Sequential stereo problems in Chimera in Mac after updating to OSX EL Capitan
Hi, No sequential stereo is working in Chimera after updating of our Macs to OS X El Capitan - 10.11.1 in the CRTs linked to MacPros Error remarks: - unable to turn on stereo viewing - "Unable to find hardware stereo support ... " (see attachment). This problem has not appeared in with earlier OSX updates! We hope this problem will be fixed soon. Cheers Peter Peter Engelhardt, PhD, docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography Nanomicroscopy Center (NMC), Department of Applied Physics Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland Department of Pathology Haartman Institute P.O.Box 21 (Haartmaninkatu 3) FIN-00014 University of Helsinki, Finland Email: Peter.Engelhardt@Helsinki.Fi Email: Peter.Engelhardt@Aalto.Fi URL: http://www.lce.hut.fi/~engelhar/ Mobil: +358-400193342 Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: +358-505113192 ________________________________________ From: chimera-users-bounces@cgl.ucsf.edu <chimera-users-bounces@cgl.ucsf.edu> on behalf of chimera-users-request@cgl.ucsf.edu <chimera-users-request@cgl.ucsf.edu> Sent: Monday, November 30, 2015 10:00 PM To: chimera-users@cgl.ucsf.edu Subject: Chimera-users Digest, Vol 151, Issue 35 Send Chimera-users mailing list submissions to chimera-users@cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request@cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. inserting missing residue (Francesco Pietra) ---------------------------------------------------------------------- Message: 1 Date: Mon, 30 Nov 2015 19:40:50 +0100 From: Francesco Pietra <chiendarret@gmail.com> To: chimera <chimera-users@cgl.ucsf.edu> Subject: [Chimera-users] inserting missing residue Message-ID: <CAEv0nmtYfsQJBkbzkypX+uzqbYU7EMLhFZrybVhzj5W1hdM_OQ@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi: II would like to insert a single non-terminal missing amino acid in a big peptide. By using MODELLER with CHIMERA, I don't find any option for NOT modeling loops. Just inserting the missing residue without moving the adjacent residues. In the sequence that appears by invoking modeling, the missing residue is not marked in any way, the sequence just continues as if no non-terminal residue were missing. thanks francesco pietra
Hi Peter, If Chimera says "Unable to find hardware stereo support … “ when you enable sequential stereo it means the graphics driver does not support quad-buffered OpenGL stereo. Unfortunately Apple has not been interested in supporting stereo so I’m surprised you had it working recently. For several years now no machines Apple sold supported stereo. We had an ancient (8 year old) Nvidia Quadro FX 5600 in a Mac Pro until about 2 years ago, but the performance became so poor we abandoned it and had to switch to Windows. The new Mac Pro cylinders did not support stereo. Unfortunately Apple also doesn’t seem to provide any information on which systems support stereo. We used to be able to get this information from the Apple OpenGL Capabilities web page https://developer.apple.com/opengl/capabilities/ <https://developer.apple.com/opengl/capabilities/> but they stopped updating that two Mac OS versions ago (10.9). Now the only thing I can find from Apple about OpenGL support is this page https://support.apple.com/en-us/HT202823 <https://support.apple.com/en-us/HT202823> that lists the OpenGL version supported by each of their computers. Quad buffered stereo is not a requirement of any OpenGL version so this page does not help find out about stereo support. With Mac OS El Capitan (10.11) Apple has talked a lot about “Metal” which is an alternative graphics programming interface. Chimera does not use it since it is Apple only and we need to support Linux and Windows. In summary, I think Apple has dropped support for stereo on your systems. Could you tell us what graphics card it was working with and which Mac OS version (Mavericks 10.10?). Also if you use Chimera menu Help / Report a Bug… we will know the configuration that no longer works which will help us advise other Chimera users. Tom
On Nov 30, 2015, at 12:54 PM, Engelhardt, Peter wrote:
Hi,
No sequential stereo is working in Chimera after updating of our Macs to OS X El Capitan - 10.11.1 in the CRTs linked to MacPros
Error remarks: - unable to turn on stereo viewing - "Unable to find hardware stereo support ... "
(see attachment).
This problem has not appeared in with earlier OSX updates!
We hope this problem will be fixed soon.
Cheers Peter
Peter Engelhardt, PhD, docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography
Nanomicroscopy Center (NMC), Department of Applied Physics Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland
Department of Pathology Haartman Institute P.O.Box 21 (Haartmaninkatu 3) FIN-00014 University of Helsinki, Finland
Email: Peter.Engelhardt@Helsinki.Fi Email: Peter.Engelhardt@Aalto.Fi URL: http://www.lce.hut.fi/~engelhar/ Mobil: +358-400193342
Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: +358-505113192
Sequential S3D is vanishing. Zspace uses it for their windows only apps. Nvidia barely supports S3D as a technology. Not sure if any other chip makers are using sequential anymore. Chip electronics have outpaced the need for sequential. SBS half, the chimera DTI option output as HDMI is your best bet, regardless of the OS. Some of the Samsung tv/monitors that do hdmi 2.0 now offer SBS half at 4k. This resolution is better than bluray S3D framepack under HDMI 1.4, and is probably the best you will get for the foreseeable future (ie, 5-15 years). Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= ================================================= ________________________________ From: chimera-users-bounces@cgl.ucsf.edu <chimera-users-bounces@cgl.ucsf.edu> on behalf of Tom Goddard <goddard@sonic.net> Sent: Monday, November 30, 2015 4:26 PM To: Engelhardt, Peter Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Sequential stereo problems in Chimera in Mac after updating to OSX EL Capitan Hi Peter, If Chimera says "Unable to find hardware stereo support … “ when you enable sequential stereo it means the graphics driver does not support quad-buffered OpenGL stereo. Unfortunately Apple has not been interested in supporting stereo so I’m surprised you had it working recently. For several years now no machines Apple sold supported stereo. We had an ancient (8 year old) Nvidia Quadro FX 5600 in a Mac Pro until about 2 years ago, but the performance became so poor we abandoned it and had to switch to Windows. The new Mac Pro cylinders did not support stereo. Unfortunately Apple also doesn’t seem to provide any information on which systems support stereo. We used to be able to get this information from the Apple OpenGL Capabilities web page https://developer.apple.com/opengl/capabilities/ OpenGL version 1.5 - Apple Developer Tools OpenGL Capabilities Tables. The following table lists OpenGL extensions and parameter values reported for each of the OS X versions, graphics adapters, and CPU ... Read more...<https://developer.apple.com/opengl/capabilities/> but they stopped updating that two Mac OS versions ago (10.9). Now the only thing I can find from Apple about OpenGL support is this page https://support.apple.com/en-us/HT202823 that lists the OpenGL version supported by each of their computers. Quad buffered stereo is not a requirement of any OpenGL version so this page does not help find out about stereo support. With Mac OS El Capitan (10.11) Apple has talked a lot about “Metal” which is an alternative graphics programming interface. Chimera does not use it since it is Apple only and we need to support Linux and Windows. In summary, I think Apple has dropped support for stereo on your systems. Could you tell us what graphics card it was working with and which Mac OS version (Mavericks 10.10?). Also if you use Chimera menu Help / Report a Bug… we will know the configuration that no longer works which will help us advise other Chimera users. Tom On Nov 30, 2015, at 12:54 PM, Engelhardt, Peter wrote: Hi, No sequential stereo is working in Chimera after updating of our Macs to OS X El Capitan - 10.11.1 in the CRTs linked to MacPros Error remarks: - unable to turn on stereo viewing - "Unable to find hardware stereo support ... " (see attachment). This problem has not appeared in with earlier OSX updates! We hope this problem will be fixed soon. Cheers Peter Peter Engelhardt, PhD, docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography Nanomicroscopy Center (NMC), Department of Applied Physics Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland Department of Pathology Haartman Institute P.O.Box 21 (Haartmaninkatu 3) FIN-00014 University of Helsinki, Finland Email: Peter.Engelhardt@Helsinki.Fi<mailto:Peter.Engelhardt@Helsinki.Fi> Email: Peter.Engelhardt@Aalto.Fi<mailto:Peter.Engelhardt@Aalto.Fi> URL: http://www.lce.hut.fi/~engelhar/ Mobil: +358-400193342 Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: +358-505113192
Further to Matt’s comment, SBS works very well for rendering/display in 3D but it is difficult to work with for interactive visualisation because you must work full screen and chimera doesn’t completely understand that the left and right halves of the screen are now superimposed. Firstly accessing menus and the command line is problematic because you must move your mouse to the left eye view, so you need to mouse across the screen and off the left hand side. This is a relatively trivial irritation however. What is more challenging is interacting with the model/volume to select rotate/pan etc. So, to work with SBS 3D you must have a second monitor to handle all of the floating windows and non-3D stuff. It would be good to be able to float the display window and tear-off the drop-down menus and command line to view separately on the 2D monitor (perhaps you can already?). Currently mouse selection tools are focussed on the left hand view, while the rotation control seems to focus on the centre of the display, so sometimes when you intend to rotate the model you end up just rotating about z (or vice-versa). Perhaps it would be better to have all mouse interactions focus on the left-hand view and to have a visual cue to let you know when your mouse is over the left or right view? I have both nVidia sequential stereo (on linux) and SBS (on a 32” 3D samsung TV on my mac), interactive work is so much more straight-forward on the sequential setup. Dr David Bhella MRC-University of Glasgow Centre for Virus Research Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch
On 1 Dec 2015, at 07:28, Dougherty, Matthew T <matthewd@bcm.edu> wrote:
Sequential S3D is vanishing. Zspace uses it for their windows only apps. Nvidia barely supports S3D as a technology. Not sure if any other chip makers are using sequential anymore. Chip electronics have outpaced the need for sequential.
