[PyMOL] 3D HDMI Videos
Hi, is there a known way to create 3D movies for DLP projectors using one of the known 3D formats for HDMI: Frame-Packing (1920 x 2205 / 2 HD pics + 35 pixel black) Top over Bottom (2x540x1920 or 2x720x1280) Side by Side (2x 960 x 1080 ) Only Frame packing will give full resolution on current projectors as far as I know. -- Joachim Reichelt Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf Richter, MBA Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477 -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] [ccp4bb] MacBookPro problems
Hi all, the problem for Zalman monitor to newer MACs etc. is : From Zalman ( j...@zalman.co.kr ) I got this Mail: I can provide the fix – a custom DVI cable specifically for the ZM-M220W. It resolves the issue of the swapped pins 15 16 of the ZM-M220W, which is not an issue with older graphic cards/GPUs(I infact use the DVI connection with my office PC that has an Nvidia GeForce 7600 card), but is an issue with newer / notebook GPUs. Basically, newer GPUs seem to have acquired a function that actively sends and receives a signal to and from the monitor to check if a connection is made, and if it does not get a return signal that it is looking for, the GPU’s output shuts down. With the ZM-M220W’s swapped pins 15 16, the newer GPUs don’t get the return signal and thinks that no monitor is connected and shuts the output off. On older GPUs, this function is not common and so the GPU outputs constantly without regarding for the pins 15 16. ... Jihoon Jihoon Jo Manager, 3D Business Development Zalman Tech Co., Ltd. #1007 Daeryung Techno Town III 448 Gasan-dong, Gumchun-gu Seoul, 153-803, Korea Tel : +82-2-2107-3109 Fax: +82-2-2107-3322 So I'l get a new DVI cable. -- Joachim -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Viewsonic VX2268wm confirmed to work in stereo under Linux
I Am 25.02.2010 14:01, schrieb greipel.joac...@mh-hannover.de: Hi, For supporting a wide variety of software I think it would be the best choice to have an openGL quad buffered stereo device running. The fact that Harry did have success with a 120 Hz TFT-Monitor, the Quadro FX3800 (3-Pin Mini-Din) with 195.x drivers and 3D-Vision Glasses under Linux is due to the fact that he uses a Linux distribution which is related to RHEL. I just tried exactly the same thing with OpenSuSE 11.2 and couldn't get it to work at all. The reason, at least how I got it after a long, long discussion with custhelp.nvidia appears to be that some distributions mount USB devices under /proc/bus/usb/devices (works...) and some under /dev/bus/usb (doesn't work). In OpenSuSE, which belongs to the latter class, the driver appears to look under the non existing /proc/bus/usb/devices, doesn't find the entry for the 3D-Vision emitter and refuses to switch on stereo. The nvidia guys tested it with RHEL 5, which belongs to the former class of distributions. Unfortunately the USB Emitter must be recognized for reasons I do not know by the driver although the sync signal runs via the 3-Pin Mini-Din. This is easy to fix: put a line in /etc/init.d/boot.local: mount /proc/bus/usb I have 4 systems up runnig openSuse 11.2 Another question of concern is wether the chipset on the FX1800 is supported by the 195.x driver at all. You should look this up with nvidia. Regards, Joachim -- Dr. rer. nat. Joachim Greipel Med. Hochschule Hannover Biophys. Chem. OE 4350 Carl-Neuberg-Str. 1 30625 Hannover Germany Fon: +49-511-532-3718 Fax: +49-511-532-8924 Von: Hugo Gutiérrez de Teran [mailto:hugo.te...@usc.es] Gesendet: Donnerstag, 25. Februar 2010 13:10 An: Harry M. Greenblatt Cc: pymol-users@lists.sourceforge.net Betreff: Re: [PyMOL] Viewsonic VX2268wm confirmed to work in stereo under Linux Dear PyMolers, We are on the process of buying a 3D monitor for stereo rendering. The main software we use for visualization is PyMOL, in Linux (preferably OpenSuse), so it is mandatory that it works well with Pymol. We might use stereo with other programs like Maestro (Schrödinger) or MOE (CCG), so if compatible with this other software, the better. Graphics Card is a nVidiaGEFORCE QUADRO FX 1800. PyMOL official recommendations was the Zalman ZMM220W, but this is not longer distributed, at least in Europe. So, before going for any of the solutions like Samgsung or Viewsonic, and getting deep into the nightmare of finding out the proper X configuration, I would like to receive as much input as possible from recent experiences of PyMOL community. Thanks in advance, Hugo -- Hugo G. de Teran, PhD. "Parga Pondal" Research fellow Fundación Pública Galega de Medicina Xenómica - SERGAS Santiago de Compostela (SPAIN) Phone +34 981563100 ext 13873 e-mail:hugo.te...