[ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation - Fwd: 3D graphics under linux for coot, pymol and chimera

[Wim Burmeister]

  
  
Hello,
I re-post my contribution from 17 may 2017.
Software versions and hardware may be obsolete, but some of the
information may still help.
Best
Wim

  
   Forwarded Message 
  

  
Subject:

3D graphics under linux for coot, pymol and chimera
  
  
Date: 
Wed, 17 May 2017 12:27:21 +0200
  
  
From: 
Wim Burmeister 
  
  
To: 
CCP4 Bulletin Board 
  

  
  
  
  
  
  Hello,
   
  we just wanted to share our experience in
finding a configuration which allows to use 3D graphics
under linux using Nvidia GeForce 3D glasses.
   
  We had quite a hard time to find a
configurations which works correctly.
   
  We finally used Debian linux with a xfce
desktop. Other recent desktops use a tiling which is not
compatible with 3D graphics.
   
  The hardware consists of
  
  
a DELL Precision T5810 
desktop computer with an Nvidia Quadro M4000 (8 Gbyte
memory, 4 DP) graphics card
Nvidia
GeForce 3D Vision 2 (NVIDIA GEF 3D VISION 2 GLASSES KIT)
active stereo glasses
a stereo
connector PNY Quadro 4000 3D for the synchronization of
graphics card and glasses
an ASUS
24" LED 3D - VG248QE display
a
DisplayPort-DisplayPort cable
  
  
  The Nvidia linux drivers from version 367.57
can handle the current version of the Nvidia glasses.
   
  For an obscure reason a direct DP-DP connection
between graphics card and display is absolutely required in
order to obtain fully working stereo. If a DP-DVI dual link
adapter is used, the stereo does not work on the top and the
bottom part of the screen. This is true for a native DELL
active adaptor or generic models. The exact reason remains
unresolved, but the solution is to use a direct DP-DP
connection. This limits the available choice of displays
which require 120 Hz for 1080*1980 screen resolution and a
DP input. We have been choosing a “Nvidia 3D ready” model.
   
  There has been a considerate about of exchange
about this problem on
   
  https://devtalk.nvidia.com/default/topic/992892/linux/partially-working-stereoscopic-effect-with-3d-vision-under-debian-linux/
   
  The setup comes with a price tag of about 1600
€ free of taxes.
   
  coot, pymol and chimera work straight without
problems in hardware stereo mode. The experience is
absolutely great.
   
  Best
   
  Wim 
  
  
  
  
  
  
  
  
  
  -- 


  Wim Burmeister
Professeur
  Institut de Biologie Structurale (IBS) CIBB
  71 avenue des Martyrs
  CS
  20192
  38044 Grenoble Cedex 9, FRANCE
  E-mail: wim.burmeis...@ibs.fr
Tel:    +33 (0) 457 42 87 41   Fax: +33 (0) 476 20
94 00
  website
  
  
  

  
  


  



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Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

[Jim Fairman]

The newest version of KDE Neon works.  You just have to turn compositing
off.
--
Jim Fairman
C: 1-240-479-6575


On Thu, Dec 20, 2018 at 2:33 PM Guenter Fritz <
guenter.fritz.phenix.c...@gmail.com> wrote:

> Dear Adarsh,
>
> just an add-on to the instructions of the others. Since GNOME is not
> anymore compatible with stereo, we use successfully Xubuntu (18.04) with
> NVIDIA drivers.
> Best , Guenter
> > Hello everyone
> >
> > We have just purchased a Dell workstation for crystallography data
> analysis. We were trying to use Nvidia 3D vision 2 glasses with it, but
> failed to do so. Please help me out with this one. Some relevant
> information is as follows:
> > OS: Ubuntu 16.04 LTS
> > Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket)
> > Monitor: Asus VG248QE
> >
> > Thanks and regards
> > Adarsh Kumar
> > Suo Lab
> > Florida State University College of Medicine
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
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>
> 
>
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[ccp4bb] Computational Crystallography Newsletter (CCN) submissions

[Nigel Moriarty]

Folks

Calling for articles and short communications of interest to
structural biologists. The deadline for submission for the January
2019 issue is 20 January 2019.

The Computational Crystallography Newsletter (CCN) is an electronic
newsletter for structural biologists, and is published online every 6
months. Feature articles, meeting announcements and reports can be
submitted to me at any time for consideration. Submission of text by
email or word-processing files using the CCN templates is requested.
Past newsletters and a Microsoft Word template are available at
www.phenix-online.org/newsletter.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909   Web  : CCI.LBL.gov



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Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

[adarsh kumar]

Thank you, Guenter. I will keep that in mind.