SBS half, the chimera DTI option output as HDMI is your best bet, regardless of the OS.
Some of the Samsung tv/monitors that do hdmi 2.0 now offer SBS half at 4k.
This resolution is better than bluray S3D framepack under HDMI 1.4, and is probably the best you will get for the foreseeable future (ie, 5-15 years).
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================
From: chimera-users-bounces@cgl.ucsf.edu <chimera-users-bounces@cgl.ucsf.edu> on behalf of Tom Goddard <goddard@sonic.net> Sent: Monday, November 30, 2015 4:26 PM To: Engelhardt, Peter Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Sequential stereo problems in Chimera in Mac after updating to OSX EL Capitan
Hi Peter,
If Chimera says "Unable to find hardware stereo support … “ when you enable sequential stereo it means the graphics driver does not support quad-buffered OpenGL stereo. Unfortunately Apple has not been interested in supporting stereo so I’m surprised you had it working recently. For several years now no machines Apple sold supported stereo. We had an ancient (8 year old) Nvidia Quadro FX 5600 in a Mac Pro until about 2 years ago, but the performance became so poor we abandoned it and had to switch to Windows. The new Mac Pro cylinders did not support stereo.
Unfortunately Apple also doesn’t seem to provide any information on which systems support stereo. We used to be able to get this information from the Apple OpenGL Capabilities web page
https://developer.apple.com/opengl/capabilities/ OpenGL version 1.5 - Apple Developer Tools OpenGL Capabilities Tables. The following table lists OpenGL extensions and parameter values reported for each of the OS X versions, graphics adapters, and CPU ... Read more...
but they stopped updating that two Mac OS versions ago (10.9). Now the only thing I can find from Apple about OpenGL support is this page
https://support.apple.com/en-us/HT202823
that lists the OpenGL version supported by each of their computers. Quad buffered stereo is not a requirement of any OpenGL version so this page does not help find out about stereo support.
With Mac OS El Capitan (10.11) Apple has talked a lot about “Metal” which is an alternative graphics programming interface. Chimera does not use it since it is Apple only and we need to support Linux and Windows.
In summary, I think Apple has dropped support for stereo on your systems. Could you tell us what graphics card it was working with and which Mac OS version (Mavericks 10.10?). Also if you use Chimera menu Help / Report a Bug… we will know the configuration that no longer works which will help us advise other Chimera users.
Tom
On Nov 30, 2015, at 12:54 PM, Engelhardt, Peter wrote:
Hi,
No sequential stereo is working in Chimera after updating of our Macs to OS X El Capitan - 10.11.1 in the CRTs linked to MacPros
Error remarks: - unable to turn on stereo viewing - "Unable to find hardware stereo support ... "
(see attachment).
This problem has not appeared in with earlier OSX updates!
We hope this problem will be fixed soon.
Cheers Peter
Peter Engelhardt, PhD, docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography
Nanomicroscopy Center (NMC), Department of Applied Physics Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland
Department of Pathology Haartman Institute P.O.Box 21 (Haartmaninkatu 3) FIN-00014 University of Helsinki, Finland
Email: Peter.Engelhardt@Helsinki.Fi Email: Peter.Engelhardt@Aalto.Fi URL: http://www.lce.hut.fi/~engelhar/ Mobil: +358-400193342
Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: +358-505113192
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Here is another approach possibly coming in the future. Maybe nvidia is getting back in the S3D game. http://www.stereoscopynews.com/index.php?option=com_content&view=article&id=... I definitely recommend two monitors, one dedicated to 3D viz and the other for control. On the mac, using chimera extensions I have created a third control surface that I push off onto an ipad. My chimera extension has a button that moves windows around, putting the layout in/out of S3D, moves it to a projector, etc. I prefer SBS over sequential, and avoid it more as a matter of long term strategy. Just getting harder to find hardware and I do not think that will improve in the future; HDMI has deemed SBS and framepack as must have features for S3D, sequential does not make the list, and the list includes a dozen other optional S3D methods. David is correct about the half view & mouse control. Not sure a change in chimera could fix that. Regardless my strategy is to avoid using the mouse on the 3D viz at every opportunity, hence the extensions. What I am realizing using S3D is that I have to up my precision of control, which is difficult to do with a mouse. In some of my situations I need 6 orders of magnitude for the range of control. With S3D, up close, rotating 1 degrees can be excessive and may require 0.01 degree movements as button pushes through USB-HID. You should also avoid using zooming in S3D and keep it at unity. Actually I recommend never using zooming, people should be using z translation which they think they are doing with zooming. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= ================================================= ________________________________________ From: David Bhella <David.Bhella@glasgow.ac.uk> Sent: Tuesday, December 1, 2015 2:23 AM To: Dougherty, Matthew T Cc: Tom Goddard; Engelhardt, Peter; chimera-users@cgl.ucsf.edu Subject: Feature suggestions - based on risk of loss of sequential stereo options Further to Matt’s comment, SBS works very well for rendering/display in 3D but it is difficult to work with for interactive visualisation because you must work full screen and chimera doesn’t completely understand that the left and right halves of the screen are now superimposed. Firstly accessing menus and the command line is problematic because you must move your mouse to the left eye view, so you need to mouse across the screen and off the left hand side. This is a relatively trivial irritation however. What is more challenging is interacting with the model/volume to select rotate/pan etc. So, to work with SBS 3D you must have a second monitor to handle all of the floating windows and non-3D stuff. It would be good to be able to float the display window and tear-off the drop-down menus and command line to view separately on the 2D monitor (perhaps you can already?). Currently mouse selection tools are focussed on the left hand view, while the rotation control seems to focus on the centre of the display, so sometimes when you intend to rotate the model you end up just rotating about z (or vice-versa). Perhaps it would be better to have all mouse interactions focus on the left-hand view and to have a visual cue to let you know when your mouse is over the left or right view? I have both nVidia sequential stereo (on linux) and SBS (on a 32” 3D samsung TV on my mac), interactive work is so much more straight-forward on the sequential setup. Dr David Bhella MRC-University of Glasgow Centre for Virus Research Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch
On 1 Dec 2015, at 07:28, Dougherty, Matthew T <matthewd@bcm.edu> wrote:
Sequential S3D is vanishing. Zspace uses it for their windows only apps. Nvidia barely supports S3D as a technology. Not sure if any other chip makers are using sequential anymore. Chip electronics have outpaced the need for sequential.
SBS half, the chimera DTI option output as HDMI is your best bet, regardless of the OS.
Some of the Samsung tv/monitors that do hdmi 2.0 now offer SBS half at 4k.
This resolution is better than bluray S3D framepack under HDMI 1.4, and is probably the best you will get for the foreseeable future (ie, 5-15 years).
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================
From: chimera-users-bounces@cgl.ucsf.edu <chimera-users-bounces@cgl.ucsf.edu> on behalf of Tom Goddard <goddard@sonic.net> Sent: Monday, November 30, 2015 4:26 PM To: Engelhardt, Peter Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Sequential stereo problems in Chimera in Mac after updating to OSX EL Capitan
Hi Peter,
If Chimera says "Unable to find hardware stereo support … “ when you enable sequential stereo it means the graphics driver does not support quad-buffered OpenGL stereo. Unfortunately Apple has not been interested in supporting stereo so I’m surprised you had it working recently. For several years now no machines Apple sold supported stereo. We had an ancient (8 year old) Nvidia Quadro FX 5600 in a Mac Pro until about 2 years ago, but the performance became so poor we abandoned it and had to switch to Windows. The new Mac Pro cylinders did not support stereo.
Unfortunately Apple also doesn’t seem to provide any information on which systems support stereo. We used to be able to get this information from the Apple OpenGL Capabilities web page
https://developer.apple.com/opengl/capabilities/ OpenGL version 1.5 - Apple Developer Tools OpenGL Capabilities Tables. The following table lists OpenGL extensions and parameter values reported for each of the OS X versions, graphics adapters, and CPU ... Read more...
but they stopped updating that two Mac OS versions ago (10.9). Now the only thing I can find from Apple about OpenGL support is this page
https://support.apple.com/en-us/HT202823
that lists the OpenGL version supported by each of their computers. Quad buffered stereo is not a requirement of any OpenGL version so this page does not help find out about stereo support.
With Mac OS El Capitan (10.11) Apple has talked a lot about “Metal” which is an alternative graphics programming interface. Chimera does not use it since it is Apple only and we need to support Linux and Windows.
In summary, I think Apple has dropped support for stereo on your systems. Could you tell us what graphics card it was working with and which Mac OS version (Mavericks 10.10?). Also if you use Chimera menu Help / Report a Bug… we will know the configuration that no longer works which will help us advise other Chimera users.
Tom
On Nov 30, 2015, at 12:54 PM, Engelhardt, Peter wrote:
Hi,
No sequential stereo is working in Chimera after updating of our Macs to OS X El Capitan - 10.11.1 in the CRTs linked to MacPros
Error remarks: - unable to turn on stereo viewing - "Unable to find hardware stereo support ... "
(see attachment).
This problem has not appeared in with earlier OSX updates!
We hope this problem will be fixed soon.
Cheers Peter
Peter Engelhardt, PhD, docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography
Nanomicroscopy Center (NMC), Department of Applied Physics Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland
Department of Pathology Haartman Institute P.O.Box 21 (Haartmaninkatu 3) FIN-00014 University of Helsinki, Finland
Email: Peter.Engelhardt@Helsinki.Fi Email: Peter.Engelhardt@Aalto.Fi URL: http://www.lce.hut.fi/~engelhar/ Mobil: +358-400193342
Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: +358-505113192
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
On Dec 1, 2015, at 12:23 AM, David Bhella <David.Bhella@glasgow.ac.uk> wrote:
It would be good to be able to float the display window and tear-off the drop-down menus and command line to view separately on the 2D monitor (perhaps you can already?).
