Hi Simon,

The ChimeraX —stereo option was unfortunately not hooked up, it didn’t even ask for a stereo OpenGL format. I fixed that just now and tested it on Windows 7 and an ancient Nvidia Quadro FX 2700 using Nvidia 3D Vision LCD glasses and emitter. Worked nicely. It required using the —stereo option, and starting from a shell, I was using a cygwin bash shell on Windows:

$ ChimeraX/bin/ChimeraX.exe —stereo

If it fails to start you can also use the —debug option, it will say it can’t get an OpenGL stereo context if you don’t have the driver settings right.

$ ChimeraX/bin/ChimeraX.exe —stereo —debug

It hasn’t been used much, it was hooked up 12 months ago for a short time and I tried it some then, we mostly focus on VR headsets. The sequential stereo zooming behavior and eye separation parameters are a bit wacky. Here are the docs on the camera command that sets the parameters.

https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/camera.html

The two stereo parameters are "eyeSeparation <e>” and “pixelEyeSeparation <p>”. The eye separation is the distance between the eyes in the scene, ie in Angstroms, default 5, and the pixelEyeSeparation is the distance between your physical eyes in screen pixels, default 200 since typical screen is about 100 pixels per inch with eyes about 2 inches apart. When you zoom Chimera 1 and probably every other stereo display system makes the model bigger or smaller without getting farther away, but in ChimeraX it simply moves it closer or further from you. I tested on a 150 Angstrom diameter structure (PDB 1oel) and with eye separation at 5 Angstrom that makes the structure 30 times my eye width so it is going to have to be 5 or 10 feet away to all be in view (with 30 degree field of view) which is way way behind the screen. So I needed to change the eye separation to 50 Angstroms to have it floating close to the screen.

camera eyeSep 50

This is a bit awkward having to adjust your eye separation in scene units to be a good match for the size of the structure you are looking at. Chimera 1 parameterizes things differently with a focal plane distance that avoids this weirdness. We will improve this as need demands.

Tom

On Jun 5, 2017, at 4:25 PM, Greg Couch wrote:

Whoops. I answered for Chimera, not ChimeraX. In the ChimeraX case, stereo does not work yet, even if your system is configured correctly. We did have stereo working a long time ago, but there have been tons of changes since then, so will need to investigate what it will take to get it working again.

If you want to test if your system is configured correctly, there is an extremely simple test program athttps://www.cgl.ucsf.edu/Overview/stereotest.html https://www.cgl.ucsf.edu/Overview/stereotest.html.

-- Greg

On 06/05/2017 04:14 PM, Greg Couch wrote:

...

You don't say if you are on Windows or Linux nor if you are using NVidia's 3D vision glasses or some other solution. Mac stereo stopped working in Mac OS X 10.11. All of those details matter.

For Windows, you to need to enable 3D stereo in the Manage 3D settings panel of the NVIDIA control panel, not the Stereoscopic 3D settings. Specifically, "Stereo - Enable" should be on and "Stereo - Display mode" should be set correctly for your hardware setup, e.g., "On-board DIN connector (with NIVDIA 3D Vision)".

On Linux, it is more complicated. Read the NVIDIA driver release notes in /usr/share/doc/nvidia*/html/index.html and edit your X11 server configuration file, /etc/Xorg.conf, appropriately.

HTH,

Greg

On 06/05/2017 11:38 AM, Simon Smith wrote:

...

Hello,

We're trying to get ChimeraX to work with our sequential stereo setup (Quadro 5000, driver 369.26).

Using the 'camera stereo' command always gives the error message 'Do not have stereo OpenGL context', even when using the --stereo command line flag. Setting the right stereo settings in Nvidia Control Panel hasn't made a difference either.

Does anyone have any hints/ideas on how to get this to work?

Thanks, Simon

---

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Thanks for the updates! We've got ChimeraX running in stereo in our lab now, using the latest build.