@usc.es http://webspersoais.usc.es/persoais/hugo.teran/ Harry M. Greenblatt wrote: BS"D Just to let you all know that we have successfully tested a Viewsonic VX2268wm (I'm guessing that is the version of the VX2265wm sold on this side of the pond) with an nVidia Quadro 3800 (3pin stereo version) under Fedora Core 12, with the nVidia 3D vision glasses, and the 195beta version of the driver. Very high quality QB stereo under PyMOL and Coot. By the way, Warren had warned us that the ATI drivers for Linux were not up to scratch (without even considering stereo). Is that still true? Thanks Harry - Harry M. Greenblatt Associate Staff Scientist Dept of Structural
Re: [PyMOL] [ccp4bb] Stereo flipping in coot and pymol
I said, we are on Linux. But I did not say: We are using Stereographic glases and emiter connected by 3-wire cable to the DIN plug on NVIDIA Quadro FX 3000 NVIDIA GLX Module 173.14.17 Mon Feb 23 16:04:17 PST 2009 If of interest, this is openSUSE 11.1 on i386 Am 28.09.2009 16:21, schrieb Dirk Kostrewa: Dear Joachim, you don't say whether its Linux, Windows or Mac OS X and which emitter and glasses you are using. I've seen this behaviour long time ago with very old Nvidia graphics card drivers under Linux. Sometimes, I still see this behaviour with new drivers but with old computer hardware. Here are a few hints that might be worth trying: - Install the most recent Nvidia driver. If it happened after updating, it might be worth to go back 1-2 versions. - If you use the emitter from NuVision, you can simply invert left and right with a small switch. - Sometimes, it helps to minimize the application and maximize it again. Good luck, Dirk. Am 28.09.2009 um 15:48 schrieb Joachim Reichelt: Dear all, our users complain that during there graphics session front and back are switched. We are on Linux using NVIDA Quadro boards with 3-pin DIN connectors. So it seems that you see sidechains behind a sheet, that are in realety front of a sheet. If they were behind it, you should not see them at all. -- Joachim -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax: +49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW: www.genzentrum.lmu.de *** -- -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Zalman 3D Monitor
Hello, does anyone know, which Quadro card supports the Zalman mode. The readme states: Stereo options 7, 8, and 9 are only supported on G8xGL and higher GPUs. Mode 7 is for the Zalman -- Joachim -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Monitors for molecular Modelling (Stereo 3D LCDs)
I just installed the NVIDIA GLX Module 185.19 Sat Apr 4 07:32:28 PST 2009 (beta) driver on Linux and found in the README.txt: Option "Stereo" "integer" Enable offering of quad-buffered stereo visuals on Quadro. Integer indicates the type of stereo equipment being used: Value Equipment -- --- 1 DDC glasses. The sync signal is sent to the glasses via the DDC signal to the monitor. These usually involve a passthrough cable between the monitor and the graphics card. This mode is not available on G8xGL and higher GPUs. 2 "Blueline" glasses. These usually involve a passthrough cable between the monitor and graphics card. The glasses know which eye to display based on the length of a blue line visible at the bottom of the screen. When in this mode, the root window dimensions are one pixel shorter in the Y dimension than requested. This mode does not work with virtual root window sizes larger than the visible root window size (desktop panning). This mode is not available on G8xGL and higher GPUs. 3 Onboard stereo support. This is usually only found on professional cards. The glasses connect via a DIN connector on the back of the graphics card. 4 TwinView clone mode stereo (also known as "passive" stereo). On graphics cards that support TwinView, the left eye is displayed on the first display, and the right eye is displayed on the second display. This is normally used in conjunction with special projectors to produce 2 polarized images which are then viewed with polarized glasses. To use this stereo mode, you must also configure TwinView in clone mode with the same resolution, panning offset, and panning domains on each display. 