[PyMOL] Hardware stereo on Fedora 8 linux
I have had a difficult time getting hardware stereo configured using CrystalEyes glasses and I thought I'd share the solution with other pymol users. I've just set up a new system with an Intel motherboard and quad-core processor and an Nvidia quadro fx1300 video card. The operating system is Fedora 8. I'm using my old SGI IR emitter with an adaptor that provides 12VDC power in place of the 5VDC the video card delivers. RealD has a diagram of the necessary cable here: http://www.reald-corporate.com/scientific/pdf/Sgi-retro-VESA-REV-B.pdf My problem was that stereo mode would fail with no message on all the applications I tried: Pymol, Chimera and VMD. It was difficult to tell whether the problem was with hardware, driver or improperly configured software. In the end the solution was lurking in my /var/log/Xorg.0.log file: (WW) NVIDIA(0): UBB is incompatible with the Composite extension. Disabling (WW) NVIDIA(0): UBB. (WW) NVIDIA(0): Stereo is incompatible with the Composite extension. (II) NVIDIA(0): Disabling stereo. Commenting out the Option Composite Enable line in the extensions section of my xorg.conf file didn't fix the problem. Apparently the Composite extension is enabled by default. Changing to: Option Composite Disable fixed the problem. I added the following to my device section for good measure: Option AddARGBGLXVisuals False because ARGB GLX visuals require the Composite extension. In the end, the relevant section of my xorg.conf file looks like this: Section Monitor Identifier Monitor0 VendorName Unknown ModelNameUnknown HorizSync30.0 - 110.0 VertRefresh 50.0 - 150.0 # 1440x1050 Stereo @ 100 Hz ModeLine 1440x1050_100 212.76 1440 1504 1824 1952 1050 1051 1054 1103 Option DPMS EndSection Section Device Identifier Videocard0 Driver nvidia Option UBB True Option Stereo 3 # ARGB GLX visuals require Composite extension which is incompatible with stereo Option AddARGBGLXVisuals False EndSection Section Screen Identifier Screen0 Device Videocard0 MonitorMonitor0 DefaultDepth 24 SubSection Display Viewport 0 0 Depth 24 Modes 1440x1050_100 EndSubSection EndSection Section Extensions # UBB and Stereo are incompatible with the Composite extension Option Composite Disable EndSection Stereo mode now works beautifully in all applications. Rendering on large complexes, even without stereo, is slower with the Composite extension disabled though. Anyway, I hope this is helpful to other Pymol users. Chad
[PyMOL] hardware stereo problem
Dear Pymol users, We have a problem with one of our hardware stereo equipped PCs. For some reason, hardware stereo works fine for about 30sec but than switches to an inverted 3D image. And it keeps switching back and forth between the 'normal' 3D image and the inverted one, every 30sec. This is pretty annoying and even after reinstalling winXP, the right nvidia driver and playing around with all possible nvidia settings, we cannot find the problem. The problem is not Pymol specific, having the same problem in DSviewer. Does anybody recognize this problem? The PC (AMD X2, 4GB, Nvidia quadro4 980XGL) is running winXP and one of the latest pymol builds (1.0r2). The monitor is a high-end 21 (EIZO Flexscan T966) and we are using a stereographics emitter. Thanks a lot in advance. Best, Joris Beld ETH Zürich Switzerland
Re: [PyMOL] hardware stereo problem
Joris, this is a well known problem with the NVIDIA cards. It gets better with the newer highend cards but does not go away completely. You may want to invest in such a card and play around with different drivers. Carsten -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of Joris Beld Sent: Wednesday, March 12, 2008 4:44 AM To: PyMOL-users@lists.sourceforge.net Subject: [PyMOL] hardware stereo problem Dear Pymol users, We have a problem with one of our hardware stereo equipped PCs. For some reason, hardware stereo works fine for about 30sec but than switches to an inverted 3D image. And it keeps switching back and forth between the 'normal' 3D image and the inverted one, every 30sec. This is pretty annoying and even after reinstalling winXP, the right nvidia driver and playing around with all possible nvidia settings, we cannot find the problem. The problem is not Pymol specific, having the same problem in DSviewer. Does anybody recognize this problem? The PC (AMD X2, 4GB, Nvidia quadro4 980XGL) is running winXP and one of the latest pymol builds (1.0r2). The monitor is a high-end 21 (EIZO Flexscan T966) and we are using a stereographics emitter. Thanks a lot in advance. Best, Joris Beld ETH Zürich Switzerland -- --- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] hardware stereo problem