If you use the X11 version of Chimera for the Mac, you can tear off the menus. You can’t with the native version. —Eric Eric Pettersen UCSF Computer Graphics Lab
Hi David, Only being able to do full-screen stereo is a pain in Chimera because you need a second display for the Chimera dialogs like Model Panel. Stereo-in-a-window allows the Chimera main window to be 3d with shutter glasses and the dialogs can be on the same display. The problem is that stereo-in-a-window is only supported on professional graphics cards as far as I know, such as the Nvidia Quadro series or AMD FirePro series. These are expensive cards. A year ago we tried an Nvidia Quadro K4000 ($800) and an AMD FirePro W7000 ($600). Both do stereo-in-a-window on Windows 7 on our lab stereo projector. We returned the K4000 because of some driver bug that effected Chimera. The AMD also does stereo-in-a-window on Linux, although it is pretty flakey (eyes swapped) and difficult to use with dual displays on Linux. The common consumer cards only do full-screen stereo such as the Nvidia Geforce series or AMD Radeon series. No graphics cards provided in Apple computers support stereo-in-a-window to my knowledge. We had a very old (2007) Mac Pro with an Nvidia Quadro FX 5600 that did stereo-in-a-window, but that is the last Mac I saw that could do it. Given all this we use professional graphics cards and Windows 7 for our stereo systems. I think all of this is independent of whether the display uses side-by-side format (SBS typical of 3d TVs) or sequential format (typical of stereo-capable computer displays). Both can do stereo-in-a-window with pro graphics, but only full-screen stereo with consumer graphics cards. I’m not completely sure that stereo-in-a-window works on the SBS and we will test that on Thursday. For the side-by-side format, even if the graphics driver does not support any stereo, Chimera can render the left and right eye images side-by-side and can be used on SBS displays — this mode is called DTI stereo in Chimera, each eye image is uses only half the screen width so resolution is not as good as sequential format stereo. Displays that take SBS format generally take full-width images for both eyes — so the a 1920x1080 display would really get a 3840x1080 image. But that requires graphics driver support for the graphics card to output a 3840x1080 image to a display device that says it is 1920x1080 in size. We haven’t done anything to make dual display Chimera where the graphics is full-screen on one display work smoothly. So for instance the Chimera command-line cannot be detached from the graphics window. Also I doubt Chimera will automatically put the dialog windows on the non-fullscreen display. Also the mouse cursor is handled by the operating system and it lines up with different objects in the left eye and the right eye which is annoying — Chimera uses the left eye alignment for selecting objects (ctrl-click). Mouse rotation considers the mouse position relative to the center of the screen. In summary, the stereo options are all expensive (stereo-in-a-window) or difficult to use (full-screen stereo) and restrict your choice of operating system (no stereo-in-a-window on Mac). The consumer uses of stereo to view 3-d movies or play 3-d video games are all full-screen so we can expect only full-screen to have decent support from the graphics card manufacturers. Tom
On Dec 1, 2015, at 12:23 AM, David Bhella wrote:
Further to Matt’s comment, SBS works very well for rendering/display in 3D but it is difficult to work with for interactive visualisation because you must work full screen and chimera doesn’t completely understand that the left and right halves of the screen are now superimposed. Firstly accessing menus and the command line is problematic because you must move your mouse to the left eye view, so you need to mouse across the screen and off the left hand side. This is a relatively trivial irritation however. What is more challenging is interacting with the model/volume to select rotate/pan etc.
So, to work with SBS 3D you must have a second monitor to handle all of the floating windows and non-3D stuff. It would be good to be able to float the display window and tear-off the drop-down menus and command line to view separately on the 2D monitor (perhaps you can already?). Currently mouse selection tools are focussed on the left hand view, while the rotation control seems to focus on the centre of the display, so sometimes when you intend to rotate the model you end up just rotating about z (or vice-versa). Perhaps it would be better to have all mouse interactions focus on the left-hand view and to have a visual cue to let you know when your mouse is over the left or right view?
I have both nVidia sequential stereo (on linux) and SBS (on a 32” 3D samsung TV on my mac), interactive work is so much more straight-forward on the sequential setup.
Dr David Bhella MRC-University of Glasgow Centre for Virus Research Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK)
Telephone: 0141-330-3685 Skype: d.bhella
Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk
CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch
On 1 Dec 2015, at 07:28, Dougherty, Matthew T wrote:
Sequential S3D is vanishing. Zspace uses it for their windows only apps. Nvidia barely supports S3D as a technology. Not sure if any other chip makers are using sequential anymore. Chip electronics have outpaced the need for sequential.
SBS half, the chimera DTI option output as HDMI is your best bet, regardless of the OS.
Some of the Samsung tv/monitors that do hdmi 2.0 now offer SBS half at 4k.
This resolution is better than bluray S3D framepack under HDMI 1.4, and is probably the best you will get for the foreseeable future (ie, 5-15 years).
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================
From: chimera-users-bounces@cgl.ucsf.edu <chimera-users-bounces@cgl.ucsf.edu> on behalf of Tom Goddard Sent: Monday, November 30, 2015 4:26 PM To: Engelhardt, Peter Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Sequential stereo problems in Chimera in Mac after updating to OSX EL Capitan
Hi Peter,
If Chimera says "Unable to find hardware stereo support … “ when you enable sequential stereo it means the graphics driver does not support quad-buffered OpenGL stereo. Unfortunately Apple has not been interested in supporting stereo so I’m surprised you had it working recently. For several years now no machines Apple sold supported stereo. We had an ancient (8 year old) Nvidia Quadro FX 5600 in a Mac Pro until about 2 years ago, but the performance became so poor we abandoned it and had to switch to Windows. The new Mac Pro cylinders did not support stereo.
Unfortunately Apple also doesn’t seem to provide any information on which systems support stereo. We used to be able to get this information from the Apple OpenGL Capabilities web page
https://developer.apple.com/opengl/capabilities/ OpenGL version 1.5 - Apple Developer Tools OpenGL Capabilities Tables. The following table lists OpenGL extensions and parameter values reported for each of the OS X versions, graphics adapters, and CPU ... Read more...
but they stopped updating that two Mac OS versions ago (10.9). Now the only thing I can find from Apple about OpenGL support is this page
https://support.apple.com/en-us/HT202823
that lists the OpenGL version supported by each of their computers. Quad buffered stereo is not a requirement of any OpenGL version so this page does not help find out about stereo support.
With Mac OS El Capitan (10.11) Apple has talked a lot about “Metal” which is an alternative graphics programming interface. Chimera does not use it since it is Apple only and we need to support Linux and Windows.
In summary, I think Apple has dropped support for stereo on your systems. Could you tell us what graphics card it was working with and which Mac OS version (Mavericks 10.10?). Also if you use Chimera menu Help / Report a Bug… we will know the configuration that no longer works which will help us advise other Chimera users.
Tom
On Nov 30, 2015, at 12:54 PM, Engelhardt, Peter wrote:
Hi,
No sequential stereo is working in Chimera after updating of our Macs to OS X El Capitan - 10.11.1 in the CRTs linked to MacPros
Error remarks: - unable to turn on stereo viewing - "Unable to find hardware stereo support ... "
(see attachment).
This problem has not appeared in with earlier OSX updates!
We hope this problem will be fixed soon.
Cheers Peter
Peter Engelhardt, PhD, docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography
Nanomicroscopy Center (NMC), Department of Applied Physics Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland
Department of Pathology Haartman Institute P.O.Box 21 (Haartmaninkatu 3) FIN-00014 University of Helsinki, Finland
Email: Peter.Engelhardt@Helsinki.Fi Email: Peter.Engelhardt@Aalto.Fi URL: http://www.lce.hut.fi/~engelhar/ Mobil: +358-400193342
Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: +358-505113192
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
FYI, stereo-in-a-window also works with AMD Radeon graphics cards that support HD3D on Windows 8. We haven't tested Windows 10 yet. So couple that with a 3D TV or monitor and you have a fairly inexpensive setup. See http://www.amd.com/HD3D for more details. -- Greg On 12/1/2015 5:48 PM, Tom Goddard wrote:
Hi David,
Only being able to do full-screen stereo is a pain in Chimera because you need a second display for the Chimera dialogs like Model Panel. Stereo-in-a-window allows the Chimera main window to be 3d with shutter glasses and the dialogs can be on the same display. The problem is that stereo-in-a-window is only supported on professional graphics cards as far as I know, such as the Nvidia Quadro series or AMD FirePro series. These are expensive cards. A year ago we tried an Nvidia Quadro K4000 ($800) and an AMD FirePro W7000 ($600). Both do stereo-in-a-window on Windows 7 on our lab stereo projector. We returned the K4000 because of some driver bug that effected Chimera. The AMD also does stereo-in-a-window on Linux, although it is pretty flakey (eyes swapped) and difficult to use with dual displays on Linux.
The common consumer cards only do full-screen stereo such as the Nvidia Geforce series or AMD Radeon series. No graphics cards provided in Apple computers support stereo-in-a-window to my knowledge. We had a very old (2007) Mac Pro with an Nvidia Quadro FX 5600 that did stereo-in-a-window, but that is the last Mac I saw that could do it.
Given all this we use professional graphics cards and Windows 7 for our stereo systems.
I think all of this is independent of whether the display uses side-by-side format (SBS typical of 3d TVs) or sequential format (typical of stereo-capable computer displays). Both can do stereo-in-a-window with pro graphics, but only full-screen stereo with consumer graphics cards. I’m not completely sure that stereo-in-a-window works on the SBS and we will test that on Thursday. For the side-by-side format, even if the graphics driver does not support any stereo, Chimera can render the left and right eye images side-by-side and can be used on SBS displays — this mode is called DTI stereo in Chimera, each eye image is uses only half the screen width so resolution is not as good as sequential format stereo. Displays that take SBS format generally take full-width images for both eyes — so the a 1920x1080 display would really get a 3840x1080 image. But that requires graphics driver support for the graphics card to output a 3840x1080 image to a display device that says it is 1920x1080 in size.
