Re: [COOT] Hardware recommendations
Hi Qiuye, 2x 12GB RTX-3060 will - for example - fit well with sufficient space between cards on the MSI MEG *X570S* Unify-X Max (with two GPU slots at 16x/8x speed) and the Gigabyte X570S Aorus Master (with three slots at 8x/8x/4x if all are populated), but as you correctly noted, you will need a really big case with plenty of fans to remove the heat such as an Corsair 7000D Airflowor or the be quiet! silent base 802 or, for the brave, build a water-cooled rig.. All cheaper X570S and all of the X570 boards do not support 16x/8x or 8x/8x speed (at least I did not find one). Best, Jeroen Am 19.04.22 um 17:41 schrieb Qiuye Li: Hi Jeroen, Thanks for the kind suggestions, they definitely help me as well as many others a lot! I recently tested coot0.9 on a 11800H+64G+A2000+1600p mobile workstation and am quite OK with the performance. I guess the same gen desktop-level hardware and configuration--something around 5950X+64G+3060 with my existing 27' 2k display--should do the work well, and can be picked up today in a local store. We already have more than a dozen consumer cards in our workstations so we'll probably worry about NVIDIA's policy later. The idea of a dual-GPU machine sounds wonderful, I need to dig a bit more myself to see if there are decent chassis and board to fit those gamer cards' little hot fans, and still be reasonably quiet in an office. Best, Qiuye On Tue, Apr 19, 2022 at 7:47 AM mesters wrote: Hi Qiuye, somehow the one-million-dollar/"budget vs. program specs vs. current/future applications//vs. access to central computing facilities/" question, is it not? As Paul indicated, for a personal/office graphics workstation (maximally 128GB ram memory), a 8-16 core CPU with a passmark <https://www.cpubenchmark.net/high_end_cpus.html> of >27.500 and for <600 US$ will do (intel i9-12900, i7-12700, i5-12600k; Ryzen 5950x, 5900x or 5800x). As heat dissipation is a major problem, AMD is a good choice for the moment (i9-12900k TDP 241 watts vs. 3950x TDP 105 watts). If there is a reasonable chance, the system is to be upgraded in the future to a small/medium 2x GPU CryoSpark workstation, plan for a 16-core CPU from the beginning and make sure to choose a motherboard that offers the possibility of 2x PCIe 4.0 at *8x/8x* speed mode (MSI MPG Z690 FORCE / Gygabyte X570*S* Aorus PRO) as many standard boards only offer 16x/4x speed mode (read the technical description carefully; most if not all boards <300 US$ offer 16x/4x only). As for the graphics card, it depends mainly on program specs, structure-model-size / e.d.-map-size and screen resolution. For a 4K screen in combination with rendering, you will indeed require a >4000 cuda-cores GPU card such as a 8GB RTX3060ti (600 €; 4864 cuda-cores; 200 watt and sadly no FE model available) or a 16GB RTX A4000 (1100 €; 6144 cuda-cores; 140 watt). Again, as heat dissipation is a major problem, the A4000 is a very good pick with 16GB memory! I recommend a professional RTX *A*xx00-series over the wide-spread 3x00-series consumer cards (*FE* models if at all!) as for the moment, Nvidia still allows the installation of the CUDA-package (AlphaFold, etc., etc.) on consumer cards outside of any central university computing facility without restrictions (read the small print in the cuda software documention), but I would not be surprized this might change in the future (recall the LHR measures taken by the company)! Nvidia can tell from the IP-adress who-is-who (office, home or central computing facility). For a 1440p screen and small- to mid-sized models/maps, an A2000 (3328 cuda-cores, 30% more cores than a 2070 super; 650-750€; 70 watt) with 6 or 12GB GDDR is good although not a bargain compared to the A4000 that offers a much better price/performance ratio. Paul's dream-machine - an 3990X combined with a Nvidia RTX 3090 Ti - will cost you, build-it-yourself, at least 8.000 €, which is just too expensive in my eyes. A build-it-yourself machine around a Ryzen 5800x, 12GB RTX A2000, 2TB M.2, 12TB HDD and 32GB ram including power-supply and case will cost about 2600 €, and with a Ryzen 5950x and 16GB RTX A4000 about 3100 €. A minimal system for about 1100€ can be build around a Ryzen 5600x or intel i5-12500 (passmark > 20.000), 16Gb ram and a 6GB GTX 1660 super (1408 cuda-cores; max. 1440p resolution; we run AlphaFold v2 on such a card, not superfast but it gets the job done), for smaller models/maps of course and with slower Coot1 fancy mode I guess It all boiles down to budget in the end I guess, good luck at taking the right decision! Jeroen Am 15.04.22 um 17:32 schrieb Qiuye Li: Dear all, We recently centralized our high-end workstations and
Re: [COOT] Hardware recommendations