5 Vertical interlaced stereo mode, for use with SeeReal Stereo Digital Flat Panels. 6 Color interleaved stereo mode, for use with Sharp3D Stereo Digital Flat Panels. 7 Horizontal interlaced stereo mode, for use with Arisawa, Hyundai, Zalman, Pavione, and Miracube Digital Flat Panels. Am 21.04.2009 17:33, schrieb Warren DeLano: FYI: I just heard back from nVidia regarding the status of the Quadro drivers for the 3D Vision glasses to be used with the Samsung 2233RZ and other 120Hz full-field LCD displays (ViewSonic): Release was originally intended by April, but so far it hasn't happened. In their own words: "I do not know the exact release date however it should be around the same time as when new QuadroFX drivers based on the Release 185 driver branch is available in the near future..." Cheers, Warren -Original Message- From: owner-chemistry+warren==delsci@ccl.net [mailto:owner- chemistry+warren==delsci@ccl.net] On Behalf Of Vincent.Leroux]|[loria.fr Sent: Tuesday, April 21, 2009 5:02 AM To: Warren DeLano Subject: CCL: Monitors for molecular Modelling Sent to CCL by: Vincent.Leroux:_:loria.fr Hi Peter, This might interest you: http://www.samsung.com/us/consumer/detail/detail.do?group=computersperiphe ralstype=monitorssubtype=lcdmodel_cd=LS22CMFKFV/ZA This is an LCD monitor capable of doing 120 Hz natively. Resolution is 1680x1050, which is the most common with computer flat screens (better forget 1280x1024)... It sells for ?300 in France right now. 2x60 Hz stereoscopic glasses can be bought separately from nVidia ($200, or $600 bundled with the Samsung monitor). They are especially interesting as the stereo support is done at the drivers level. http://www.nvidia.com/object/GeForce_3D_Vision_Main.html For the moment, unfortunately, the stereo drivers are only available for mainstream GeForce cards under Windows Vista, but it should not take long before nVidia provides Linux drivers. Support for the Quadro range was announced for spring 2009, this might be done at the same time. The glasses are also compatible with any CRT monitor capable of = 100 Hz - so the old 21" 30kg CRT monsters from Mitsubishi/Sony/Illyama, which can be found 2nd hand for about nothing, are interesting. This is good to know if you want to stick to 1280x1024, as
[PyMOL] Cofactor Spheres size
Dear all, we are interested in Molecules with Atoms unknown to pymol. So pymol does not know the vdW radius of these atome. Where can I define those values? -- Joachim
Re: [PyMOL] zoom relative and absolute
So there something missing in the "manual" at http://www.pymolwiki.org/index.php/Zoom zoom [ selection [,buffer [, state [, complete Where is the distance here??? Did you just add this today to the text? Am 17.09.2008 23:09, DeLano Scientific schrieb: Joachim, The trick with that is the same as in real life: you must place the camera the same distance from each object you intend to photograph. But how can we do this with PyMOL? Ah ha! I've got it The "center" command positions and points the camera at the molecule. center object-name And then you can use the "zoom" command with the "center" keyword to specify how much to zoom around that point. For example: zoom center, distance Just use the same value (e.g. 20) with the "zoom center, ..." command and you'll always get the same scaling (for a fixed aperture / window size / aspect ratio). load obj1.pdb center obj1 zoom center, 20 ray png img1.png delete all load obj2.pdb center obj2 zoom center, 20 ray png img2.png Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Joachim Reichelt Sent: Wednesday, September 17, 2008 5:03 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] zoom relative and absolute Hallo, we want to create a set of pictures from different molecules but the zoom value should all be the same. ANd is there an easy way to zoom in or out by e.g. 5%? -- Joachim - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=""> ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --
[PyMOL] zoom relative and absolute
Hallo, we want to create a set of pictures from different molecules but the zoom value should all be the same. ANd is there an easy way to zoom in or out by e.g. 5%? -- Joachim
[PyMOL] 3D controller
Hi, one of us just bought a 3Dconnexion SpaceNavigator. There is no problem to install the base software on Linux, but how to use it in pymol? -- Joachim Reichelt