We haven’t done anything to make dual display Chimera where the graphics is full-screen on one display work smoothly. So for instance the Chimera command-line cannot be detached from the graphics window. Also I doubt Chimera will automatically put the dialog windows on the non-fullscreen display. Also the mouse cursor is handled by the operating system and it lines up with different objects in the left eye and the right eye which is annoying — Chimera uses the left eye alignment for selecting objects (ctrl-click). Mouse rotation considers the mouse position relative to the center of the screen.
In summary, the stereo options are all expensive (stereo-in-a-window) or difficult to use (full-screen stereo) and restrict your choice of operating system (no stereo-in-a-window on Mac). The consumer uses of stereo to view 3-d movies or play 3-d video games are all full-screen so we can expect only full-screen to have decent support from the graphics card manufacturers.
Tom
On Dec 1, 2015, at 12:23 AM, David Bhella wrote:
Further to Matt’s comment, SBS works very well for rendering/display in 3D but it is difficult to work with for interactive visualisation because you must work full screen and chimera doesn’t completely understand that the left and right halves of the screen are now superimposed. Firstly accessing menus and the command line is problematic because you must move your mouse to the left eye view, so you need to mouse across the screen and off the left hand side. This is a relatively trivial irritation however. What is more challenging is interacting with the model/volume to select rotate/pan etc.
So, to work with SBS 3D you must have a second monitor to handle all of the floating windows and non-3D stuff. It would be good to be able to float the display window and tear-off the drop-down menus and command line to view separately on the 2D monitor (perhaps you can already?). Currently mouse selection tools are focussed on the left hand view, while the rotation control seems to focus on the centre of the display, so sometimes when you intend to rotate the model you end up just rotating about z (or vice-versa). Perhaps it would be better to have all mouse interactions focus on the left-hand view and to have a visual cue to let you know when your mouse is over the left or right view?
I have both nVidia sequential stereo (on linux) and SBS (on a 32” 3D samsung TV on my mac), interactive work is so much more straight-forward on the sequential setup.
Dr David Bhella MRC-University of Glasgow Centre for Virus Research Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK)
Telephone: 0141-330-3685 Skype: d.bhella
Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk
CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch
On 1 Dec 2015, at 07:28, Dougherty, Matthew T wrote:
Sequential S3D is vanishing. Zspace uses it for their windows only apps. Nvidia barely supports S3D as a technology. Not sure if any other chip makers are using sequential anymore. Chip electronics have outpaced the need for sequential.
SBS half, the chimera DTI option output as HDMI is your best bet, regardless of the OS.
Some of the Samsung tv/monitors that do hdmi 2.0 now offer SBS half at 4k.
This resolution is better than bluray S3D framepack under HDMI 1.4, and is probably the best you will get for the foreseeable future (ie, 5-15 years).
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================
From: chimera-users-bounces@cgl.ucsf.edu <chimera-users-bounces@cgl.ucsf.edu> on behalf of Tom Goddard Sent: Monday, November 30, 2015 4:26 PM To: Engelhardt, Peter Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Sequential stereo problems in Chimera in Mac after updating to OSX EL Capitan
Hi Peter,
If Chimera says "Unable to find hardware stereo support … “ when you enable sequential stereo it means the graphics driver does not support quad-buffered OpenGL stereo. Unfortunately Apple has not been interested in supporting stereo so I’m surprised you had it working recently. For several years now no machines Apple sold supported stereo. We had an ancient (8 year old) Nvidia Quadro FX 5600 in a Mac Pro until about 2 years ago, but the performance became so poor we abandoned it and had to switch to Windows. The new Mac Pro cylinders did not support stereo.
Unfortunately Apple also doesn’t seem to provide any information on which systems support stereo. We used to be able to get this information from the Apple OpenGL Capabilities web page
https://developer.apple.com/opengl/capabilities/ OpenGL version 1.5 - Apple Developer Tools OpenGL Capabilities Tables. The following table lists OpenGL extensions and parameter values reported for each of the OS X versions, graphics adapters, and CPU ... Read more...
but they stopped updating that two Mac OS versions ago (10.9). Now the only thing I can find from Apple about OpenGL support is this page
https://support.apple.com/en-us/HT202823
that lists the OpenGL version supported by each of their computers. Quad buffered stereo is not a requirement of any OpenGL version so this page does not help find out about stereo support.
With Mac OS El Capitan (10.11) Apple has talked a lot about “Metal” which is an alternative graphics programming interface. Chimera does not use it since it is Apple only and we need to support Linux and Windows.
In summary, I think Apple has dropped support for stereo on your systems. Could you tell us what graphics card it was working with and which Mac OS version (Mavericks 10.10?). Also if you use Chimera menu Help / Report a Bug… we will know the configuration that no longer works which will help us advise other Chimera users.
Tom
On Nov 30, 2015, at 12:54 PM, Engelhardt, Peter wrote:
Hi,
No sequential stereo is working in Chimera after updating of our Macs to OS X El Capitan - 10.11.1 in the CRTs linked to MacPros
Error remarks: - unable to turn on stereo viewing - "Unable to find hardware stereo support ... "
(see attachment).
This problem has not appeared in with earlier OSX updates!
We hope this problem will be fixed soon.
Cheers Peter
Peter Engelhardt, PhD, docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography
Nanomicroscopy Center (NMC), Department of Applied Physics Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland
Department of Pathology Haartman Institute P.O.Box 21 (Haartmaninkatu 3) FIN-00014 University of Helsinki, Finland
Email: Peter.Engelhardt@Helsinki.Fi Email: Peter.Engelhardt@Aalto.Fi URL: http://www.lce.hut.fi/~engelhar/ Mobil: +358-400193342
Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: +358-505113192
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
regarding /www.amd.com/HD3D AMD seems to have the same problem as nividia's 3dvision, most of the displays are no longer available. Both websites seem to stop updating around 2011, when the S3D market tanked. This is not to say S3D is dead; S3D has cycled through boom to bust, 5-10 times over the last 100 years (this includes photography). On the last cycle the incremental improvement was getting a standard in place for HDMI S3D. The key concept is including metadata ('vendor specific info packets'), that directs the hardware to automatically switch between mono mode and S3D, providing sufficient detail as to the type of S3D (eg, SBS-half, SBS-full, T/B, framepack, quincunx); something the pro market never could figure out. Safest strategy is to plan for HDMI compliance. I agree with Tom, go with consumer products. Buying s3D displays is now the biggest limitation, and for the forseeable future. The movie industry and 4k TV manufacturers are the ones keeping the S3D business financially viable. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= ================================================= ________________________________________ From: chimera-users-bounces@cgl.ucsf.edu <chimera-users-bounces@cgl.ucsf.edu> on behalf of Greg Couch <gregc@cgl.ucsf.edu> Sent: Wednesday, December 2, 2015 3:00 PM To: Tom Goddard; David Bhella Cc: chimera-users@cgl.ucsf.edu; Engelhardt, Peter Subject: Re: [Chimera-users] Feature suggestions - based on risk of loss of sequential stereo options FYI, stereo-in-a-window also works with AMD Radeon graphics cards that support HD3D on Windows 8. We haven't tested Windows 10 yet. So couple that with a 3D TV or monitor and you have a fairly inexpensive setup. See http://www.amd.com/HD3D for more details. -- Greg On 12/1/2015 5:48 PM, Tom Goddard wrote:
Hi David,
Only being able to do full-screen stereo is a pain in Chimera because you need a second display for the Chimera dialogs like Model Panel. Stereo-in-a-window allows the Chimera main window to be 3d with shutter glasses and the dialogs can be on the same display. The problem is that stereo-in-a-window is only supported on professional graphics cards as far as I know, such as the Nvidia Quadro series or AMD FirePro series. These are expensive cards. A year ago we tried an Nvidia Quadro K4000 ($800) and an AMD FirePro W7000 ($600). Both do stereo-in-a-window on Windows 7 on our lab stereo projector. We returned the K4000 because of some driver bug that effected Chimera. The AMD also does stereo-in-a-window on Linux, although it is pretty flakey (eyes swapped) and difficult to use with dual displays on Linux.
The common consumer cards only do full-screen stereo such as the Nvidia Geforce series or AMD Radeon series. No graphics cards provided in Apple computers support stereo-in-a-window to my knowledge. We had a very old (2007) Mac Pro with an Nvidia Quadro FX 5600 that did stereo-in-a-window, but that is the last Mac I saw that could do it.
Given all this we use professional graphics cards and Windows 7 for our stereo systems.
I think all of this is independent of whether the display uses side-by-side format (SBS typical of 3d TVs) or sequential format (typical of stereo-capable computer displays). Both can do stereo-in-a-window with pro graphics, but only full-screen stereo with consumer graphics cards. I’m not completely sure that stereo-in-a-window works on the SBS and we will test that on Thursday. For the side-by-side format, even if the graphics driver does not support any stereo, Chimera can render the left and right eye images side-by-side and can be used on SBS displays — this mode is called DTI stereo in Chimera, each eye image is uses only half the screen width so resolution is not as good as sequential format stereo. Displays that take SBS format generally take full-width images for both eyes — so the a 1920x1080 display would really get a 3840x1080 image. But that requires graphics driver support for the graphics card to output a 3840x1080 image to a display device that says it is 1920x1080 in size.