Hi Qiuye, somehow the one-million-dollar/"budget vs. program specs vs. current/future applications//vs. access to central computing facilities/" question, is it not? As Paul indicated, for a personal/office graphics workstation (maximally 128GB ram memory), a 8-16 core CPU with a passmark <https://www.cpubenchmark.net/high_end_cpus.html> of >27.500 and for <600 US$ will do (intel i9-12900, i7-12700, i5-12600k; Ryzen 5950x, 5900x or 5800x). As heat dissipation is a major problem, AMD is a good choice for the moment (i9-12900k TDP 241 watts vs. 3950x TDP 105 watts). If there is a reasonable chance, the system is to be upgraded in the future to a small/medium 2x GPU CryoSpark workstation, plan for a 16-core CPU from the beginning and make sure to choose a motherboard that offers the possibility of 2x PCIe 4.0 at *8x/8x* speed mode (MSI MPG Z690 FORCE / Gygabyte X570*S* Aorus PRO) as many standard boards only offer 16x/4x speed mode (read the technical description carefully; most if not all boards <300 US$ offer 16x/4x only). As for the graphics card, it depends mainly on program specs, structure-model-size / e.d.-map-size and screen resolution. For a 4K screen in combination with rendering, you will indeed require a >4000 cuda-cores GPU card such as a 8GB RTX3060ti (600 €; 4864 cuda-cores; 200 watt and sadly no FE model available) or a 16GB RTX A4000 (1100 €; 6144 cuda-cores; 140 watt). Again, as heat dissipation is a major problem, the A4000 is a very good pick with 16GB memory! I recommend a professional RTX *A*xx00-series over the wide-spread 3x00-series consumer cards (*FE* models if at all!) as for the moment, Nvidia still allows the installation of the CUDA-package (AlphaFold, etc., etc.) on consumer cards outside of any central university computing facility without restrictions (read the small print in the cuda software documention), but I would not be surprized this might change in the future (recall the LHR measures taken by the company)! Nvidia can tell from the IP-adress who-is-who (office, home or central computing facility). For a 1440p screen and small- to mid-sized models/maps, an A2000 (3328 cuda-cores, 30% more cores than a 2070 super; 650-750€; 70 watt) with 6 or 12GB GDDR is good although not a bargain compared to the A4000 that offers a much better price/performance ratio. Paul's dream-machine - an 3990X combined with a Nvidia RTX 3090 Ti - will cost you, build-it-yourself, at least 8.000 €, which is just too expensive in my eyes. A build-it-yourself machine around a Ryzen 5800x, 12GB RTX A2000, 2TB M.2, 12TB HDD and 32GB ram including power-supply and case will cost about 2600 €, and with a Ryzen 5950x and 16GB RTX A4000 about 3100 €. A minimal system for about 1100€ can be build around a Ryzen 5600x or intel i5-12500 (passmark > 20.000), 16Gb ram and a 6GB GTX 1660 super (1408 cuda-cores; max. 1440p resolution; we run AlphaFold v2 on such a card, not superfast but it gets the job done), for smaller models/maps of course and with slower Coot1 fancy mode I guess It all boiles down to budget in the end I guess, good luck at taking the right decision! Jeroen Am 15.04.22 um 17:32 schrieb Qiuye Li: Dear all, We recently centralized our high-end workstations and no longer have easy access to their displays, and thus need a modeling computer. I found coot 0.9/wincoot 0.9 are a bit laggy on our less frequently updated office computers, and the all-new coot 1 probably requires even more hardware resources? With this recent launch of coot 1, it is probably a good time to kindly ask for hardware suggestions, like CPU, RAM, SSD, and dGPU. With coot, I typically visualize a .mrc map using a radius of ~25 A and work with real-space refinement/other simple manual adjustments. Other than coot, I often have 1-2 active chimera/Phenix windows open, a few SSH tunnels, and some web pages. I'll be happy to provide more details if needed. Any suggestions are appreciated! Best, Qiuye To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1> -- signature.html *Dr. /math. et dis. nat./ Jeroen R. Mesters *Deputy, Lecturer, Program Coordinator Infection Biology <https://www.uni-luebeck.de/en/university-education/degree-programmes/infection-biology.html> Visiting Professorship (South Bohemian University <https://www.jcu.cz/?set_language=en>) in Biophysics *University of Lübeck* Center for Structural and Cell Biology in Medicine* Institute of Biochemistry* Tel +49 451 3101 3105 (Secretariate 3101) Fax +49 451 3101 3104 * *jeroen.mest...@uni-luebeck.de https://www.biochem.uni-luebeck.de https://orcid.org/-0001-8532-6699 *Ratzeburger A
Re: [COOT] Hardware recommendations
