Hi Greg, Thanks so much for the tips. Now I am more confident of having a functional machine again! I will keep you and Tom updated. Cheers and have a good weekend! Wei On Fri, Oct 30, 2020 at 3:22 PM Greg Pintilie <gregdp@gmail.com> wrote:

Hi Wei, Tom,

I had the Nvidia 3D vision system working on Ubuntu 14/16, the following instructions were very helpful:

http://eigenvaluables.blogspot.ca/2011/10/installing-nvidia-3d-vision-on-ubu...

I am actually not sure if it was on 14 or 16, I set it up years ago so it’s a bit of a blur, but it worked well for many years. Just this year I tried to upgrade to 18 (to use ChimeraX, which doesn’t seem to work with 14/16?) but on this version I could not get it to work using the method above.

I then installed Windows 10, and on this it works well with both Chimera and ChimeraX, but I had to use an older driver for the Quadro card, still downloadable from the Nvidia site, it’s version 392.58. With newer drivers it did not work. I haven’t tried going back to a similar older driver with Ubuntu 18/20, not sure if it’s possible, but maybe that could make it work.

Let us know how it works for you, and if you manage to get it working with 18/20 especially. If you try 14/16 or Windows 10 and have problems let me know, I can try to dig up more details if needed. I suspect that since drivers have dropped the support it may be harder and harder to keep it going as Tom said.

Regards,

Greg

On Oct 30, 2020, at 12:38 AM, Wei Zhang <zhangwei@umn.edu> wrote:

Tom,

Thank you for these suggestions. I will look into these options.

Best regards,

Wei

On Thu, Oct 29, 2020 at 8:58 PM Tom Goddard <goddard@sonic.net> wrote:

...

Hi Wei,

I'd suggest using Ubuntu 20.04, the latest Ubuntu, the current Chimera 1.14 or daily build will work fine on that. I am not certain that Quadro FX 4800 graphics drivers will be available for Ubuntu 20, probably they will be, but you might want to look for that online before proceeding. That graphics cards is very old, from 2008.

The other thing to know is that Nvidia discontinued support for Nvidia 3D Vision stereo glasses in 2019

https://nvidia.custhelp.com/app/answers/detail/a_id/4845

meaning those glasses and emitter will no longer work using just the current Nvidia graphics driver. But they claim that there is a separate driver for the USB emitter that allows it to work.

https://www.nvidia.com/en-us/drivers/nv3dvisionusb/390_41/nv3dvisionusb-driv...

I have not tried it. If you get it to work I'd be interested in hearing about it since we have an old Nvidia 3D Vision system.

Tom

On Oct 29, 2020, at 6:41 PM, Wei Zhang <zhangwei@umn.edu> wrote:

Hi Tom,

Hope everything is well.

One university's computer lab recently retired some workstations that were used for 3D visualization before. I managed to get a couple workstations with the 3D glasses and emitters. But I need to reinstall the operating system on those machines.

The graphic card of the workstation is Nvidia Quadro FX4800. The emitter is NVIDIA P854. The glasses are NVIDIA-P854 and ViewSonic-PGD250.

I plan to install Ubuntu. I am wondering which version of Ubuntu is suitable for using UCSF Chimera. Do we need to install cuda to make it work? Do we need to install an older version of Chimera?

Sorry I just sent the message to you to follow the previous chain of conversation. Shall I email the chimera-user in the future with such questions?