Joris: There is a thread (at least one, anyway) at the nvidia support forum, that may address this problem: http://www.nvnews.net/vbulletin/showthread.php?t=85807 Note, however, that the problem the thread addresses is under linux, not windows. -- Steve Lane System, Network and Security Administrator Doudna Lab Biomolecular Structure and Mechanism Group UC Berkeley On Wed, Mar 12, 2008 at 08:46:02AM -0400, Schubert, Carsten [PRDUS] wrote: Joris, This is a well known problem with the NVIDIA cards. It gets better with the newer highend cards but does not go away completely. You may want to invest in such a card and play around with different drivers. Carsten -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of Joris Beld Sent: Wednesday, March 12, 2008 4:44 AM To: PyMOL-users@lists.sourceforge.net Subject: [PyMOL] hardware stereo problem Dear Pymol users, We have a problem with one of our hardware stereo equipped PCs. For some reason, hardware stereo works fine for about 30sec but than switches to an inverted 3D image. And it keeps switching back and forth between the 'normal' 3D image and the inverted one, every 30sec. This is pretty annoying and even after reinstalling winXP, the right nvidia driver and playing around with all possible nvidia settings, we cannot find the problem. The problem is not Pymol specific, having the same problem in DSviewer. Does anybody recognize this problem? The PC (AMD X2, 4GB, Nvidia quadro4 980XGL) is running winXP and one of the latest pymol builds (1.0r2). The monitor is a high-end 21 (EIZO Flexscan T966) and we are using a stereographics emitter. Thanks a lot in advance. Best, Joris Beld ETH Z?rich Switzerland -- --- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] hardware stereo problem
Joris, We used to experience this problem occasionally on Linux, but not anymore. Your best bet is to update to the latest drivers. If that does not work, then this may be an unsolvable hardware issue on older cards. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Joris Beld Sent: Wednesday, March 12, 2008 1:44 AM To: PyMOL-users@lists.sourceforge.net Subject: [PyMOL] hardware stereo problem Dear Pymol users, We have a problem with one of our hardware stereo equipped PCs. For some reason, hardware stereo works fine for about 30sec but than switches to an inverted 3D image. And it keeps switching back and forth between the 'normal' 3D image and the inverted one, every 30sec. This is pretty annoying and even after reinstalling winXP, the right nvidia driver and playing around with all possible nvidia settings, we cannot find the problem. The problem is not Pymol specific, having the same problem in DSviewer. Does anybody recognize this problem? The PC (AMD X2, 4GB, Nvidia quadro4 980XGL) is running winXP and one of the latest pymol builds (1.0r2). The monitor is a high-end 21 (EIZO Flexscan T966) and we are using a stereographics emitter. Thanks a lot in advance. Best, Joris Beld ETH Zürich Switzerland -- --- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] hardware stereo winXP
Dear people, Have just finished an install of winXP (32) on an AMD-X2, 4GB RAM, Nvidia Quadro4-980XGL-AGP. Found the driver for this graphic card and the monitor is an 21 CRT EIZO Flexscan T966. Now running 1280x...@120hz with fH 122.8 and fV 119.4. Pymol runs great...but it will not start the hardware stereo. We use pymol-1_0r0-bin-win32. Do i have to do something else to get it to work? Thanks a lot in advance. Best, Joris Beld ETH Zürich Switzerland
[PyMOL] Hardware Stereo
I am running Pymol on a linux desktop with x86_64 architecture using Redhat Enterprise. The stereo component is a nuvision system, event after setting the Option Stereo 3 in my xorg.conf file, I am unable to get the hardware stereo to work. The monitor is a Sony CRT and model is CPD-G400. The Horizintalsync is 30 - 107 and the VerticalRefresh is set to 48 - 120. Suggestions to resolve the above problem is greatly appreciated. Thanks Sridhar
[PyMOL] Hardware Stereo OSX Tiger 10.4
Hi Can anyone lend support on getting full screen stereo to work with either MacPymol 0.98 or the latest beta 0.99. I am running Mac OS X version 10.4.2 on a dual G5 system with an ATI Radeon 9650 graphics card and a Monitor Z-screen 2000i. I have been able to run the GLUTStereo demo from the apple site, so I believe the hardware is working correctly. http://developer.apple.com/samplecode/GLUTStereo/GLUTStereo.html Any suggestions would be appreciated. thanks, Steve -- Stephen U. Dunham TEL 610 625-7103 Department of ChemistryFAX 610 625-7918 Moravian College 1200 Main Street Bethlehem, PA 18018 www.biochem.moravian.edu/biochemmain.html
RE: [PyMOL] Hardware Stereo OSX Tiger 10.4