My two cents, if one has access to centralized computing power i.e. CPUs and GPUs for doing the heavy calculations, one will hardly need a 64-core threadripper 3990X (4300 €) in the office especially since most programs profit from quality (speed), not quantity (total number of cores). A 3960x will do just fine and will provide 75% computing power of an 3990x (both are rated at 280 wattswhich sets the total performance level for the major part) at just 33% of the costs. Extra money is much better spent on other components such as sufficient ram, M.2 SSDs, sufficient HDDs, a professional CUDA card such as the 20GB, 7168 CUDA-core RTX 4500 (2300 €) and most of all, *two* (!) 1440p displays Happy easter wishes (holidays) to everybody, Jeroen Am 17.04.22 um 01:38 schrieb Paul Emsley: On 15/04/2022 16:32, Qiuye Li wrote: We recently centralized our high-end workstations and no longer have easy access to their displays, Someone drew the short straw there :-( I found coot 0.9/wincoot 0.9 are a bit laggy on our less frequently updated office computers, You mean hardware updates? Yes, if you go back a gen or two, you will notice this. and the all-new coot 1 probably requires even more hardware resources? It was my intention that Coot 1 be faster than 0.9.x in Basic mode - Coot 1 is using the GPU in the way it was intended to be used - not transferring the map line by line from the CPU to the GPU each frame. So, with my machine, in the coot spin test, with a sampling rate of 2.5 and a radius of 99, Coot 0.9.8.1 spins at 5fps, and Coot 1 spins at 60fps for all render modes (limited by monitor sync). Coot 1 has three render modes: Basic, Standard and Fancy. Basic mode draws models with lines (like Coot 0.x does), Standard mode uses (only) ambient, diffuse and specular lighting, Fancy mode adds brightness, gamma, depth blur, SSAO and shadows. Fancy mode in 4K fullscreen with a ribosome drops the frame rate to less than 60 fps on my computer (RTX 2070 Super). With this recent launch of coot 1, it is probably a good time to kindly ask for hardware suggestions, like CPU, RAM, SSD, and dGPU. With coot, I typically visualize a .mrc map using a radius of ~25 A and work with real-space refinement/other simple manual adjustments. Other than coot, I often have 1-2 active chimera/Phenix windows open, a few SSH tunnels, and some web pages. [] Any suggestions are appreciated! OK, so Coot 1 now takes more than 1 second to open in graphics mode on my computers (SSD and m.2 NVMe PCIe 4). Coot 0.9.x was 0.35s. I haven't tested it from a hard drive, but I can believe that Coot 1 would take more than 10 seconds - that could be irritating. So m.2 NVMe 4 or 5 it is. Since 2017 any function/algorithm that I've written that takes more than 1 second to complete is now written as multi-threaded (and I have refactored several older algorithms to be multi-threaded also). So the more of and faster the cores the better. I only have access to workstation/Xeon processor at work - they are less speedy (and more expensive (reliable though)). Although I haven't tried them myself I'd recommend AMD Ryzen 5900X, 5950X or (the new) 5800X3D (the increased size of the L3 cache could improve contouring and FFT speed). Process size: I've seen coot get up to more than 20Gb - typically when using map masking for cryo-EM maps. I have 32 Gb RAM on my main machine and I haven't see Coot crash due to lack of memory. So I'd recommend at least that especially if you have a multi-tabbed browser and other graphics going also. If you have a 4K monitor (if you don't have one, you should get one) and want fullscreen 4K Fancy mode goodness (and to make pretty screenshots) you'd want something better than my card, so the 3000 series, RTX 3070 or 3080. I don't follow AMD graphics cards sad to say. I intend to make the interface to Blender increasingly powerful and easy to use - that also will benefit from big memory and a fast graphics card. So, get yourself a ballin gamer rig, and you'll have a ballin Coot workstation :-) The Best Coot Workstation today would be build around the AMD Threadripper 3990X and Nvidia RTX 3090 Ti card and Dell UltraSharp U4320Q monitor. Paul. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- signature.html *Dr. /math. et dis. nat./ Jeroen R. Mesters *Deputy, Lecturer, Program Coordinator Infection Biology <https://www.uni-luebeck.de/en/university-education/degree-programmes/infection-biology.html> Visiting Professorship (South Bohemian University <https://www.jcu.cz/?set_language=en>) in Biophysi
Re: [COOT] [EXTERNAL] Re: Coot Stereo Issue
Hello Yong, concerning the driver problematics, anybody interested can find more information on "https://nvidia.custhelp.com/app/answers/detail/a_id/4845/~/3d-vision-end-of-life---faq; where nvidia makes for example the following statements: 1) R418 graphics drivers will be the last driver to contain the 3D Vision driver package. The R418 branch will be supported until January 2020. 