We haven’t done anything to make dual display Chimera where the graphics is full-screen on one display work smoothly. So for instance the Chimera command-line cannot be detached from the graphics window. Also I doubt Chimera will automatically put the dialog windows on the non-fullscreen display. Also the mouse cursor is handled by the operating system and it lines up with different objects in the left eye and the right eye which is annoying — Chimera uses the left eye alignment for selecting objects (ctrl-click). Mouse rotation considers the mouse position relative to the center of the screen.
In summary, the stereo options are all expensive (stereo-in-a-window) or difficult to use (full-screen stereo) and restrict your choice of operating system (no stereo-in-a-window on Mac). The consumer uses of stereo to view 3-d movies or play 3-d video games are all full-screen so we can expect only full-screen to have decent support from the graphics card manufacturers.
Tom
On Dec 1, 2015, at 12:23 AM, David Bhella wrote:
Further to Matt’s comment, SBS works very well for rendering/display in 3D but it is difficult to work with for interactive visualisation because you must work full screen and chimera doesn’t completely understand that the left and right halves of the screen are now superimposed. Firstly accessing menus and the command line is problematic because you must move your mouse to the left eye view, so you need to mouse across the screen and off the left hand side. This is a relatively trivial irritation however. What is more challenging is interacting with the model/volume to select rotate/pan etc.
So, to work with SBS 3D you must have a second monitor to handle all of the floating windows and non-3D stuff. It would be good to be able to float the display window and tear-off the drop-down menus and command line to view separately on the 2D monitor (perhaps you can already?). Currently mouse selection tools are focussed on the left hand view, while the rotation control seems to focus on the centre of the display, so sometimes when you intend to rotate the model you end up just rotating about z (or vice-versa). Perhaps it would be better to have all mouse interactions focus on the left-hand view and to have a visual cue to let you know when your mouse is over the left or right view?
I have both nVidia sequential stereo (on linux) and SBS (on a 32” 3D samsung TV on my mac), interactive work is so much more straight-forward on the sequential setup.
Dr David Bhella MRC-University of Glasgow Centre for Virus Research Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK)
Telephone: 0141-330-3685 Skype: d.bhella
Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk
CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch
On 1 Dec 2015, at 07:28, Dougherty, Matthew T wrote:
Sequential S3D is vanishing. Zspace uses it for their windows only apps. Nvidia barely supports S3D as a technology. Not sure if any other chip makers are using sequential anymore. Chip electronics have outpaced the need for sequential.
SBS half, the chimera DTI option output as HDMI is your best bet, regardless of the OS.
Some of the Samsung tv/monitors that do hdmi 2.0 now offer SBS half at 4k.
This resolution is better than bluray S3D framepack under HDMI 1.4, and is probably the best you will get for the foreseeable future (ie, 5-15 years).
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================
From: chimera-users-bounces@cgl.ucsf.edu <chimera-users-bounces@cgl.ucsf.edu> on behalf of Tom Goddard Sent: Monday, November 30, 2015 4:26 PM To: Engelhardt, Peter Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Sequential stereo problems in Chimera in Mac after updating to OSX EL Capitan
Hi Peter,
If Chimera says "Unable to find hardware stereo support … “ when you enable sequential stereo it means the graphics driver does not support quad-buffered OpenGL stereo. Unfortunately Apple has not been interested in supporting stereo so I’m surprised you had it working recently. For several years now no machines Apple sold supported stereo. We had an ancient (8 year old) Nvidia Quadro FX 5600 in a Mac Pro until about 2 years ago, but the performance became so poor we abandoned it and had to switch to Windows. The new Mac Pro cylinders did not support stereo.
Unfortunately Apple also doesn’t seem to provide any information on which systems support stereo. We used to be able to get this information from the Apple OpenGL Capabilities web page
https://developer.apple.com/opengl/capabilities/ OpenGL version 1.5 - Apple Developer Tools OpenGL Capabilities Tables. The following table lists OpenGL extensions and parameter values reported for each of the OS X versions, graphics adapters, and CPU ... Read more...
but they stopped updating that two Mac OS versions ago (10.9). Now the only thing I can find from Apple about OpenGL support is this page
https://support.apple.com/en-us/HT202823
that lists the OpenGL version supported by each of their computers. Quad buffered stereo is not a requirement of any OpenGL version so this page does not help find out about stereo support.
With Mac OS El Capitan (10.11) Apple has talked a lot about “Metal” which is an alternative graphics programming interface. Chimera does not use it since it is Apple only and we need to support Linux and Windows.
In summary, I think Apple has dropped support for stereo on your systems. Could you tell us what graphics card it was working with and which Mac OS version (Mavericks 10.10?). Also if you use Chimera menu Help / Report a Bug… we will know the configuration that no longer works which will help us advise other Chimera users.
Tom
On Nov 30, 2015, at 12:54 PM, Engelhardt, Peter wrote:
Hi,
No sequential stereo is working in Chimera after updating of our Macs to OS X El Capitan - 10.11.1 in the CRTs linked to MacPros
Error remarks: - unable to turn on stereo viewing - "Unable to find hardware stereo support ... "
(see attachment).
This problem has not appeared in with earlier OSX updates!
We hope this problem will be fixed soon.
Cheers Peter
Peter Engelhardt, PhD, docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography
Nanomicroscopy Center (NMC), Department of Applied Physics Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland
Department of Pathology Haartman Institute P.O.Box 21 (Haartmaninkatu 3) FIN-00014 University of Helsinki, Finland
Email: Peter.Engelhardt@Helsinki.Fi Email: Peter.Engelhardt@Aalto.Fi URL: http://www.lce.hut.fi/~engelhar/ Mobil: +358-400193342
Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: +358-505113192
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Good Morning to all of you, We thank you all for your valuable comments on Chimera stereo and sorry for delay in answering. The simplest way to have sequential stereo back here was to remove El Capitan and go back to Yosemite that took some time! The Chimera sequential stereo is now working again in the adjacent VGA Display of our "old MacPro" - (Early 2008) with NVIDIA Quadro FX 5600 MB. More, we are unable to get a any 'workable SBS stereo' using DTI - only side by side deformed images are visible that are impossible to superimpose to stereo - on any big TV screens or displays? Before converting back from El Capitan to Yosemite of our second "old MacPro" (Early 2009) with NVIDIA Quodro FX 4800 1536 MB - we wonder now - if Chimera 'El Capitan update' could somehow 'restore' the sequential stereo? We thank you in advance and hope to hear your comments. Cheers Peter ________________________________________ From: Dougherty, Matthew T <matthewd@bcm.edu> Sent: Wednesday, December 2, 2015 11:52 PM To: Greg Couch; Tom Goddard; David Bhella Cc: chimera-users@cgl.ucsf.edu; Engelhardt, Peter Subject: Re: [Chimera-users] Feature suggestions - based on risk of loss of sequential stereo options regarding /www.amd.com/HD3D AMD seems to have the same problem as nividia's 3dvision, most of the displays are no longer available. Both websites seem to stop updating around 2011, when the S3D market tanked. This is not to say S3D is dead; S3D has cycled through boom to bust, 5-10 times over the last 100 years (this includes photography). On the last cycle the incremental improvement was getting a standard in place for HDMI S3D. The key concept is including metadata ('vendor specific info packets'), that directs the hardware to automatically switch between mono mode and S3D, providing sufficient detail as to the type of S3D (eg, SBS-half, SBS-full, T/B, framepack, quincunx); something the pro market never could figure out. Safest strategy is to plan for HDMI compliance. I agree with Tom, go with consumer products. Buying s3D displays is now the biggest limitation, and for the forseeable future. The movie industry and 4k TV manufacturers are the ones keeping the S3D business financially viable. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= ================================================= ________________________________________ From: chimera-users-bounces@cgl.ucsf.edu <chimera-users-bounces@cgl.ucsf.edu> on behalf of Greg Couch <gregc@cgl.ucsf.edu> Sent: Wednesday, December 2, 2015 3:00 PM To: Tom Goddard; David Bhella Cc: chimera-users@cgl.ucsf.edu; Engelhardt, Peter Subject: Re: [Chimera-users] Feature suggestions - based on risk of loss of sequential stereo options FYI, stereo-in-a-window also works with AMD Radeon graphics cards that support HD3D on Windows 8. We haven't tested Windows 10 yet. So couple that with a 3D TV or monitor and you have a fairly inexpensive setup. See http://www.amd.com/HD3D for more details. -- Greg On 12/1/2015 5:48 PM, Tom Goddard wrote:
Hi David,
Only being able to do full-screen stereo is a pain in Chimera because you need a second display for the Chimera dialogs like Model Panel. Stereo-in-a-window allows the Chimera main window to be 3d with shutter glasses and the dialogs can be on the same display. The problem is that stereo-in-a-window is only supported on professional graphics cards as far as I know, such as the Nvidia Quadro series or AMD FirePro series. These are expensive cards. A year ago we tried an Nvidia Quadro K4000 ($800) and an AMD FirePro W7000 ($600). Both do stereo-in-a-window on Windows 7 on our lab stereo projector. We returned the K4000 because of some driver bug that effected Chimera. The AMD also does stereo-in-a-window on Linux, although it is pretty flakey (eyes swapped) and difficult to use with dual displays on Linux.
The common consumer cards only do full-screen stereo such as the Nvidia Geforce series or AMD Radeon series. No graphics cards provided in Apple computers support stereo-in-a-window to my knowledge. We had a very old (2007) Mac Pro with an Nvidia Quadro FX 5600 that did stereo-in-a-window, but that is the last Mac I saw that could do it.
Given all this we use professional graphics cards and Windows 7 for our stereo systems.
