sure – squinting (for cross-eyed stereo) is easier. to exploit cross-eyed stereo (for example in pymol):- place your screen (preferably with a nice wide aspect ratio) a comfortable distance from and perpendicular to your eyes so that things are nicely in focus. then start to squint so that the images move together – they will of course be out of focus. squint further until the images coincide. the vertical coincidence is important: adjust it by angling your head slightly in each direction. when the images coincide, just keep looking for a few seconds, perhaps playing with the positions a bit. suddenly your brain will notice that stereoscopic information is available and - hey presto! – your eyes snap into focus. if you've never done this before, it might take a couple of minutes to work. when it does, you will look rather silly – but what's new? jon
Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Goldman, Adrian Gesendet: Donnerstag, 27. Februar 2025 14:14 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] [ccp4bb] 3D/Stereoscopic hardware options in 2025? Hi, 1) I agree with Richard - wall-eyed stereo is easy as long as the width of the images is about that of your eyes (6-7 cm or so). But to make your eyes go outward - now that’s a trick. That’s why I uses mirrors and glasses, so I can do wall-eyed stereo over the width of the monitor. 2) we don’t have to worry about it - chatGPT has solved the protein folding problem - right ;)? Adrian On 27 Feb 2025, at 14:57, Richard Alan Engh <0001053f39af3698-dmarc-requ...@jiscmail.ac.uk<mailto:0001053f39af3698-dmarc-requ...@jiscmail.ac.uk>> wrote: Hi everyone, I have been using wall-eyed stereo for most of my life, including childhood when I would relax my eyes to superimpose the candles on either side of church altars to see them take strange depth patterns. Same with ceiling lights or mosquito netting. The stereo images in my first organic chemistry textbook (Streiwieser & Heathcock) were then a real "eye-opening" experience! Two points here: 1) Wall-eyed viewing doesn't have to be too painful, it's just a bit of trick to learn to decouple focussing from the relative eye angles. But I do have to have the window pretty narrow on computer screens, so that's a reason to use mirrors, lenses, or stereo glasses. 2) I cannot understand why there is not more demand for stereo. The experience is simply a sudden understanding of the 3D scene. Naively, two images can maximally double the information content, and because the images must be highly correlated it is really much less. But the perception (useful information) increase is much more. Try playing table tennis without stereo vision. So I asked ChatGPT to quantify this. An excerpt of the info regarding perception: ------------------------------------------------------------ * Monocular image: Contains only (x, y) spatial information for each pixel. * Stereo image: Allows reconstruction of (x, y, z) coordinates. If we assume uniform information density, adding the third dimension increases the available information by a factor of: Area of a 2D projectionVolume of a 3D space∼depth resolution For an intuitive example, if we represent a table tennis scene in 2D as a 1920×1080 pixel image, it has about 2 million pixels. If stereo vision lets us resolve depth into, say, 256 discrete levels, then the effective number of distinguishable spatial points increases to: 1920×1080×256=552,960,000 This suggests an increase of two orders of magnitude (~100x), not just 2x. 2. Shannon Entropy Perspective A rough estimate from studies in stereo vision compression suggests that while the pixel-level entropy gain is about 30-50%, the semantic information gain (useful scene understanding) is closer to 10×–100×, depending on the scene complexity. ------------------------------------------------------------ Maybe there is a way to get younger people excited about stereo viewing and keep simple systems working... -Rick ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Dirk Kostrewa <dirk.kostr...@lmu.de<mailto:dirk.kostr...@lmu.de>> Sent: Thursday, February 27, 2025 13:01 To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: Re: [ccp4bb] AW: [ccp4bb] 3D/Stereoscopic hardware options in 2025? You don't often get email from dirk.kostr...@lmu.de<mailto:dirk.kostr...@lmu.de>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Dear all, you can get quad-buffered 3D stereo working under Linux with Nvidia emitter and glasses and a more recent Nvidia graphics card if the card supports the separate Nvidia bracket with the 3-pin mini-DIN socket, required to connect the emitter. However, more recent Nvidia drivers recognize the emitter (green light on it), but fail to activate it upon switching to 3D stereo! The reason is a bug, that Nvidia introduced with driver 530 (see bug report<https://forums.developer.nvidia.com/t/3d-vision-bug-in-530-30-02/248188>; there might come a future driver 570 without that bug). In order to get Nvidia 3D stereo working, I had to install driver 525 via the CUDA 12.0.1 repository (see CUDA toolkit archive download site for 12.0.1<https://developer.nvidia.com/cuda-12-0-1-download-archive>). I've also tried the stand-alone Nvidia-run-file installer for driver 525, but this didn't work. The xorg configuration file requires the usual 'Option "Stereo" "10"' entry for the Nvidia driver to use the Nvidia emitter. The main problem is probably to still get a monitor that supports Nvidia 3D stereo. So, I have a workstation under Rocky Linux 8 with an RTX A4000 graphics card connected to the 3-pin mini-DIN bracket and functioning Nvidia 3D stereo. However in our lab, I am the last one (aka "dinosaur") who uses 3D stereo 😉. Best regards, Dirk On 27.02.25 11:24, Oliver Einsle wrote: Dear all, Hi Wulf! I have to get in on this one, because I remember Juan Fontecilla-Camps *very* vividly recounting on how every muscle around his eyes hurt after doing cross- or wall-eyed stereo for a few hours. Also, the mirror glasses with a wood frame and a head strap that we had in some bottom drawer during my PhD time in Martinsried are quite reminiscent of an Apple vision pro in terms of long-term wearing comfort. Alternatively, we are still happily running Linux, and with a little effort you can get stereo going reasonably well (even if the younglings these days show absolutely no interest in using it, btw). What you need is a stereo-capable graphics card. We are still using approx.. 