2) NVIDIA will decouple the 3D Vision USB driver from the graphics driver. NVIDIA will provide the 3D Vision USB driver package as a separate installer on NVIDIA.com . This will allow users to upgrade the graphics driver while continuing to use the standalone 3D Vision USB driver. So one can upgrade the windows driver for the GPU only but will need a stand-alone 3D Vision driver as explained. Some people are trying to solve the "Linux problem" by reverse engineering, see http://www.open-terrain.org/index.php/Projects/3DVision But as you noted, the 3D Vision kit is history. Concerning Epiphany, not sure you can still purchase this brand. Seems there are only few companies left that produce shutter glasses and emitters. One of them is XPAND https://xpandvision.com which is well known and produces glasses for Sony, NEC and other brands. They also sell emitters that come with a 3-pin DIN stereo plug for connecting directly to the GPU or bracket. I think the prices for the glasses are okay if compared to the original Streographics Crystal Eyes 3D glasses, see http://www.ultimate3dheaven.com/stcrey33dgl3.html. Regards, Jeroen Am 02.03.22 um 17:26 schrieb Yong Wang: signature.html The discontinuation of support for 3D Vision in the driver actually does not impair the use of stereo as quad buffered stereo is still supported. Use of driver beyond 390.41 is fine. Sometimes you are forced to use the latest version because of some other incompatibility. The trouble is with the hardware support, no more 3D Vision hardware kit. An important piece of information from Zhuang is the hardware “from a not-so-often-heard vendor called epiphany”. Anybody else has good experience with this vendor? I don’t see 3D glasses or emitter from their catalog. Yong *From:* Mailing list for users of COOT Crystallographic Software *On Behalf Of *mesters *Sent:* Wednesday, March 2, 2022 7:46 AM *To:* COOT@JISCMAIL.AC.UK *Subject:* [EXTERNAL] Re: Coot Stereo Issue *EXTERNAL EMAIL: *Use caution before replying, clicking links, and opening attachments. Hi Pedro, Zhuang's problem was finally solved by installation of the latest nvidia graphics card driver 511.79. WinCoot works on windows 10, no doubt: Nvidia however stopped supporting the 3D Vision kit from within (professional) graphics drivers and instead offers a stand-alone separate 3D Vision driver 390.41 that will not be updated in the future (only in case of security issues). So, how long this work-around will be useful is unknown. For the future this means, one probably needs to purchase the much more expensive GPUs... For linux, there is an absolute requirement for the 3-pin connector (either build-in or attachable via bracket) as the USB-based 3D Vision kit was never actively supported by Nvidia under linux (and that is indeed a commercial decision...). "Specs" will not help to select the GPU as even the small P400 or P620 offers - according to specs - 3D quad-buffered openGL stereo support (that is, under Windows and making use of the 3D Vision kit). What you need under Linux is an nvidia GPU with an on-board 3-pin DIN stereo connector or, a GPU with a connector for the 3-pin DIN stereo bracket (NVIDIA 699-50764--001 or PNY 930-50764). So, for the GPU, one needs to pick a second hand model such as K / M /P4000, or newer models such as rtx 4000 or rtx a4000 (a2000 will not work)... Cheers, Jeroen Am 02.03.22 um 13:07 schrieb Pedro Matias: Hi there, Coot stereo not working under Windows is a common problem. There seems to be a driver incompatibility that causes the issues you described. In our lab, we were able to use Coot stereo only under Windows 7, not on later Windows versions. As for the Linux hardware you do need a more expensive graphics card - as far as I know there is no technical reason for the 3-pin connector requirement and it may be just a commercial decision by NVIDIA to require this. However, since NVIDIA discontinued the 3D Vision support these cards may be more difficult ro obtain. Basically you need a NVIDIA Quadro K4000, similar or higher specs - it should support 3D Vision stereo (maybe this is indicated in the specs and/or in the box). Regards, Pedro Em 01/03/2022 14:03, Li, Zhuang escreveu: Hi Jeroen, Thank you so much for your response. I use a Win10 pro with Nvidia graphics driver 442.92 and 3D vision controller driver 390.41, and BenQ XL2411P 3
Re: [COOT] Coot Stereo Issue
Hi Pedro, Zhuang's problem was finally solved by installation of the latest nvidia graphics card driver 511.79. WinCoot works on windows 10, no doubt: Nvidia however stopped supporting the 3D Vision kit from within (professional) graphics drivers and instead offers a stand-alone separate 3D Vision driver 390.41 that will not be updated in the future (only in case of security issues). So, how long this work-around will be useful is unknown. For the future this means, one probably needs to purchase the much more expensive GPUs... For linux, there is an absolute requirement for the 3-pin connector (either build-in or attachable via bracket) as the USB-based 3D Vision kit was never actively supported by Nvidia under linux (and that is indeed a commercial decision...). "Specs" will not help to select the GPU as even the small P400 or P620 offers - according to specs - 3D quad-buffered openGL stereo support (that is, under Windows and making use of the 3D Vision kit). What you need under Linux is an nvidia GPU with an on-board 3-pin DIN stereo connector or, a GPU with a connector for the 3-pin DIN stereo bracket (NVIDIA 699-50764--001 or PNY 930-50764). So, for the GPU, one needs to pick a second hand model such as K / M /P4000, or newer