*Regards*



*Adarsh Kumar, PhD*

*Suo Lab*

*Florida State University College of Medicine*


*Tallahassee, FL - 32304*



On Thu, Dec 20, 2018 at 5:33 PM Guenter Fritz <
guenter.fritz.phenix.c...@gmail.com> wrote:

> Dear Adarsh,
>
> just an add-on to the instructions of the others. Since GNOME is not
> anymore compatible with stereo, we use successfully Xubuntu (18.04) with
> NVIDIA drivers.
> Best , Guenter
> > Hello everyone
> >
> > We have just purchased a Dell workstation for crystallography data
> analysis. We were trying to use Nvidia 3D vision 2 glasses with it, but
> failed to do so. Please help me out with this one. Some relevant
> information is as follows:
> > OS: Ubuntu 16.04 LTS
> > Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket)
> > Monitor: Asus VG248QE
> >
> > Thanks and regards
> > Adarsh Kumar
> > Suo Lab
> > Florida State University College of Medicine
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>



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Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

[Guenter Fritz]

Dear Adarsh,

just an add-on to the instructions of the others. Since GNOME is not 
anymore compatible with stereo, we use successfully Xubuntu (18.04) with 
NVIDIA drivers.

Best , Guenter

Hello everyone

We have just purchased a Dell workstation for crystallography data analysis. We 
were trying to use Nvidia 3D vision 2 glasses with it, but failed to do so. 
Please help me out with this one. Some relevant information is as follows:
OS: Ubuntu 16.04 LTS
Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket)
Monitor: Asus VG248QE

Thanks and regards
Adarsh Kumar
Suo Lab
Florida State University College of Medicine



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Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

[adarsh kumar]

Hi

Did you use 3-DIN connector?

Regards
Adarsh Kumar, PhD
Suo lab
Florida State University School of Medicine
Tallahassee FL - 32304

On Thu, Dec 20, 2018, 16:48 Guillermo Montoya  we are using a similar setup ( i do not know if the asus monitor is the
> same)
> and I managed to make it work following this
>
>
> https://devtalk.nvidia.com/default/topic/1004126/general-discussion/nvidia-3d-stereo-under-linux-ubuntu-16/
>
>  but you need to use metacity as window manager
>
> I hope it helps
>
> best
>
>
> G.
>
>
> > On 20 Dec 2018, at 21:45, Adarsh Kumar 
> wrote:
> >
> > Hello everyone
> >
> > We have just purchased a Dell workstation for crystallography data
> analysis. We were trying to use Nvidia 3D vision 2 glasses with it, but
> failed to do so. Please help me out with this one. Some relevant
> information is as follows:
> > OS: Ubuntu 16.04 LTS
> > Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket)
> > Monitor: Asus VG248QE
> >
> > Thanks and regards
> > Adarsh Kumar
> > Suo Lab
> > Florida State University College of Medicine
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>



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Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

[Christine Gee]

Hi Adarsh,

As others have commented, you need your IR emitter to be connected to the
P4000 graphics card through the 3 pin connector to get stereo with the
vision 2 glasses unless you have a screen with a built in emitter. We
recently set up a system using a Quadro P4000 and the additional 3 pin
connector (which we bought with the P4000).
If it helps, we also use the MATE instead of GNOME desktop. And in the
/etc/X11/xorg.conf file you will need to add set the stereo option to 10,
at least we did with our ASUS ROG PG278QR monitor and we also set composite
to disable. Please reach out if you would like any more information.
Regards
Christine



On Thu, Dec 20, 2018 at 12:46 PM Adarsh Kumar 
wrote:

> Hello everyone
>
> We have just purchased a Dell workstation for crystallography data
> analysis. We were trying to use Nvidia 3D vision 2 glasses with it, but
> failed to do so. Please help me out with this one. Some relevant
> information is as follows:
> OS: Ubuntu 16.04 LTS
> Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket)
> Monitor: Asus VG248QE
>
> Thanks and regards
> Adarsh Kumar
> Suo Lab
> Florida State University College of Medicine
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

[Guillermo Montoya]

we are using a similar setup ( i do not know if the asus monitor is the same)
and I managed to make it work following this 

https://devtalk.nvidia.com/default/topic/1004126/general-discussion/nvidia-3d-stereo-under-linux-ubuntu-16/

 but you need to use metacity as window manager

I hope it helps

best 


G.