15 yr old Quadro FX3700 without much problems. You also need a desktop manager that allows to disable the “composite” extension (e.g. KDE) and a Linux driver that still has the 3D vision functionality and supports your card. Our current solution is to have a few designated Workstations running a recent OpenSuSE with KDE, and a patched driver for compatibility between the old card and the newer OS. There is some flicker I did not observe in the old days, but the system runs smoothly and stably in hardware stereo @120 Hz, both on the Asus and with Emitters. This solution will not last forever, but stereo has become so much more useful again when looking at cryo-EM maps, so it would be great to see a viable solution coming back. Best wishes, Oliver. From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK><mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of "Hughes, Jonathan" <jon.hug...@bot3.bio.uni-giessen.de><mailto:jon.hug...@bot3.bio.uni-giessen.de> Reply to: "Hughes, Jonathan" <jon.hug...@bot3.bio.uni-giessen.de><mailto:jon.hug...@bot3.bio.uni-giessen.de> Date: Thursday, 27. February 2025 at 11:02 To: "CCP4BB@JISCMAIL.AC.UK"<mailto:CCP4BB@JISCMAIL.AC.UK> <CCP4BB@JISCMAIL.AC.UK><mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] AW: [ccp4bb] 3D/Stereoscopic hardware options in 2025? isn't the answer simple biology? almost everyone can squint (it's good for your eyes, btw), so with a bit of practice you can see structures in 3D with "cross-eyed stereo" dual images easily, especially with a wide screen. cheers jon Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK><mailto:CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Goldman, Adrian Gesendet: Donnerstag, 27. Februar 2025 10:41 An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Betreff: Re: [ccp4bb] 3D/Stereoscopic hardware options in 2025? I went very old school (as in 1970s—1980s) and use side by side either with mirror glasses that I put on my face or indeed by making a double mirror system like we had at Yale with the ps2. Rather than having a finely machined device with anodised black aluminium and glass mirrors, I used cardboard and Mylar. It also works :) Adrian Sent from my iPhone On 27 Feb 2025, at 10:49, Pedro Matias <mat...@itqb.unl.pt<mailto:mat...@itqb.unl.pt>> wrote: Hi Wulf, We never got our NVIDIA 3D to work with Windows 10, only with Windows 7. The Windows advantage is that the graphics cards are much cheaper than those for Linux. I believe there is a NVIDIA 3D Vision standalone driver that may work in Windows 11. Alternatively, my suggestion would be to use a PC disconnected from the internal institute network and keep running Windows 10 on it. File transfer would be a bit of an hassle but workable. Good luck & best regards, Pedro On 27/02/2025 07:05, Blankenfeldt, Wulf wrote: Dear all, I have just been shocked by our IT department’s announcement that they will force us into migration to Win11 very soon. I know I am a dinosaur, but I still use and love my old nvidia Quadro/Asus/shutter glasses combi (over 10 years old) for hardware stereo viewing of protein structures under Win10. I am afraid that this will simply not work anymore once I have been upgraded, since nvdia has disabled hardware stereo in its drivers long time ago. Personally, I cannot understand how modern structural biology can live without it and I would love to still be able view structures in “real” 3D. I know that the ccp4 community is graphics- and tech-savvy, I am therefore asking if you know of any modern day and established/sustainable hardware solution for 3D viewing in our favorite programs (Coot, PyMol, …). Thank you in advance for your advice, Wulf Prof. Wulf Blankenfeldt Struktur und Funktion der Proteine (SFPR) HZI - Helmholtz-Zentrum für Infektionsforschung GmbH SCIENCE CAMPUS Braunschweig-Süd Inhoffenstraße 7, 38124 Braunschweig Tel. +49 5316181-7000 wulf.blankenfe...@helmholtz-hzi.de<mailto:wulf.blankenfe...@helmholtz-hzi.de> www.helmholtz-hzi.de<http://www.helmholtz-hzi.de/> <Helmholtz_HZI_Logo_RGB_DE_nebeneinander_beschnitt2_1acc279d-0673-4590-b45d-24938b462e30.jpg> ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de<http://www.helmholtz-hzi.de/> Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Wissenschaftlicher Geschäftsführer: Prof. Dr. Josef Penninger - Administrativer Geschäftsführer: Christian Scherf Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477 Unsere Hinweise zum Datenschutz finden Sie hier: https://www.helmholtz-hzi.de/de/service/datenschutz/ ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 -- Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit ___________________________________ Phones : (351-21) 446-9100 Ext. 1669 (351-21) 446-9669 (direct) Fax : (351-21) 441-1277 or 443-3644 email : mat...@itqb.unl.pt<mailto:mat...@itqb.unl.pt> http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit Mailing address : Instituto de Tecnologia Quimica e Biologica António Xavier Universidade Nova de Lisboa Av. da República 2780-157 Oeiras PORTUGAL ITQB NOVA, a great choice for your PhD https://youtu.be/de6j-aaTWNQ Master Programme in Biochemistry for Health https://youtu.be/UKstDCFjYI8 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 -- ****************************************** Dirk Kostrewa Gene Center and Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 E-mail: dirk.kostr...@lmu.de<mailto:dirk.kostr...@lmu.de> WWW: www.genzentrum.lmu.de<http://www.genzentrum.lmu.de/> ****************************************** ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