I think all of this is independent of whether the display uses side-by-side format (SBS typical of 3d TVs) or sequential format (typical of stereo-capable computer displays). Both can do stereo-in-a-window with pro graphics, but only full-screen stereo with consumer graphics cards. I’m not completely sure that stereo-in-a-window works on the SBS and we will test that on Thursday. For the side-by-side format, even if the graphics driver does not support any stereo, Chimera can render the left and right eye images side-by-side and can be used on SBS displays — this mode is called DTI stereo in Chimera, each eye image is uses only half the screen width so resolution is not as good as sequential format stereo. Displays that take SBS format generally take full-width images for both eyes — so the a 1920x1080 display would really get a 3840x1080 image. But that requires graphics driver support for the graphics card to output a 3840x1080 image to a display device that says it is 1920x1080 in size.
We haven’t done anything to make dual display Chimera where the graphics is full-screen on one display work smoothly. So for instance the Chimera command-line cannot be detached from the graphics window. Also I doubt Chimera will automatically put the dialog windows on the non-fullscreen display. Also the mouse cursor is handled by the operating system and it lines up with different objects in the left eye and the right eye which is annoying — Chimera uses the left eye alignment for selecting objects (ctrl-click). Mouse rotation considers the mouse position relative to the center of the screen.
In summary, the stereo options are all expensive (stereo-in-a-window) or difficult to use (full-screen stereo) and restrict your choice of operating system (no stereo-in-a-window on Mac). The consumer uses of stereo to view 3-d movies or play 3-d video games are all full-screen so we can expect only full-screen to have decent support from the graphics card manufacturers.
Tom
On Dec 1, 2015, at 12:23 AM, David Bhella wrote:
Further to Matt’s comment, SBS works very well for rendering/display in 3D but it is difficult to work with for interactive visualisation because you must work full screen and chimera doesn’t completely understand that the left and right halves of the screen are now superimposed. Firstly accessing menus and the command line is problematic because you must move your mouse to the left eye view, so you need to mouse across the screen and off the left hand side. This is a relatively trivial irritation however. What is more challenging is interacting with the model/volume to select rotate/pan etc.
So, to work with SBS 3D you must have a second monitor to handle all of the floating windows and non-3D stuff. It would be good to be able to float the display window and tear-off the drop-down menus and command line to view separately on the 2D monitor (perhaps you can already?). Currently mouse selection tools are focussed on the left hand view, while the rotation control seems to focus on the centre of the display, so sometimes when you intend to rotate the model you end up just rotating about z (or vice-versa). Perhaps it would be better to have all mouse interactions focus on the left-hand view and to have a visual cue to let you know when your mouse is over the left or right view?
I have both nVidia sequential stereo (on linux) and SBS (on a 32” 3D samsung TV on my mac), interactive work is so much more straight-forward on the sequential setup.
Dr David Bhella MRC-University of Glasgow Centre for Virus Research Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK)
Telephone: 0141-330-3685 Skype: d.bhella
Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk
CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch
On 1 Dec 2015, at 07:28, Dougherty, Matthew T wrote:
Sequential S3D is vanishing. Zspace uses it for their windows only apps. Nvidia barely supports S3D as a technology. Not sure if any other chip makers are using sequential anymore. Chip electronics have outpaced the need for sequential.
SBS half, the chimera DTI option output as HDMI is your best bet, regardless of the OS.
Some of the Samsung tv/monitors that do hdmi 2.0 now offer SBS half at 4k.
This resolution is better than bluray S3D framepack under HDMI 1.4, and is probably the best you will get for the foreseeable future (ie, 5-15 years).
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================
From: chimera-users-bounces@cgl.ucsf.edu <chimera-users-bounces@cgl.ucsf.edu> on behalf of Tom Goddard Sent: Monday, November 30, 2015 4:26 PM To: Engelhardt, Peter Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Sequential stereo problems in Chimera in Mac after updating to OSX EL Capitan
Hi Peter,
If Chimera says "Unable to find hardware stereo support … “ when you enable sequential stereo it means the graphics driver does not support quad-buffered OpenGL stereo. Unfortunately Apple has not been interested in supporting stereo so I’m surprised you had it working recently. For several years now no machines Apple sold supported stereo. We had an ancient (8 year old) Nvidia Quadro FX 5600 in a Mac Pro until about 2 years ago, but the performance became so poor we abandoned it and had to switch to Windows. The new Mac Pro cylinders did not support stereo.
Unfortunately Apple also doesn’t seem to provide any information on which systems support stereo. We used to be able to get this information from the Apple OpenGL Capabilities web page
https://developer.apple.com/opengl/capabilities/ OpenGL version 1.5 - Apple Developer Tools OpenGL Capabilities Tables. The following table lists OpenGL extensions and parameter values reported for each of the OS X versions, graphics adapters, and CPU ... Read more...
but they stopped updating that two Mac OS versions ago (10.9). Now the only thing I can find from Apple about OpenGL support is this page
https://support.apple.com/en-us/HT202823
that lists the OpenGL version supported by each of their computers. Quad buffered stereo is not a requirement of any OpenGL version so this page does not help find out about stereo support.
With Mac OS El Capitan (10.11) Apple has talked a lot about “Metal” which is an alternative graphics programming interface. Chimera does not use it since it is Apple only and we need to support Linux and Windows.
In summary, I think Apple has dropped support for stereo on your systems. Could you tell us what graphics card it was working with and which Mac OS version (Mavericks 10.10?). Also if you use Chimera menu Help / Report a Bug… we will know the configuration that no longer works which will help us advise other Chimera users.
Tom
On Nov 30, 2015, at 12:54 PM, Engelhardt, Peter wrote:
Hi,
No sequential stereo is working in Chimera after updating of our Macs to OS X El Capitan - 10.11.1 in the CRTs linked to MacPros
Error remarks: - unable to turn on stereo viewing - "Unable to find hardware stereo support ... "
(see attachment).
This problem has not appeared in with earlier OSX updates!
We hope this problem will be fixed soon.
Cheers Peter
Peter Engelhardt, PhD, docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography
Nanomicroscopy Center (NMC), Department of Applied Physics Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland
Department of Pathology Haartman Institute P.O.Box 21 (Haartmaninkatu 3) FIN-00014 University of Helsinki, Finland
Email: Peter.Engelhardt@Helsinki.Fi Email: Peter.Engelhardt@Aalto.Fi URL: http://www.lce.hut.fi/~engelhar/ Mobil: +358-400193342
Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: +358-505113192
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
More, we are unable to get a any 'workable SBS stereo' using DTI - only side by side deformed images are visible that are impossible to superimpose to stereo - on any big TV screens or displays?
Not clear on sentence/question. SBS-half (DTI) is a mandatory requirement of HDMI 1.4+, should work on any any 3DTV™ monitor. Because you are not generating vendor specific info packets that have stereo3D metadata, it will not switch automatically so you must manually activate/deactivate stereo3D on the display (usually by the remote). === The sequential problem is in the OS; apple has removed the capability. And apple no longer supports add on cards. You can kludge it with some 3rd party thunderbolt to PCI boxes, but the odds of making it work are slim because low lever OS I/O drivers have to interact with the graphics card, which means you will have to write them. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= ================================================= ________________________________________ From: Engelhardt, Peter <peter.engelhardt@helsinki.fi> Sent: Tuesday, December 8, 2015 12:34 PM To: Dougherty, Matthew T; Greg Couch; Tom Goddard; David Bhella Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Feature suggestions - based on risk of loss of sequential stereo options Good Morning to all of you, We thank you all for your valuable comments on Chimera stereo and sorry for delay in answering. The simplest way to have sequential stereo back here was to remove El Capitan and go back to Yosemite that took some time! The Chimera sequential stereo is now working again in the adjacent VGA Display of our "old MacPro" - (Early 2008) with NVIDIA Quadro FX 5600 MB. More, we are unable to get a any 'workable SBS stereo' using DTI - only side by side deformed images are visible that are impossible to superimpose to stereo - on any big TV screens or displays? Before converting back from El Capitan to Yosemite of our second "old MacPro" (Early 2009) with NVIDIA Quodro FX 4800 1536 MB - we wonder now - if Chimera 'El Capitan update' could somehow 'restore' the sequential stereo? We thank you in advance and hope to hear your comments. Cheers Peter ________________________________________ From: Dougherty, Matthew T <matthewd@bcm.edu> Sent: Wednesday, December 2, 2015 11:52 PM To: Greg Couch; Tom Goddard; David Bhella Cc: chimera-users@cgl.ucsf.edu; Engelhardt, Peter Subject: Re: [Chimera-users] Feature suggestions - based on risk of loss of sequential stereo options regarding /www.amd.com/HD3D AMD seems to have the same problem as nividia's 3dvision, most of the displays are no longer available. Both websites seem to stop updating around 2011, when the S3D market tanked. This is not to say S3D is dead; S3D has cycled through boom to bust, 5-10 times over the last 100 years (this includes photography). On the last cycle the incremental improvement was getting a standard in place for HDMI S3D. The key concept is including metadata ('vendor specific info packets'), that directs the hardware to automatically switch between mono mode and S3D, providing sufficient detail as to the type of S3D (eg, SBS-half, SBS-full, T/B, framepack, quincunx); something the pro market never could figure out. Safest strategy is to plan for HDMI compliance. I agree with Tom, go with consumer products. Buying s3D displays is now the biggest limitation, and for the forseeable future. The movie industry and 4k TV manufacturers are the ones keeping the S3D business financially viable. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= ================================================= ________________________________________ From: chimera-users-bounces@cgl.ucsf.edu <chimera-users-bounces@cgl.ucsf.edu> on behalf of Greg Couch <gregc@cgl.ucsf.edu> Sent: Wednesday, December 2, 2015 3:00 PM To: Tom Goddard; David Bhella Cc: chimera-users@cgl.ucsf.edu; Engelhardt, Peter Subject: Re: [Chimera-users] Feature suggestions - based on risk of loss of sequential stereo options FYI, stereo-in-a-window also works with AMD Radeon graphics cards that support HD3D on Windows 8. We haven't tested Windows 10 yet. So couple that with a 3D TV or monitor and you have a fairly inexpensive setup. See http://www.amd.com/HD3D for more details. -- Greg On 12/1/2015 5:48 PM, Tom Goddard wrote:
Hi David,
Only being able to do full-screen stereo is a pain in Chimera because you need a second display for the Chimera dialogs like Model Panel. Stereo-in-a-window allows the Chimera main window to be 3d with shutter glasses and the dialogs can be on the same display. The problem is that stereo-in-a-window is only supported on professional graphics cards as far as I know, such as the Nvidia Quadro series or AMD FirePro series. These are expensive cards. A year ago we tried an Nvidia Quadro K4000 ($800) and an AMD FirePro W7000 ($600). Both do stereo-in-a-window on Windows 7 on our lab stereo projector. We returned the K4000 because of some driver bug that effected Chimera. The AMD also does stereo-in-a-window on Linux, although it is pretty flakey (eyes swapped) and difficult to use with dual displays on Linux.