I've had the same problem as well. I'm using a dual G5 with a Radeon 9800 Pro using the CrystalEyes system. I've also tried getting it work on several different systems running 10.4, and full screen stereo will not work on any of them. If I boot the G5 into 10.3.9, full screen stereo works fine. I can also run full screen stereo on the G5 running 10.4 using Nanasaur 2 (heck of a way to test full screen stereo!). Dan --- Dr. Daniel Moriarty Dept. of Chemistry Biochemistry Siena College 515 Loudon Road Loudonville, NY 12211 (518) 783-2472 http://www.siena.edu/chemistry/ -Original Message- From: pymol-users-ad...@lists.sourceforge.net on behalf of Stephen Dunham Sent: Tue 9/27/2005 12:15 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Hardware Stereo OSX Tiger 10.4 Hi Can anyone lend support on getting full screen stereo to work with either MacPymol 0.98 or the latest beta 0.99. I am running Mac OS X version 10.4.2 on a dual G5 system with an ATI Radeon 9650 graphics card and a Monitor Z-screen 2000i. I have been able to run the GLUTStereo demo from the apple site, so I believe the hardware is working correctly. http://developer.apple.com/samplecode/GLUTStereo/GLUTStereo.html Any suggestions would be appreciated. thanks, Steve -- Stephen U. Dunham TEL 610 625-7103 Department of ChemistryFAX 610 625-7918 Moravian College 1200 Main Street Bethlehem, PA 18018 www.biochem.moravian.edu/biochemmain.html
RE: [PyMOL] hardware stereo on window XP
Jie, The stereo-capable CRT monitor we recommend for PyMOL is the NEC-Mitsubishi FP2141SB-BK 22. It's what I use, and I usually drive this at 1400x1024 @ 110 Hz for 55 Hz stereo to each eye. Cheers, Warren From: pymol-users-ad...@lists.sourceforge.net on behalf of jiey...@ucsd.edu Sent: Wed 06/07/2005 10:58 To: 'PYMOLBB' Subject: RE: [PyMOL] hardware stereo on window XP Hi, Thank you all for your kind help. From the info I got, there are two choices, one is the IIyama HM204DT, another is viewsonic P225f. IIyama HM204DT is SUPER in all features, but I could not find a seller in US, seems it is popular in Europe but nobody is selling that in US?! That is really sad. So I guess I have to go to viewsonic p225f(b). But before I place the order, I would like to ask your opinion again about a sgi monitor? Would it be a better choice to select a sgi monitor? Or it would be more troublesome when put them all together? Thank you very much again Jie -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Dirk Kostrewa Sent: Wednesday, July 06, 2005 12:16 AM To: jiey...@ucsd.edu Cc: PYMOLBB Subject: Re: [PyMOL] hardware stereo on window XP Hi Jie Yang, it's getting harder to buy a stereo-capable CRT monitor with all the fancy TFTs. One monitor that I know to be still available is the iiyama Vision Master Pro 514 (HM204DT). It is a 22'' CRT with a maximum horizontal refresh rate of 140 kHz (!) and a maximum vertical refresh rate of 200 Hz, that I use for stereo (1280x960 at 120 Hz). There might be still some other stereo-capable monitors available . . . Best regards, Dirk Kostrewa. jiey...@ucsd.edu wrote: I am a new user of pymol, I have learned a lot from the pymol list. Thank you all. Now I am trying to set up a hardware stereo viewing system on a PC running windows XP. I read the pymol list, and got some idea of installing hardware on window XP system, which is to get a nVidia graphic card FX3200 (which I already have now), and a CRT monitor with fast refresh rate (100), like NEC -multisync FP2141SB-BK, as suggested by Pymol users. But I just found out that this model is discontinued now. I am wondering who can suggest another monitor(s) for this purpose? any suggestions, warnings, recommendations on this issue is highly appreciated. Thank you. Jie Yang -- Dirk Kostrewa Paul Scherrer Institut Life Sciences, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax: +41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch
Re: [PyMOL] hardware stereo on window XP
Hi Jie Yang, it's getting harder to buy a stereo-capable CRT monitor with all the fancy TFTs. One monitor that I know to be still available is the iiyama Vision Master Pro 514 (HM204DT). It is a 22'' CRT with a maximum horizontal refresh rate of 140 kHz (!) and a maximum vertical refresh rate of 200 Hz, that I use for stereo (1280x960 at 120 Hz). There might be still some other stereo-capable monitors available . . . Best regards, Dirk Kostrewa. jiey...@ucsd.edu wrote: I am a new user of pymol, I have learned a lot from the pymol list. Thank you all. Now I am trying to set up a hardware stereo viewing system on a PC running windows XP. I read the pymol list, and got some idea of installing hardware on window XP system, which is to get a nVidia graphic card FX3200 (which I already have now), and a CRT monitor with fast refresh rate (100), like NEC -multisync FP2141SB-BK, as suggested by Pymol users. But I just found out that this model is discontinued now. I am wondering who can suggest another monitor(s) for this purpose? any suggestions, warnings, recommendations on this issue is highly appreciated. Thank you. Jie Yang -- Dirk Kostrewa Paul Scherrer Institut Life Sciences, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax:+41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch
RE: [PyMOL] hardware stereo on window XP
Hi, Thank you all for your kind help. From the info I got, there are two choices, one is the IIyama HM204DT, another is viewsonic P225f. IIyama HM204DT is SUPER in all features, but I could not find a seller in US, seems it is popular in Europe but nobody is selling that in US?! That is really sad. So I guess I have to go to viewsonic p225f(b). But before I place the order, I would like to ask your opinion again about a sgi monitor? Would it be a better choice to select a sgi monitor? Or it would be more troublesome when put them all together? Thank you very much again Jie -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Dirk Kostrewa Sent: Wednesday, July 06, 2005 12:16 AM To: jiey...@ucsd.edu Cc: PYMOLBB Subject: Re: [PyMOL] hardware stereo on window XP Hi Jie Yang, it's getting harder to buy a stereo-capable CRT monitor with all the fancy TFTs. One monitor that I know to be still available is the iiyama Vision Master Pro 514 (HM204DT). It is a 22'' CRT with a maximum horizontal refresh rate of 140 kHz (!) and a maximum vertical refresh rate of 200 Hz, that I use for stereo (1280x960 at 120 Hz). There might be still some other stereo-capable monitors available . . . Best regards, Dirk Kostrewa. jiey...@ucsd.edu wrote: I am a new user of pymol, I have learned a lot from the pymol list. Thank you all. Now I am trying to set up a hardware stereo viewing system on a PC running windows XP. I read the pymol list, and got some idea of installing hardware on window XP system, which is to get a nVidia graphic card FX3200 (which I already have now), and a CRT monitor with fast refresh rate (100), like NEC -multisync FP2141SB-BK, as suggested by Pymol users. But I just found out that this model is discontinued now. I am wondering who can suggest another monitor(s) for this purpose? any suggestions, warnings, recommendations on this issue is highly appreciated. Thank you. Jie Yang -- Dirk Kostrewa Paul Scherrer Institut Life Sciences, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax: +41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch
[PyMOL] hardware stereo on window XP
I am a new user of pymol, I have learned a lot from the pymol list. Thank you all. Now I am trying to set up a hardware stereo viewing system on a PC running windows XP. I read the pymol list, and got some idea of installing hardware on window XP system, which is to get a nVidia graphic card FX3200 (which I already have now), and a CRT monitor with fast refresh rate (100), like NEC -multisync FP2141SB-BK, as suggested by Pymol users. But I just found out that this model is discontinued now. I am wondering who can suggest another monitor(s) for this purpose? any suggestions, warnings, recommendations on this issue is highly appreciated. Thank you. Jie Yang
[PyMOL] hardware stereo
Hello PYMOLers, I've recently installed Pymol v0.97 on an SGI but the hardware stereo mode was not detected. Is there somebody successfully using PyMol with this mode on an SGI ? If yes, could you please help me to fix this problem? My SGI: - Irix 64 Release 6.5 - Model Indigo 2 Impact 1 - Main Mem: 128 MB - CPU: 175 MHz Thanks a lot, Nicolas Ambert. -- --- AMBERT Nicolas (UMR 7100) Ecole Supérieure de Biotechnologie de Strasbourg (ESBS) PARC INNOVATION - BOULEVARD SEBASTIEN BRANT BP 10413 - F-67412 ILLKIRCH - CEDEX Office: 33 3 90 24 47 30 Email amb...@titus.u-strasbg.fr
Re: [PyMOL] hardware stereo
Hi, For SGI run 'xsetmon', if you see any resolution modes with an 's' after the refresh (e.g. 1024x768_96s) then click that mode and click 'load'. You can also check if your video card supports stereo by running 'glxinfo'. If you see a 'y' underneath anything in the 'stnewlinero' column then stereo in a window may work. Depending on your video card Pymol may automatically change your desktop resolution to the highest stereo supporting resolution. For example I'm running 1280x1024_30f and when I switch on Quad Buffered Stereo in pymol-0_98beta27-bin-irix65-r10k the screen resolution automatically changes to 1024x768_96s from 1280x1024_30f (I wish it would switch back when i turn off hardware stereo, but it does not). Hope that helps, Sabuj Pattanayek Ambert Nicolas wrote: Hello PYMOLers, I've recently installed Pymol v0.97 on an SGI but the hardware stereo mode was not detected. Is there somebody successfully using PyMol with this mode on an SGI ? If yes, could you please help me to fix this problem? My SGI: - Irix 64 Release 6.5 - Model Indigo 2 Impact 1 - Main Mem: 128 MB - CPU: 175 MHz Thanks a lot, Nicolas Ambert.