Thank you,

Wei

_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

To clarify, the emitter has 2 connections, one USB and one stereo sync. In Win 10 you only need the USB connection to the emitter, but in linux you need a separate cable from the Nvidia card to the emitter that provides the sync signal. The emitter send it's signal to the glasses in sync with the monitor, which is directly connected to the video card. You need a cable that has the 3 pin DIN one end and 'audio stereo' plug on the other. I have included a png of the P5000 with it's small cable for linux. kas Kenneth A. Satyshur, M.S., Ph.D. Senior Scientist, College of Ag and Life Sciences: Department of Bacteriology; School of Medicine and Public Health: Departments of Biomolecular Chemistry, Neuroscience, Oncology, and Carbone Cancer Center (Small Molecule Screening Facility) University of Wisconsin-Madison Madison, Wisconsin, 53706 608-215-5207 ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Tuesday, November 3, 2020 12:09 PM To: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Cc: Kenneth Satyshur <kenneth.satyshur@wisc.edu> Subject: Re: [Chimera-users] How to setup Nvidia 3D Vision on Ubuntu Kenneth Satyshur describes below how he sets up 3D stereo glasses with CentOS 7. Seems his instructions are for emitters that get their sync signal from the 5 or 3-pin DIN connector on older Quadro graphics cards rather than the USB Nvidia 3D Vision emitter. Tom Begin forwarded message: From: Kenneth Satyshur <kenneth.satyshur@wisc.edu<mailto:kenneth.satyshur@wisc.edu>> Subject: Re: Questions about an old 3D visualization system Date: November 3, 2020 at 7:09:20 AM PST To: Wei Zhang <zhangwei@umn.edu<mailto:zhangwei@umn.edu>> Cc: SBGrid Bug Reports <bugs@sbgrid.org<mailto:bugs@sbgrid.org>>, "goddard@cgl.ucsf.edu<mailto:goddard@cgl.ucsf.edu>" <goddard@cgl.ucsf.edu<mailto:goddard@cgl.ucsf.edu>> Sorry for the late reply. Yes I can get you going. I have a document explaining the steps needed and will sent it to you this week when it is finished. Briefly 1. Need nvidia 3D stereo glasses and emitter system. Also, a 3D stereo ready monitor the works at 122 Hz of higher. Not any high frequency monitor will work. You need those approved by Nvidia. I have several, and Asus VG 248. Unfortunately they are hard to find. 2. Nvidia Quadro card with a separate plugin cable 5pin DIN for the sync signal. (Out of stock. My son can make one for you.) You have FX4800 as do 3 of my 4 legacy stereo systems. Good card. 3. Linux OS Centos 7. Centos 8 will do 3D stereo, but it will not do stereo-in-a-window but stereo in a desktop. Also, Mate Desktop. The Gnome desktops will not do 3D stereo-in-a-window, but in-a-desktop. That means the entire desktop and not just pymol will be in stereo. That's because, after 10 years, Nvidia no longer supports 3D stereo systems, but only VR systems. 4. 3D is driven by the gaming industry. They are all VR or AR now. To be so blinded that you cannot see the keyboard is not the way to do 3D. But we are at the mercy of the gaming industry and the quest for market share. 5. X11 is dead. It is being replaced in linux by Wayland. I have not experimented with Wayland for stereo-in-a-window (SIW). So you need to disable the nouveau and install the legacy driver for nvidia card you have. And change the /etc/x11/xorg.conf file to include 'composite disable'. https://wiki.archlinux.org/index.php/nouveau The driver for FX4800 is stuck at NVIDIA-Linux-x86_64-340.108.run. After Nouveau disable you need to update Centos7 and run the NVidia drive script as root and reboot. You can also use dkms https://github.com/shawfdong/hyades/wiki/DKMS-on-CentOS-7 Short on details but this is the big picture. Much of this can be googled if you have a linux savvy tech person. I have 4 legacy systems with FX4800, 2 P5000 newer systems and my home dual core K4000 all running 3D stereo. (One of them is attached to a 3D projector for the 3D teaching lab.) I will send more specifics later. kas p.s. please feel free to share. I am continuing to test Wayland to see if it will do SIW. and not just SID. Kenneth A. Satyshur, M.S., Ph.D. Senior Scientist, College of Ag and Life Sciences: Department of Bacteriology; School of Medicine and Public Health: Departments of Biomolecular Chemistry, Neuroscience, Oncology, and Carbone Cancer Center (Small Molecule Screening Facility) University of Wisconsin-Madison Madison, Wisconsin, 53706 608-215-5207