Simon

________________________________ From: Tom Goddard goddard@sonic.net Sent: Monday, June 5, 2017 8:09:15 PM To: chimerax-users@cgl.ucsf.edu Cc: Simon Smith Subject: Re: [chimerax-users] Getting stereo to work

Forgot to say that the “—stereo” option will work in tonight’s builds if those builds succeed.

Tom

On Jun 5, 2017, at 6:01 PM, Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> wrote:

Hi Simon,

The ChimeraX —stereo option was unfortunately not hooked up, it didn’t even ask for a stereo OpenGL format. I fixed that just now and tested it on Windows 7 and an ancient Nvidia Quadro FX 2700 using Nvidia 3D Vision LCD glasses and emitter. Worked nicely. It required using the —stereo option, and starting from a shell, I was using a cygwin bash shell on Windows:

$ ChimeraX/bin/ChimeraX.exe —stereo

If it fails to start you can also use the —debug option, it will say it can’t get an OpenGL stereo context if you don’t have the driver settings right.

$ ChimeraX/bin/ChimeraX.exe —stereo —debug

It hasn’t been used much, it was hooked up 12 months ago for a short time and I tried it some then, we mostly focus on VR headsets. The sequential stereo zooming behavior and eye separation parameters are a bit wacky. Here are the docs on the camera command that sets the parameters.

https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/camera.html

The two stereo parameters are "eyeSeparation <e>” and “pixelEyeSeparation <p>”. The eye separation is the distance between the eyes in the scene, ie in Angstroms, default 5, and the pixelEyeSeparation is the distance between your physical eyes in screen pixels, default 200 since typical screen is about 100 pixels per inch with eyes about 2 inches apart. When you zoom Chimera 1 and probably every other stereo display system makes the model bigger or smaller without getting farther away, but in ChimeraX it simply moves it closer or further from you. I tested on a 150 Angstrom diameter structure (PDB 1oel) and with eye separation at 5 Angstrom that makes the structure 30 times my eye width so it is going to have to be 5 or 10 feet away to all be in view (with 30 degree field of view) which is way way behind the screen. So I needed to change the eye separation to 50 Angstroms to have it floating close to the screen.

camera eyeSep 50

This is a bit awkward having to adjust your eye separation in scene units to be a good match for the size of the structure you are looking at. Chimera 1 parameterizes things differently with a focal plane distance that avoids this weirdness. We will improve this as need demands.

Tom

On Jun 5, 2017, at 4:25 PM, Greg Couch wrote:

Whoops. I answered for Chimera, not ChimeraX. In the ChimeraX case, stereo does not work yet, even if your system is configured correctly. We did have stereo working a long time ago, but there have been tons of changes since then, so will need to investigate what it will take to get it working again.

If you want to test if your system is configured correctly, there is an extremely simple test program athttps://www.cgl.ucsf.edu/Overview/stereotest.html.

-- Greg

On 06/05/2017 04:14 PM, Greg Couch wrote: You don't say if you are on Windows or Linux nor if you are using NVidia's 3D vision glasses or some other solution. Mac stereo stopped working in Mac OS X 10.11. All of those details matter.

For Windows, you to need to enable 3D stereo in the Manage 3D settings panel of the NVIDIA control panel, not the Stereoscopic 3D settings. Specifically, "Stereo - Enable" should be on and "Stereo - Display mode" should be set correctly for your hardware setup, e.g., "On-board DIN connector (with NIVDIA 3D Vision)".

On Linux, it is more complicated. Read the NVIDIA driver release notes in /usr/share/doc/nvidia*/html/index.html and edit your X11 server configuration file, /etc/Xorg.conf, appropriately.

HTH,

Greg

On 06/05/2017 11:38 AM, Simon Smith wrote: Hello,

We're trying to get ChimeraX to work with our sequential stereo setup (Quadro 5000, driver 369.26).

Using the 'camera stereo' command always gives the error message 'Do not have stereo OpenGL context', even when using the --stereo command line flag. Setting the right stereo settings in Nvidia Control Panel hasn't made a difference either.

Does anyone have any hints/ideas on how to get this to work?

Thanks, Simon

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