The common consumer cards only do full-screen stereo such as the Nvidia Geforce series or AMD Radeon series. No graphics cards provided in Apple computers support stereo-in-a-window to my knowledge. We had a very old (2007) Mac Pro with an Nvidia Quadro FX 5600 that did stereo-in-a-window, but that is the last Mac I saw that could do it.
Given all this we use professional graphics cards and Windows 7 for our stereo systems.
I think all of this is independent of whether the display uses side-by-side format (SBS typical of 3d TVs) or sequential format (typical of stereo-capable computer displays). Both can do stereo-in-a-window with pro graphics, but only full-screen stereo with consumer graphics cards. I’m not completely sure that stereo-in-a-window works on the SBS and we will test that on Thursday. For the side-by-side format, even if the graphics driver does not support any stereo, Chimera can render the left and right eye images side-by-side and can be used on SBS displays — this mode is called DTI stereo in Chimera, each eye image is uses only half the screen width so resolution is not as good as sequential format stereo. Displays that take SBS format generally take full-width images for both eyes — so the a 1920x1080 display would really get a 3840x1080 image. But that requires graphics driver support for the graphics card to output a 3840x1080 image to a display device that says it is 1920x1080 in size.
We haven’t done anything to make dual display Chimera where the graphics is full-screen on one display work smoothly. So for instance the Chimera command-line cannot be detached from the graphics window. Also I doubt Chimera will automatically put the dialog windows on the non-fullscreen display. Also the mouse cursor is handled by the operating system and it lines up with different objects in the left eye and the right eye which is annoying — Chimera uses the left eye alignment for selecting objects (ctrl-click). Mouse rotation considers the mouse position relative to the center of the screen.
In summary, the stereo options are all expensive (stereo-in-a-window) or difficult to use (full-screen stereo) and restrict your choice of operating system (no stereo-in-a-window on Mac). The consumer uses of stereo to view 3-d movies or play 3-d video games are all full-screen so we can expect only full-screen to have decent support from the graphics card manufacturers.
Tom
On Dec 1, 2015, at 12:23 AM, David Bhella wrote:
Further to Matt’s comment, SBS works very well for rendering/display in 3D but it is difficult to work with for interactive visualisation because you must work full screen and chimera doesn’t completely understand that the left and right halves of the screen are now superimposed. Firstly accessing menus and the command line is problematic because you must move your mouse to the left eye view, so you need to mouse across the screen and off the left hand side. This is a relatively trivial irritation however. What is more challenging is interacting with the model/volume to select rotate/pan etc.
So, to work with SBS 3D you must have a second monitor to handle all of the floating windows and non-3D stuff. It would be good to be able to float the display window and tear-off the drop-down menus and command line to view separately on the 2D monitor (perhaps you can already?). Currently mouse selection tools are focussed on the left hand view, while the rotation control seems to focus on the centre of the display, so sometimes when you intend to rotate the model you end up just rotating about z (or vice-versa). Perhaps it would be better to have all mouse interactions focus on the left-hand view and to have a visual cue to let you know when your mouse is over the left or right view?
I have both nVidia sequential stereo (on linux) and SBS (on a 32” 3D samsung TV on my mac), interactive work is so much more straight-forward on the sequential setup.
Dr David Bhella MRC-University of Glasgow Centre for Virus Research Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK)
Telephone: 0141-330-3685 Skype: d.bhella
Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk
CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch
On 1 Dec 2015, at 07:28, Dougherty, Matthew T wrote:
Sequential S3D is vanishing. Zspace uses it for their windows only apps. Nvidia barely supports S3D as a technology. Not sure if any other chip makers are using sequential anymore. Chip electronics have outpaced the need for sequential.
SBS half, the chimera DTI option output as HDMI is your best bet, regardless of the OS.
Some of the Samsung tv/monitors that do hdmi 2.0 now offer SBS half at 4k.
This resolution is better than bluray S3D framepack under HDMI 1.4, and is probably the best you will get for the foreseeable future (ie, 5-15 years).
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================
From: chimera-users-bounces@cgl.ucsf.edu <chimera-users-bounces@cgl.ucsf.edu> on behalf of Tom Goddard Sent: Monday, November 30, 2015 4:26 PM To: Engelhardt, Peter Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Sequential stereo problems in Chimera in Mac after updating to OSX EL Capitan
Hi Peter,
If Chimera says "Unable to find hardware stereo support … “ when you enable sequential stereo it means the graphics driver does not support quad-buffered OpenGL stereo. Unfortunately Apple has not been interested in supporting stereo so I’m surprised you had it working recently. For several years now no machines Apple sold supported stereo. We had an ancient (8 year old) Nvidia Quadro FX 5600 in a Mac Pro until about 2 years ago, but the performance became so poor we abandoned it and had to switch to Windows. The new Mac Pro cylinders did not support stereo.
Unfortunately Apple also doesn’t seem to provide any information on which systems support stereo. We used to be able to get this information from the Apple OpenGL Capabilities web page
https://developer.apple.com/opengl/capabilities/ OpenGL version 1.5 - Apple Developer Tools OpenGL Capabilities Tables. The following table lists OpenGL extensions and parameter values reported for each of the OS X versions, graphics adapters, and CPU ... Read more...
but they stopped updating that two Mac OS versions ago (10.9). Now the only thing I can find from Apple about OpenGL support is this page
https://support.apple.com/en-us/HT202823
that lists the OpenGL version supported by each of their computers. Quad buffered stereo is not a requirement of any OpenGL version so this page does not help find out about stereo support.
With Mac OS El Capitan (10.11) Apple has talked a lot about “Metal” which is an alternative graphics programming interface. Chimera does not use it since it is Apple only and we need to support Linux and Windows.
In summary, I think Apple has dropped support for stereo on your systems. Could you tell us what graphics card it was working with and which Mac OS version (Mavericks 10.10?). Also if you use Chimera menu Help / Report a Bug… we will know the configuration that no longer works which will help us advise other Chimera users.
Tom
On Nov 30, 2015, at 12:54 PM, Engelhardt, Peter wrote:
Hi,
No sequential stereo is working in Chimera after updating of our Macs to OS X El Capitan - 10.11.1 in the CRTs linked to MacPros
Error remarks: - unable to turn on stereo viewing - "Unable to find hardware stereo support ... "
(see attachment).
This problem has not appeared in with earlier OSX updates!
We hope this problem will be fixed soon.
Cheers Peter
Peter Engelhardt, PhD, docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography
Nanomicroscopy Center (NMC), Department of Applied Physics Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland
Department of Pathology Haartman Institute P.O.Box 21 (Haartmaninkatu 3) FIN-00014 University of Helsinki, Finland
Email: Peter.Engelhardt@Helsinki.Fi Email: Peter.Engelhardt@Aalto.Fi URL: http://www.lce.hut.fi/~engelhar/ Mobil: +358-400193342
Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: +358-505113192
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Peter, As Matt says, it appears Apple removed stereo support from El Capitan for your Nvidia Quadro graphics cards. There is nothing we can do to Chimera to fix that since the graphics driver is part of the operating system. Also we confirm Matt's statement that to make Chimera DTI side-by-side stereo work on a 3D TV we needed to use the TV remote control to manually switch it to SBS-half mode. Last week we tried that using Windows 10 and Nvidia Geforce and AMD Radeon HD graphics and had quite a bit of trouble. We got the Nvidia Geforce card to do it full-screen only and only when our Nvidia 3DVision stereo emitter was plugged into the computer. We used the TV stereo glasses and TV emitter but apparently the 3DVision emitter box was needed to activate Nvidia 3DPlay, a software component needed for Nvidia Geforce graphics to work with 3D TVs. With Windows 7(?) and an old AMD Radeon HD card it would sometime work with Chimera DTI side-by-side but was not stable -- it worked only intermittently. So our experience with stereo and 3D TVs and Windows is that it can work but is not easy to find a working configuration. Tom
On Dec 8, 2015, at 10:34 AM, Engelhardt, Peter wrote:
Good Morning to all of you,
We thank you all for your valuable comments on Chimera stereo and sorry for delay in answering. The simplest way to have sequential stereo back here was to remove El Capitan and go back to Yosemite that took some time! The Chimera sequential stereo is now working again in the adjacent VGA Display of our "old MacPro" - (Early 2008) with NVIDIA Quadro FX 5600 MB.
More, we are unable to get a any 'workable SBS stereo' using DTI - only side by side deformed images are visible that are impossible to superimpose to stereo - on any big TV screens or displays?
Before converting back from El Capitan to Yosemite of our second "old MacPro" (Early 2009) with NVIDIA Quodro FX 4800 1536 MB - we wonder now - if Chimera 'El Capitan update' could somehow 'restore' the sequential stereo?
We thank you in advance and hope to hear your comments.