> On 20 Dec 2018, at 21:45, Adarsh Kumar  wrote:
> 
> Hello everyone
> 
> We have just purchased a Dell workstation for crystallography data analysis. 
> We were trying to use Nvidia 3D vision 2 glasses with it, but failed to do 
> so. Please help me out with this one. Some relevant information is as follows:
> OS: Ubuntu 16.04 LTS
> Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket)
> Monitor: Asus VG248QE
> 
> Thanks and regards
> Adarsh Kumar
> Suo Lab
> Florida State University College of Medicine
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

[Kay Diederichs]

Unfortunately, monitors with built-in emitter are no longer being manufactured. 
The NVIDIA website has not been updated for years. So that path leads nowhere.

Stereo has worked well for us (for existing monitors with built-in emitter, and 
with Quadro cards /USB emitter) until and including CentOS 7.5. Recently, this 
stopped after updating to CentOS 7.6 - coot finds the stereo-capable hardware 
and reports the switch to stereo, but the monitor does not flip the pictures. 
We are investigating. We are using the Nvidia drivers through the EPEL 
repository.

best,

Kay


On Thu, 20 Dec 2018 16:11:56 -0500, David Schuller  wrote:

>I can see two possible paths here:
>
>1) Make the card work with an emitter
>
>or 2) Switch to a monitor with a built-in emitter
>
>Datasheet on the graphics card:
>
>
>"3D Stereo support with Stereo Connector1
>...
>1 VGA/DVI/HDMI/stereo support via adapter/connector/bracket"
>
>The task then is to identify the correct bracket to work with this card, 
>and find a source for purchase.
>Something like this:
>
>https://www.bhphotovideo.com/c/product/652465-REG/PNY_Technologies_900_50762__000_Stereo_Bracket_for_Quadro.html
>"PNY Technoligies Stereo Bracket for Quadro FX 3800"
> > Is this part also compatible with the Quadro P4000? I do not know.
>
>http://www8.hp.com/h20195/v2/GetPDF.aspx/c04658472.pdf
>"NVidia 3D Stereo Bracket...
>Supports NVIDIA Quadro® K4000, K5000, K6000, K4200, K5200,
>M4000, M5000, M6000, P4000, P5000, P6000 graphics cards"
>
> > Seems promising.
>
>-
>Here is a web page listing compatible monitors. You can filter for those 
>with "built-in emitter"
>
>https://www.nvidia.com/object/3d-vision-displays.html
>
>
>
>
>
>On 12/20/18 3:45 PM, Adarsh Kumar wrote:
>> Hello everyone
>>
>> We have just purchased a Dell workstation for crystallography data analysis. 
>> We were trying to use Nvidia 3D vision 2 glasses with it, but failed to do 
>> so. Please help me out with this one. Some relevant information is as 
>> follows:
>> OS: Ubuntu 16.04 LTS
>> Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket)
>> Monitor: Asus VG248QE
>>
>> Thanks and regards
>> Adarsh Kumar
>> Suo Lab
>> Florida State University College of Medicine
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>-- 
>===
>All Things Serve the Beam
>===
>David J. Schuller
>modern man in a post-modern world
>MacCHESS, Cornell University
>schul...@cornell.edu
>
>
>
>
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Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

[David Schuller]

I can see two possible paths here:

1) Make the card work with an emitter

or 2) Switch to a monitor with a built-in emitter

Datasheet on the graphics card:


"3D Stereo support with Stereo Connector1
...
1 VGA/DVI/HDMI/stereo support via adapter/connector/bracket"

The task then is to identify the correct bracket to work with this card, 
and find a source for purchase.

Something like this:

https://www.bhphotovideo.com/c/product/652465-REG/PNY_Technologies_900_50762__000_Stereo_Bracket_for_Quadro.html
"PNY Technoligies Stereo Bracket for Quadro FX 3800"
> Is this part also compatible with the Quadro P4000? I do not know.

http://www8.hp.com/h20195/v2/GetPDF.aspx/c04658472.pdf
"NVidia 3D Stereo Bracket...
Supports NVIDIA Quadro® K4000, K5000, K6000, K4200, K5200,
M4000, M5000, M6000, P4000, P5000, P6000 graphics cards"

> Seems promising.

-
Here is a web page listing compatible monitors. You can filter for those 
with "built-in emitter"


https://www.nvidia.com/object/3d-vision-displays.html





On 12/20/18 3:45 PM, Adarsh Kumar wrote:

Hello everyone

We have just purchased a Dell workstation for crystallography data analysis. We 
were trying to use Nvidia 3D vision 2 glasses with it, but failed to do so. 
Please help me out with this one. Some relevant information is as follows:
OS: Ubuntu 16.04 LTS
Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket)
Monitor: Asus VG248QE

Thanks and regards
Adarsh Kumar
Suo Lab
Florida State University College of Medicine



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--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu




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Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

[adarsh kumar]

Thank you Jim. I will try that.


