Re: [ccp4bb] Postdoc Fellowship Opportunity: Structure-based antigen engineering Calgary Alberta Canada
Postdoctoral Fellowship Opportunity Structure-based antigen engineering Working in the laboratory of Dr. Tony Schryvers (University of Calgary), the postdoctoral scholar will spearhead protein engineering and structural studies to develop novel vaccine antigens. The ideal candidate will have expertise in protein crystallography and structural modeling and be within three years of receiving their PhD. In collaboration with Dr. Trevor Moraes (protein crystallography, University of Toronto) and Dr. David Schriemer (mass spectrometry, University of Calgary) the scholar will integrate these approaches to generate detailed models of interactions between native or engineered antigens and host proteins (antibodies and transferrin) and correlate these with functional activities such as complement activation, bacterial killing, or protection. These studies will enable us to probe the encouraging but unexpected findings from recent challenge experiments that potentially will lead to new concepts in vaccine design and development. The successful scholar will have ample opportunities for parallel professional development through courses, teaching or participating in various activities in the academic or industrial spheres depending upon interests. This position is funded by a University of Calgary program “Eyes High” which provides $50,000/a for two years. Applicants should provide a cover letter, CV, and contact information for three references to Carla Davidson, PhD, Project Manager AIHS Interdisciplinary Team on Vaccine Design and Implementation, cjdav...@ucalgary.ca. Trevor F. Moraes (Ph.D.) Assistant Professor Canada Research Chair (Structural Biology of Membrane Proteins) Department of Biochemistry University of Toronto 1 King's College Circle Medical Sciences Building, Room 5366 Toronto, Ontario, Canada M5S 1A8 Email: trevor.mor...@utoronto.ca Phone: (416) 946-3048 Fax: (416) 946-8228 Web address: http://biochemistry.utoronto.ca/moraes/bch.html
[ccp4bb] Registration deadline: EMBO practical course on Computational Structural Biology - from data to structure to function
Dear colleagues, Registration closes this Friday (15th Feb.) for the 2013 EMBO practical course on Computational Structural Biology - from data to structure to function http://events.embo.org/13-comp-structure/ The course covers computational aspects of protein structure determination, validation and analysis, including background in X-ray crystallography, Nuclear Magnetic Resonance Spectroscopy, Electron Microscopy and Small-angle X-ray scattering and hands-on experience in model building from X-ray diffraction data, comparing and integrating different types of structural data, and the differences in interpretation. Students will also learn to critically examine and validate data from these techniques. The course is aimed at PhD students and post-docs working on the collection and analysis of protein structure data. The goal is to provide them with insight into the protein structure determination process, how to critically assess the quality of data from models, and to provide expertise in the integration and visualisation of data from different techniques, thus allowing the analysis of protein structure data for functional relationships. We look forward to receiving your application! Kind regards, Gary Battle On behalf of the organising committee, Gerard Kleywegt Victor Lamzin Christine Orengo Gert Vriend Rosemary Wilson -- Gary Battle Protein Data Bank in Europe (PDBe) http://www.facebook.com/proteindatabank http://twitter.com/PDBeurope
Re: [ccp4bb] Any tool to calculate surface accessible by ... another protein?
Hi Emmanuel - You might consider using MSMS. If you wish to visualize it, there is a PyMOL script available: http://pymolwiki.org/index.php/Msms. Relatedly, one should keep in mind that, while a 10 or 50 Angstrom probe will give you a general idea of accessible surface, if there is any shape complimentarity between two interacting proteins, it won't provide the whole picture. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center Old Public Health Building, Room 610 341 East 25th Street New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Feb 12, 2013, at 2:51 PM, Emmanuel Levy emmanuel.l...@gmail.commailto:emmanuel.l...@gmail.com wrote: Hello, I have been looking for a tool to measure the Protein accessible surface area, which could be defined exactly as the solvent ASA except with a probe of larger radius. Most tools that calculate ASA however do not work with a probe radius of a size equal to 10 or 50 Angstroms. Plus, ideally one would like to know the largest probe size that can access each atom or residue. So using classic ASA programs means one would have to run it ~30 times, each time with different probe radius for each protein. So my question is, do you know of a tool that could help us in obtaining this type of information? Thanks in advance for any hint, All the best, Emmanuel
Re: [ccp4bb] Any tool to calculate surface accessible by ... another protein?