Cheers Peter
________________________________________ From: Dougherty, Matthew T Sent: Wednesday, December 2, 2015 11:52 PM To: Greg Couch; Tom Goddard; David Bhella Cc: chimera-users@cgl.ucsf.edu; Engelhardt, Peter Subject: Re: [Chimera-users] Feature suggestions - based on risk of loss of sequential stereo options
regarding /www.amd.com/HD3D
AMD seems to have the same problem as nividia's 3dvision, most of the displays are no longer available. Both websites seem to stop updating around 2011, when the S3D market tanked. This is not to say S3D is dead; S3D has cycled through boom to bust, 5-10 times over the last 100 years (this includes photography). On the last cycle the incremental improvement was getting a standard in place for HDMI S3D. The key concept is including metadata ('vendor specific info packets'), that directs the hardware to automatically switch between mono mode and S3D, providing sufficient detail as to the type of S3D (eg, SBS-half, SBS-full, T/B, framepack, quincunx); something the pro market never could figure out.
Safest strategy is to plan for HDMI compliance. I agree with Tom, go with consumer products. Buying s3D displays is now the biggest limitation, and for the forseeable future. The movie industry and 4k TV manufacturers are the ones keeping the S3D business financially viable.
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================
________________________________________ From: chimera-users-bounces@cgl.ucsf.edu <chimera-users-bounces@cgl.ucsf.edu> on behalf of Greg Couch Sent: Wednesday, December 2, 2015 3:00 PM To: Tom Goddard; David Bhella Cc: chimera-users@cgl.ucsf.edu; Engelhardt, Peter Subject: Re: [Chimera-users] Feature suggestions - based on risk of loss of sequential stereo options
FYI, stereo-in-a-window also works with AMD Radeon graphics cards that support HD3D on Windows 8. We haven't tested Windows 10 yet. So couple that with a 3D TV or monitor and you have a fairly inexpensive setup. See http://www.amd.com/HD3D for more details.
-- Greg
On 12/1/2015 5:48 PM, Tom Goddard wrote:
Hi David,
Only being able to do full-screen stereo is a pain in Chimera because you need a second display for the Chimera dialogs like Model Panel. Stereo-in-a-window allows the Chimera main window to be 3d with shutter glasses and the dialogs can be on the same display. The problem is that stereo-in-a-window is only supported on professional graphics cards as far as I know, such as the Nvidia Quadro series or AMD FirePro series. These are expensive cards. A year ago we tried an Nvidia Quadro K4000 ($800) and an AMD FirePro W7000 ($600). Both do stereo-in-a-window on Windows 7 on our lab stereo projector. We returned the K4000 because of some driver bug that effected Chimera. The AMD also does stereo-in-a-window on Linux, although it is pretty flakey (eyes swapped) and difficult to use with dual displays on Linux.
The common consumer cards only do full-screen stereo such as the Nvidia Geforce series or AMD Radeon series. No graphics cards provided in Apple computers support stereo-in-a-window to my knowledge. We had a very old (2007) Mac Pro with an Nvidia Quadro FX 5600 that did stereo-in-a-window, but that is the last Mac I saw that could do it.
Given all this we use professional graphics cards and Windows 7 for our stereo systems.
I think all of this is independent of whether the display uses side-by-side format (SBS typical of 3d TVs) or sequential format (typical of stereo-capable computer displays). Both can do stereo-in-a-window with pro graphics, but only full-screen stereo with consumer graphics cards. I’m not completely sure that stereo-in-a-window works on the SBS and we will test that on Thursday. For the side-by-side format, even if the graphics driver does not support any stereo, Chimera can render the left and right eye images side-by-side and can be used on SBS displays — this mode is called DTI stereo in Chimera, each eye image is uses only half the screen width so resolution is not as good as sequential format stereo. Displays that take SBS format generally take full-width images for both eyes — so the a 1920x1080 display would really get a 3840x1080 image. But that requires graphics driver support for the graphics card to output a 3840x1080 image to a display device that says it is 1920x1080 in size.
We haven’t done anything to make dual display Chimera where the graphics is full-screen on one display work smoothly. So for instance the Chimera command-line cannot be detached from the graphics window. Also I doubt Chimera will automatically put the dialog windows on the non-fullscreen display. Also the mouse cursor is handled by the operating system and it lines up with different objects in the left eye and the right eye which is annoying — Chimera uses the left eye alignment for selecting objects (ctrl-click). Mouse rotation considers the mouse position relative to the center of the screen.
In summary, the stereo options are all expensive (stereo-in-a-window) or difficult to use (full-screen stereo) and restrict your choice of operating system (no stereo-in-a-window on Mac). The consumer uses of stereo to view 3-d movies or play 3-d video games are all full-screen so we can expect only full-screen to have decent support from the graphics card manufacturers.
Tom
On Dec 1, 2015, at 12:23 AM, David Bhella wrote:
Further to Matt’s comment, SBS works very well for rendering/display in 3D but it is difficult to work with for interactive visualisation because you must work full screen and chimera doesn’t completely understand that the left and right halves of the screen are now superimposed. Firstly accessing menus and the command line is problematic because you must move your mouse to the left eye view, so you need to mouse across the screen and off the left hand side. This is a relatively trivial irritation however. What is more challenging is interacting with the model/volume to select rotate/pan etc.
So, to work with SBS 3D you must have a second monitor to handle all of the floating windows and non-3D stuff. It would be good to be able to float the display window and tear-off the drop-down menus and command line to view separately on the 2D monitor (perhaps you can already?). Currently mouse selection tools are focussed on the left hand view, while the rotation control seems to focus on the centre of the display, so sometimes when you intend to rotate the model you end up just rotating about z (or vice-versa). Perhaps it would be better to have all mouse interactions focus on the left-hand view and to have a visual cue to let you know when your mouse is over the left or right view?
I have both nVidia sequential stereo (on linux) and SBS (on a 32” 3D samsung TV on my mac), interactive work is so much more straight-forward on the sequential setup.
Dr David Bhella MRC-University of Glasgow Centre for Virus Research Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK)
Telephone: 0141-330-3685 Skype: d.bhella
Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk
CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch
On 1 Dec 2015, at 07:28, Dougherty, Matthew T wrote:
Sequential S3D is vanishing. Zspace uses it for their windows only apps. Nvidia barely supports S3D as a technology. Not sure if any other chip makers are using sequential anymore. Chip electronics have outpaced the need for sequential.
SBS half, the chimera DTI option output as HDMI is your best bet, regardless of the OS.
Some of the Samsung tv/monitors that do hdmi 2.0 now offer SBS half at 4k.
This resolution is better than bluray S3D framepack under HDMI 1.4, and is probably the best you will get for the foreseeable future (ie, 5-15 years).
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================
From: chimera-users-bounces@cgl.ucsf.edu <chimera-users-bounces@cgl.ucsf.edu> on behalf of Tom Goddard Sent: Monday, November 30, 2015 4:26 PM To: Engelhardt, Peter Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Sequential stereo problems in Chimera in Mac after updating to OSX EL Capitan
Hi Peter,
If Chimera says "Unable to find hardware stereo support … “ when you enable sequential stereo it means the graphics driver does not support quad-buffered OpenGL stereo. Unfortunately Apple has not been interested in supporting stereo so I’m surprised you had it working recently. For several years now no machines Apple sold supported stereo. We had an ancient (8 year old) Nvidia Quadro FX 5600 in a Mac Pro until about 2 years ago, but the performance became so poor we abandoned it and had to switch to Windows. The new Mac Pro cylinders did not support stereo.
Unfortunately Apple also doesn’t seem to provide any information on which systems support stereo. We used to be able to get this information from the Apple OpenGL Capabilities web page
https://developer.apple.com/opengl/capabilities/ OpenGL version 1.5 - Apple Developer Tools OpenGL Capabilities Tables. The following table lists OpenGL extensions and parameter values reported for each of the OS X versions, graphics adapters, and CPU ... Read more...
but they stopped updating that two Mac OS versions ago (10.9). Now the only thing I can find from Apple about OpenGL support is this page
https://support.apple.com/en-us/HT202823
that lists the OpenGL version supported by each of their computers. Quad buffered stereo is not a requirement of any OpenGL version so this page does not help find out about stereo support.
With Mac OS El Capitan (10.11) Apple has talked a lot about “Metal” which is an alternative graphics programming interface. Chimera does not use it since it is Apple only and we need to support Linux and Windows.
In summary, I think Apple has dropped support for stereo on your systems. Could you tell us what graphics card it was working with and which Mac OS version (Mavericks 10.10?). Also if you use Chimera menu Help / Report a Bug… we will know the configuration that no longer works which will help us advise other Chimera users.
Tom
On Nov 30, 2015, at 12:54 PM, Engelhardt, Peter wrote:
Hi,
No sequential stereo is working in Chimera after updating of our Macs to OS X El Capitan - 10.11.1 in the CRTs linked to MacPros
Error remarks: - unable to turn on stereo viewing - "Unable to find hardware stereo support ... "
(see attachment).
This problem has not appeared in with earlier OSX updates!
We hope this problem will be fixed soon.
Cheers Peter
Peter Engelhardt, PhD, docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography
Nanomicroscopy Center (NMC), Department of Applied Physics Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland
Department of Pathology Haartman Institute P.O.Box 21 (Haartmaninkatu 3) FIN-00014 University of Helsinki, Finland
Email: Peter.Engelhardt@Helsinki.Fi Email: Peter.Engelhardt@Aalto.Fi URL: http://www.lce.hut.fi/~engelhar/ Mobil: +358-400193342
Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: +358-505113192
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (6)
-
David Bhella -
Dougherty, Matthew T -
Engelhardt, Peter -
Eric Pettersen -
Greg Couch -
Tom Goddard