*Regards*



*Adarsh Kumar, PhD*

*Suo Lab*

*Florida State University College of Medicine*


*Tallahassee, FL - 32304*



On Thu, Dec 20, 2018 at 3:55 PM Jim Fairman  wrote:

> If you want to use it with linux, the 3-pin connector is required.  You
> can buy a cable that plugs into an output on the video card and then
> provides an "Nvidia 3D Stereo Bracket" 3-pin adapter to plug the little
> pyramid into.
>
> Here is a link to Dell's site, but you can get it elsewhere as well:
> http://accessories.dell.com/sna/productdetail.aspx?c=us=en=fed=16=A7035595
>
> I can vouch for the VG248QE monitors working with 3D Vision 2, I have 2 of
> them.
>
> Cheers, Jim
> --
> Jim Fairman
> C: 1-240-479-6575
>
>
> On Thu, Dec 20, 2018 at 12:46 PM Adarsh Kumar 
> wrote:
>
>> Hello everyone
>>
>> We have just purchased a Dell workstation for crystallography data
>> analysis. We were trying to use Nvidia 3D vision 2 glasses with it, but
>> failed to do so. Please help me out with this one. Some relevant
>> information is as follows:
>> OS: Ubuntu 16.04 LTS
>> Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket)
>> Monitor: Asus VG248QE
>>
>> Thanks and regards
>> Adarsh Kumar
>> Suo Lab
>> Florida State University College of Medicine
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>



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Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

[Jim Fairman]

If you want to use it with linux, the 3-pin connector is required.  You can
buy a cable that plugs into an output on the video card and then provides
an "Nvidia 3D Stereo Bracket" 3-pin adapter to plug the little pyramid into.

Here is a link to Dell's site, but you can get it elsewhere as well:
http://accessories.dell.com/sna/productdetail.aspx?c=us=en=fed=16=A7035595

I can vouch for the VG248QE monitors working with 3D Vision 2, I have 2 of
them.

Cheers, Jim
--
Jim Fairman
C: 1-240-479-6575


On Thu, Dec 20, 2018 at 12:46 PM Adarsh Kumar 
wrote:

> Hello everyone
>
> We have just purchased a Dell workstation for crystallography data
> analysis. We were trying to use Nvidia 3D vision 2 glasses with it, but
> failed to do so. Please help me out with this one. Some relevant
> information is as follows:
> OS: Ubuntu 16.04 LTS
> Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket)
> Monitor: Asus VG248QE
>
> Thanks and regards
> Adarsh Kumar
> Suo Lab
> Florida State University College of Medicine
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

[Adarsh Kumar]

Hello everyone

We have just purchased a Dell workstation for crystallography data analysis. We 
were trying to use Nvidia 3D vision 2 glasses with it, but failed to do so. 
Please help me out with this one. Some relevant information is as follows:
OS: Ubuntu 16.04 LTS
Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket)
Monitor: Asus VG248QE

Thanks and regards
Adarsh Kumar
Suo Lab
Florida State University College of Medicine



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[ccp4bb] off-topic: AUC facility

[Engin Özkan]

Hi everybody,

We do not have access to a local analytical ultracentrifuge (Chicago 
area), and are in need of a reasonably priced facility for our urgent 
AUC needs. We are interested in KD's and thus sedimentation equilibrium.

Recommendations are highly appreciated.

Thank you,

Engin

-- 
Engin Özkan, Ph.D.
Assistant Professor
Dept of Biochemistry and Molecular Biology
University of Chicago
Phone: (773) 834-5498
http://ozkan.uchicago.edu




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[ccp4bb] Postdoctoral Position Available

[Andrew Lovering]

Dear All,

A Wellcome-Trust postdoctoral position (for 2 years, possibly extendible to 4) 
is open in the Lovering laboratory, using x-ray crystallography to study the 
means by which predatory bacteria can form a pore in the prey outer membrane.

The link for the position is https://bit.ly/2EET1ta

More information on the lab can be found here: 
https://www.birmingham.ac.uk/staff/profiles/biosciences/lovering-andrew.aspx

Have a good xmas!
Andy



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[ccp4bb] JRH report on International Data Week 2018

[John R Helliwell]

Dear Colleagues,
I mention that my report on International Data Week 2018 can be found here:-
http://forums.iucr.org/viewtopic.php?f=39=409
and which I imagine will be of general interest. 
All best wishes,
John 
Emeritus Professor John R Helliwell DSc
IUCr Representative to CODATA and Chairman of the IUCr Committee on Data



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