Re: [PyMOL] hardware stereo using pymol
On Saturday 17 January 2004 03:25, Dr. S. Frank Yan wrote: I'm using stereographics crystaleye with e-2 emitter and Quadro2 Pro graphics card, which does support the emitter. I am able to set the stereo on, and the screen starts to flick a little; however, the emitter is not turned on by the program and therefore no stereo. Stereographics claims that the emitter has to be turned on/off by application program when the stereo is enabled/disabled. I was wondering if anyone has experience with that. Thanks a lot, Frank Which OS is that? If you are on Linux, make sure you configure your X11 properly: 1) use the nvidia driver 2) load the glx module 3) remove the dri and GLcore modules 4) Most important: add Option Stereo 3 to the nvidia device section to turn on support for onboard stereo Regards Andreas -- Andreas Aemissegger, Laboratory of Organic Chemistry ETH Hoenggerberg - HCI F322, 8093 Zurich, Switzerland Phone: +41 1 632 2972, Fax: +41 1 632 1486 Mail: aemisseg...@org.chem.ethz.ch, WWW: http://www.protein.ethz.ch PGP key on request
Re: [PyMOL] hardware stereo using pymol
Hi, Thanks for the reply. We set them; however, it is still not working yet. I can see the pymol screen is flickering, but the emitter is apparently not turned on (no red light). --- Andreas Aemissegger aemisseg...@org.chem.ethz.ch wrote: On Saturday 17 January 2004 03:25, Dr. S. Frank Yan wrote: I'm using stereographics crystaleye with e-2 emitter and Quadro2 Pro graphics card, which does support the emitter. I am able to set the stereo on, and the screen starts to flick a little; however, the emitter is not turned on by the program and therefore no stereo. Stereographics claims that the emitter has to be turned on/off by application program when the stereo is enabled/disabled. I was wondering if anyone has experience with that. Thanks a lot, Frank Which OS is that? If you are on Linux, make sure you configure your X11 properly: 1) use the nvidia driver 2) load the glx module 3) remove the dri and GLcore modules 4) Most important: add Option Stereo 3 to the nvidia device section to turn on support for onboard stereo Regards Andreas -- Andreas Aemissegger, Laboratory of Organic Chemistry ETH Hoenggerberg - HCI F322, 8093 Zurich, Switzerland Phone: +41 1 632 2972, Fax: +41 1 632 1486 Mail: aemisseg...@org.chem.ethz.ch, WWW: http://www.protein.ethz.ch PGP key on request --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users __ Do you Yahoo!? Yahoo! Hotjobs: Enter the Signing Bonus Sweepstakes http://hotjobs.sweepstakes.yahoo.com/signingbonus
[PyMOL] hardware stereo using pymol
I'm using stereographics crystaleye with e-2 emitter and Quadro2 Pro graphics card, which does support the emitter. I am able to set the stereo on, and the screen starts to flick a little; however, the emitter is not turned on by the program and therefore no stereo. Stereographics claims that the emitter has to be turned on/off by application program when the stereo is enabled/disabled. I was wondering if anyone has experience with that. Thanks a lot, Frank __ Do you Yahoo!? Yahoo! Hotjobs: Enter the Signing Bonus Sweepstakes http://hotjobs.sweepstakes.yahoo.com/signingbonus