models such as rtx 4000 or rtx a4000 (a2000 will not work)... Cheers, Jeroen Am 02.03.22 um 13:07 schrieb Pedro Matias: Hi there, Coot stereo not working under Windows is a common problem. There seems to be a driver incompatibility that causes the issues you described. In our lab, we were able to use Coot stereo only under Windows 7, not on later Windows versions. As for the Linux hardware you do need a more expensive graphics card - as far as I know there is no technical reason for the 3-pin connector requirement and it may be just a commercial decision by NVIDIA to require this. However, since NVIDIA discontinued the 3D Vision support these cards may be more difficult ro obtain. Basically you need a NVIDIA Quadro K4000, similar or higher specs - it should support 3D Vision stereo (maybe this is indicated in the specs and/or in the box). Regards, Pedro Em 01/03/2022 14:03, Li, Zhuang escreveu: Hi Jeroen, Thank you so much for your response. I use a Win10 pro with Nvidia graphics driver 442.92 and 3D vision controller driver 390.41, and BenQ XL2411P 3D monitor. The IR emitter is connected to the computer only via USB, and together with 3D glasses, was from a not-so-often-heard vendor called epiphan. It works pretty fine in UCSF chimera and PyMOL, so I assume the hardware and software configuration is correct. I did enable the stereo mode in Nvidia control panel. This is the first time I setup a 3D work environment, and I used Win10 to make thing less complicated. Next time I would like to set up 3D workstation in Linux. Could you please kindly provide the hardware list that is guaranteed working with Linux? Could you please clarify what a 3-PIN connector is and how is it making things different? Thank you in advance. Zhuang ---- *From:* mesters *Sent:* Tuesday, March 1, 2022 8:42 AM *To:* Li, Zhuang *Subject:* Fwd: Coot Stereo Issue Please also check the following.. 1. On Windows 10, make sure “3D display mode” is set to “On” in Windows settings: Settings --> Display --> Advanced 2. Make sure OpenGL is turned on: --> Manage 3D Settings --> Global Presets --> OpenGL rendering GPU --> 3. Make sure Stereo is turned on: --> Manage 3D Settings --> Global Presets --> Stereo - Enabled > 4. if steps 1-3 do not help, rollback the driver: 12/29/2016 Version 21.21.13.7654 Weitergeleitete Nachricht Betreff:Re: Coot Stereo Issue Datum: Tue, 1 Mar 2022 14:35:59 +0100 Von: mesters <mailto:mest...@biochem.uni-luebeck.de> An: Li, Zhuang <mailto:li3...@purdue.edu> More info would be good What windows version? What nvidia driver version? Monitor type? Quadro P620? This one does not have a 3-pin connector for signal output Are you by any chance trying to use "Nvidia Vision" glasses with an usb-emitter to view the 3D output? This option is no longer supported with the newer nvidia drivers J. Am 01.03.22 um 13:19 schrieb Li, Zhuang: Hi guys, When I switched mono to hardware stereo, my coot window stuck. I tried 0.9.7 0.9.6 0.8.7, they look all the same. I used an AMD CPU and Quadro P620 card, and the hardware setup is working for PyMOL and UCSF Chimera. Please see screenshot as attached, and any input would be appreciated. Zhuang To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=C
Re: [COOT] COOT 0.89 crashes when Hardware-Stereo (Quad-buffered, NVIDIA 3Dvision2) is enabled
Not sure but (especially the first point is often overlooked as far as I remember) 1) *On Windows 10, make sure “3D display mode” is set to “On”* in Windows settings: Settings --> Display --> Advanced 1. 2) Make sure OpenGL is turned on: --> Manage 3D Settings --> Global Presets --> OpenGL rendering GPU --> graphics cards> 3) Make sure Stereo is turned on: --> Manage 3D Settings --> Global Presets --> Stereo - Enabled > Good luck Jeroen Am 19.03.18 um 13:08 schrieb Christoph Parthier: Hello, I'm currently preparing a set of new Windows10-workstations to be used with COOT and other macromolecular software supporting quad-buffered OpenGL Stereo with NVDIAs 3DVision2 kit using USB IR emitters (without 3-pin mini DIN cable connected) and a NVIDIA quadro K620 (low profile) graphics card. The currently installed NVIDIA driver version is 391.03 (64-bit Win10) downloaded from Nvidia (after latest Win10 updates). Quad-buffered Stereo using NVidia 3D-Vision glasses is enabled and working nicely e.g. for PyMOL 2.1.0 and the NVIDIA demos (e.g. stereoscopic picture viewer). Unfortunately WinCoot crashes and terminates when enabling the 'Hardware stereo' option in the menu 'Draw/Stereo...'