>         think these GPU cards do not support 3D visualization. One
>>>>         colleague of mine has such a workstation and he uses Zaleman
>>>>         monitor and can display the stereo map using Chimera.
>>>>         Zakeman monitor is out of market for a number of years, I am
>>>>         wondering if you are aware of any other type monitor that
>>>>         can be used for this purpose.
>>>>
>>>>         Thank you,
>>>>
>>>>         Wei
>>>>         _______________________________________________
>>>>         Chimera-dev mailing list
>>>>         Chimera-dev at cgl.ucsf.edu <mailto:Chimera-dev at cgl.ucsf.edu>
>>>>         http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev
>>>
>>
> 
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