. I tried WinCoot versions 0.86, 0.87, 0.88 and the current 0.89. All behave the same. Worth noting: - Pymol (working stereo) and WinCoot (not...) both use the same profile for the 3D settings in the NVIDIA control panel. - When setting the 'Stereo - Enable' to 'Off' in the NVIDIA control panel (Manage 3D settings) WinCoot does NOT crash when enabling the 'Hardware stereo' in Coot, but, of course, it will display not in stereo. So I assume the crash really occurs when turning the 'quad-buffered' stereo on in WinCoot. Any advice? Any debuggung info I can provide? Thanks, Christoph -- Dr.math. et dis. nat. Jeroen R. Mesters Deputy, Senior Researcher & Lecturer Program Coordinator /Infection Biology/ <http://www.uni-luebeck.de/studium/studiengaenge/infection-biology/introduction.html> Institute of Biochemistry, University of Lübeck Ratzeburger Allee 160, 23538 Lübeck, Germany phone: +49-451-31013105 (secretariate -31013101) fax: +49-451-31013104 http://jobs.zeit.de/image-upload/logo_10564.jpg http://www.biochem.uni-luebeck.de http://www.eine-stadt-sieht-gelb.de http://www.uni-luebeck.de/studium/studiengaenge/infection-biology http://www.iobcr.org Visiting Professorship in Biophysics, University of South Bohemia (CZ) President of the International Organization for Biological Crystallization (IOBCr) -- If you can look into the seeds of time and tell which grain will grow and which will not, speak then to me who neither beg nor fear (Shakespeare's Macbeth, Act I, Scene 3) -- "Aujourd'hui je sais qu'il n'y a pas de limites à la bêtise humaine - qu'elle est infinie." (Gustave Flaubert, French novelist, 1821-1880) -- It is invariably the case that high resolution X-ray structures show significantly better agreement with solution observables such as coupling constants, 13C chemical shifts, and proton chemical shifts, than the corresponding NMR structures, including the very best ones. Hence, in most cases, a high-resolution crystal structure (< 2.0 Å)will provide a better description of the structure in solution than the corresponding NMR structure (Kuszewski, Gronenborn & Clore, 1996, Protein Science 5:1067-80) -- Disclaimer * This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. * E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. If verification is required please request a hard-copy version. Please send us by fax any message containing deadlines as incoming e-mails are not screened for response deadlines. * Employees of the Institute are expressly required not to make defamatory statements and not to infringe or authorize any infringement of copyright or any other legal right by email communications. Any such communication is contrary to Institute policy and outside the scope of the employment of the individual concerned. The Institute will not accept any liability in respect of such communication, and the employee responsible will be personally liable for any damages or other liability arising. Employees who receive such an email must notify their supervisor immediately. --
[COOT] auto open MTZ problem
Hi, I currently run ccp4 version 7.0.028 on a Mac Air with OS X 10.11.6 and experience no problems if start Coot from within qtRView (model and maps are displayed correctly) If a start Coot by itself and load a PDB model and then use "auto open MTZ" and select the model in order to calculate the maps, it comes up with the following: /In /Applications/ccp4-7.0/share/guile/gtk-2.0/gtk.scm:// // 147: 0* [apply # ()]// //In unknown file:// // ?: 1 [#]// //In /Applications/ccp4-7.0/share/coot/scheme/coot-gui.scm:// // 750: 2* (let* ((active-mol-no #)) (if (not #) (begin #) (begin #)))// // 754: 3 (if (not #) (begin #) (begin #))// //In /Applications/ccp4-7.0/share/coot/scheme/refmac.scm:// //...// // 514: 4 (let* (# # # ...) (write-pdb-file imol pdb-in) ...)// // 525: 5* [run-refmac-by-filename "coot-refmac/refmac-for-phases.pdb" ...]// //In unknown file:// // ?: 6 (letrec # # # ...)// //In /Applications/ccp4-7.0/share/coot/scheme/refmac.scm:// //...// // 241: 7 (let* (#) (local-format #t "INFO:: test-refmac-status: ~s~%" ...) ...)// // 241: 8* [goosh-command "refmac5" () ...]// //In /Applications/ccp4-7.0/share/coot/scheme/coot-utils.scm:// // 676: 9 (if (not #) (begin # 255) (let* # # #))// //In unknown file:// //...// // ?: 10 [call-with-output-file "refmac-from-coot-refmac-for-phases-0.log" ...]// // ?: 11 (let* ((file #) (ans #)) (close-output-port file) ans)// // ?: 12* [open-output-file "refmac-from-coot-refmac-for-phases-0.log"]// // ?: 13 [open-file "refmac-from-coot-refmac-for-phases-0.log" "w"]// //: In procedure open-file in expression (open-file str OPEN_WRITE):// //: Permission denied: "refmac-from-coot-refmac-for-phases-0.log"/ Actually, I updated Quartz very recently and today, reinstalled both Quartz and CCP4 in an attempt to solve this problem. Any ideas? Regards Jeroen -- Dr.math. et dis. nat. Jeroen R. Mesters Deputy, Senior Researcher & Lecturer Program Coordinator /Infection Biology/ <http://www.uni-luebeck.de/studium/studiengaenge/infection-biology/introduction.html> Institute of Biochemistry, University of Lübeck Ratzeburger Allee 160, 23538 Lübeck, Germany phone: +49-451-31013105 (secretariate -31013101) fax: +49-451-31013104 http://www.biochem.uni-luebeck.de http://www.eine-stadt-sieht-gelb.de http://www.uni-luebeck.de/studium/studiengaenge/infection-biology http://www.iobcr.org -- If you can look into the seeds of time and tell which grain will grow and which will not, speak then to me who neither beg nor fear (Shakespeare's Macbeth, Act I, Scene 3) -- Only two things are infinite, the universe and human stupidity, and I'm not sure about the former (Albert Einstein) -- Disclaimer * This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. * E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. If verification is required please request a hard-copy version. Please send us by fax any message containing deadlines as incoming e-mails are not screened for response deadlines. * Employees of the Institute are expressly required not to make defamatory statements and not to infringe or authorize any infringement of copyright or any other legal right by email communications. Any such communication is contrary to Institute policy and outside the scope of the employment of the individual concerned. The Institute will not accept any liability in respect of such communication, and the employee responsible will be personally liable for any damages or other liability arising. Employees who receive such an email must notify their supervisor immediately. --
[COOT] Sep. 17-20, Hamburg - Crystallization for novel radiation sources - ICCBM15
Exciting program featuring many highly-esteemed colleagues from all over the world (http://www.iccbm15.org). *Early abstract submission deadline May 16th if to be considered for an oral presentation*, last possible submission date is July 31th, if to be included in the Abstract book. *15th International Conference on the Crystallization of Biological Macromolecules ** * Focus on crystallization for novel radiation sources and use of complementary methods (such as CryoEM) The conference is preceded by a hands-on crystallization workshop (Sep. 14-16) Chairpersons: Christian Betzel and Jeroen Mesters
[COOT] Save the date: ICCBM15, Sep. 17-20, Hamburg - Crystallization for novel radiation sources.
Save the date: ICCBM15, Sep. 17-20, Hamburg, Germany 15th International Conference on the Crystallization of Biological Macromolecules (http://www.iccbm15.org) Focus on crystallization for novel radiation sources and cryo electron microscopy The conference is preceded by a hands-on crystallization workshop (Sep. 14-16) Chairpersons: Christian Betzel and Jeroen Mesters 2014: International Year of Crystallography -- Dr. Jeroen R. Mesters Deputy and Group Leader Institute of Biochemistry, University of Lübeck Ratzeburger Allee 160, 23538 Lübeck, Germany phone: +49-451-5004065 (secretariate 5004061) fax: +49-451-5004068 http://www.biochem.uni-luebeck.de http://www.iobcr.org -- If you can look into the seeds of time and tell which grain will grow and which will not, speak then to me who neither beg nor fear (Shakespeare's Macbeth, Act I, Scene 3) --
Re: [COOT] Hardware stereo setup help
Hi, under linux, USB support will not work as far as I am informed. So, better to use the 3-pin for both operating systems. Not sure the nvidia demo is a useful reference because it can send a HD-TV 1920 × 1080 pixel @ 24 Hz signal to the monitor (what monitor are you using and how is it connected, HDMI, DVI-D???). Under windows, you have to set a few things in the nvidia system driver: 1) change monitor settings to advanced stereo 2) change 3d options to 3d opengl stereo with stereo activation on You have to play a little around here. Under Linux, you have to set a few things in the xorg.conf file by hand! To find out why it is not working, send us of the xorg.conf file the sections Monitor to Extentions. This will help to locate the problem. - J. - Am 02.09.13 23:59, schrieb David Schuller: In addition to using STEREO mode 10, try adding this section to xorg.conf: Section Extensions Option Composite Disable EndSection Full xorg.conf file included at the bottom of this post. On 09/02/13 11:52, Arnaud Basle wrote: Dear Coot and Pymol users, I have the same problem with both softwares so I thought I would send a joined message. We recently acquired a quadro 4000 with a 3-pin connector and the NVIDIA 3D Vision 2 kit (suppose to be supported by NVIDIA on linux for openGL applications http://www.nvidia.com/object/quadro_pro_graphics_boards_linux.html) I have inserted /etc/X11/xorg.conf in device section the following: option stereo 3 following instructions here (http://us.download.nvidia.com/XFree86/Linux-x86/310.40/README/xconfigoptions.html) I am using Mint 13 (based on ubuntu) and the NVIDIA drivers are 319.32. When stating pymol using the following: pymol -S -t 1, I get the following error message: Error: The requested stereo 3D visualization mode is not available. Coot give me the following error when switching to hardware stereo: WARNING:: Can't enable stereo visual - falling back so I guess I did not installed properly my drivers but I am stuck in what to try next. Any help from those of you who managed to get hardware stereo to work would be greatly appreciated (I am even willing to try a different linux flavour if need be). I would like to add that the hardware works fine (at least the NVIDIA demo stuff) on windows 7 but even under windows i could not get pymol/coot to work. Both switch to stereo hardware and the display get blurry but the shutter glasses do not work... Cheers, Arnaud a working xorg.conf from Scientific Linux 6.x : Section ServerLayout Identifier Layout0 Screen 0 Screen0 0 0 InputDeviceKeyboard0 CoreKeyboard InputDeviceMouse0 CorePointer EndSection Section Files ModulePath /usr/lib64/xorg/modules/extensions/nvidia ModulePath /usr/lib64/xorg/modules FontPath /usr/share/fonts/default/Type1 EndSection Section InputDevice # generated from default Identifier Mouse0 Driver mouse OptionProtocol auto OptionDevice /dev/input/mice OptionEmulate3Buttons no OptionZAxisMapping 4 5 EndSection Section InputDevice # generated from data in /etc/sysconfig/keyboard Identifier Keyboard0 Driver kbd OptionXkbLayout us OptionXkbModel pc105 EndSection Section Monitor Identifier Monitor0 VendorName Planar ModelNameSA2311W HorizSync30.0 - 140.0 VertRefresh 56.0 - 120.0 OptionDPMS EndSection Section Device Identifier Device0 Driver nvidia VendorName NVIDIA Corporation EndSection Section Screen Identifier Screen0 Device Device0 MonitorMonitor0 DefaultDepth 24 Option Stereo 10 SubSection Display Modes 1920x1080 1920x1080_120 Depth 24 EndSubSection EndSection Section Extensions Option Composite Disable EndSection -- -- Dr. Jeroen R. Mesters Gruppenleiter Strukturelle Neurobiologie und Kristallogenese Institut für Biochemie Universität zu Lübeck Zentrum für Medizinische Struktur- und Zellbiologie Ratzeburger Allee 160, D-23538 Lübeck Tel: +49-451-5004065 Fax: +49-451-5004068 Http://www.biochem.uni-luebeck.de Http://www.iobcr.org Http://www.selfish-brain.org Http://www.opticryst.org -- Any intelligent fool can make things bigger and more complex. It takes a lot of genius and a lot of courage to move in the opposite direction (Albert Einstein, 1879-1955) Ifyou can look into the seeds of time and say which grain will grow and which will not - speak then to me(Macbeth) -- Disclaimer * Employees of the Institute are expressly required not to make defamatory statements and not to infringe or authorize any infringement of copyright or any other legal right by email communications. Any such communication is contrary to Institute policy and outside the scope
Re: [COOT] HD3D on Linux?
Today I managed to get Coot (and Pymol etc) running under Linux in stereo. Here is the setup for those that are interested: For the stereophiles with a linux box, System: Dell precision 3600 with nvidia quadro 2000 (no 3-pin connector) Linux: Latest version of openSuse but we had to download and install latest nvidia driver ourselves Screen: ASUS VG278H (with build-in IR emitter!! for driving nvidia stereo glasses) First set the resolution to 1920x1080@120Hz and then edit the xorg.conf file in /etc/X11/ as follows: 1) in Section Screen change Option Stereo 0 to 11 (7, 8, 9, 10, or 12 did not work at all!). 11 activates nvidia vision pro 2) did NOT add the line with 3DVisionDisplayType 1 because the ASUS monitor is nvidia certified 3) added the following too (but did not test if this is really needed) Section Extensions Option Composite Disable EndSection 4) save the file, log out, log in again. Hoppla, the 3D light is switches on (also happened with Stereo 10 but stereo was not active at all) and Coot in stereo looks just great! Pymol also works. Jeroen. p.s. season's greetings to all of you out there! -- Dr. Jeroen R. Mesters Gruppenleiter Strukturelle Neurobiologie und Kristallogenese Institut für Biochemie Universität zu Lübeck Zentrum für Medizinische Struktur- und Zellbiologie Ratzeburger Allee 160, D-23538 Lübeck Tel: +49-451-5004065 Fax: +49-451-5004068 Http://www.biochem.uni-luebeck.de Http://www.iobcr.org Http://www.selfish-brain.org Http://www.opticryst.org -- Any intelligent fool can make things bigger and more complex. It takes a lot of genius and a lot of courage to move in the opposite direction (Albert Einstein, 1879-1955) Ifyou can look into the seeds of time and say which grain will grow and which will not - speak then to me(Macbeth) -- Disclaimer * Employees of the Institute are expressly required not to make defamatory statements and not to infringe or authorize any infringement of copyright or any other legal right by email communications. Any such communication is contrary to Institute policy and outside the scope of the employment of the individual concerned. The Institute will not accept any liability in respect of such communication, and the employee responsible will be personally liable for any damages or other liability arising. Employees who receive such an email must notify their supervisor immediately. * This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. * E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. If verification is required please request a hard-copy version. Please send us by fax any message containing deadlines as incoming e-mails are not screened for response deadlines. --