Hi Emmanuel, On Wed, 2013-02-13 16:30 EST, Sampson, Jared jared.samp...@nyumc.org wrote: You might consider using MSMS. If you wish to visualize it, there is a PyMOL script available: http://pymolwiki.org/index.php/Msms. Relatedly, one should keep in mind that, while a 10 or 50 Angstrom probe will give you a general idea of accessible surface, if there is any shape complimentarity between two interacting proteins, it won't provide the whole picture. I would second Jared's suggestion of MSMS. It is straightforward to set up a script to calculate the areas for each atom at many different probe radii. Note that when run with a very large probe size, the calculation takes substantially longer -- total run times on a protein of 185 residues takes less than a second for radii up to 15 A, but increases to 5 minutes for a 20 A probe radius. I didn't bother trying a 50 A probe. MSMS when run with the -af option will generate a file containing the accessible areas for each atom. I have several python scripts that will calculate total areas for various atom classes (hydrophobic, charged, etc.) and also save an output file with areas for each atom and/or residue. These can be run from within PyMOL or as standalone scripts. Similar to the script Jared mentions, my msms_pymol.py script will also allow visualization of the MSMS surface in PyMOL. My various python scripts can be found here: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ Cheers, Rob On Feb 12, 2013, at 2:51 PM, Emmanuel Levy emmanuel.l...@gmail.commailto:emmanuel.l...@gmail.com wrote: Hello, I have been looking for a tool to measure the Protein accessible surface area, which could be defined exactly as the solvent ASA except with a probe of larger radius. Most tools that calculate ASA however do not work with a probe radius of a size equal to 10 or 50 Angstroms. Plus, ideally one would like to know the largest probe size that can access each atom or residue. So using classic ASA programs means one would have to run it ~30 times, each time with different probe radius for each protein. So my question is, do you know of a tool that could help us in obtaining this type of information? Thanks in advance for any hint, All the best, Emmanuel -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical Molecular Sciences Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc
[ccp4bb] GeForce Graphics cards
Hi there, I have an off-toptic question about Graphics card. My searches on pymolwiki and ccp4bb archives resulted in the following conclusion: Coot and pymol are not compatible with the new GeForce graphics cards. Hoewver, most of the posts I found were from 2009 and 2010. Does anyone here have any experience with GeForce 660 or 680 for stereo applications of Coot, Pymol or UCSF chimera? Will quadro cards work equally smooth in the stereo mode of these programs? Do 3D applications put too much pressure on the Graphics card which would justify installing dual Graphics card? (not sure if is relevant, but just for the record, we want to buy passive 3D monitor due to the budget restrictions). Thanks, Alex
Re: [ccp4bb] GeForce Graphics cards
BSD Dear Alex, I'm not sure why you think the new Geforce cards will be an issue. Please clarify. As far as stereo is concerned, Geforce cards only give stereo under Windows, not Linux. If you want stereo under Linux you need the Quadro cards with the stereo option (for example, Quadro 4000 or 5000). Not all Quadro cards support this option, and so would only give stereo under Windows, like the Geforce cards. Not sure about the passive type of stereo; I have a feeling that will also only work under Windows. I'm also not sure it works with Pymol and Coot. Perhaps someone can clarify this. As far as I know the stereo under Linux is only the active variety, using the NVidia 3D Vision glasses. Harry From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Alex Kavian [alek6...@gmail.com] Sent: Wednesday, February 13, 2013 9:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] GeForce Graphics cards Hi there, I have an off-toptic question about Graphics card. My searches on pymolwiki and ccp4bb archives resulted in the following conclusion: Coot and pymol are not compatible with the new GeForce graphics cards. Hoewver, most of the posts I found were from 2009 and 2010. Does anyone here have any experience with GeForce 660 or 680 for stereo applications of Coot, Pymol or UCSF chimera? Will quadro cards work equally smooth in the stereo mode of these programs? Do 3D applications put too much pressure on the Graphics card which would justify installing dual Graphics card? (not sure if is relevant, but just for the record, we want to buy passive 3D monitor due to the budget restrictions). Thanks, Alex
Re: [ccp4bb] GeForce Graphics cards
Harry, I found this on pymol wiki NVidia 3D NVision kit only supports DirectX software for GeForce (gaming cards) on Windows; users are reporting that they are not able to run PyMOL with NVision with these cards. Get a newer model low end quadro ( G8x graphics core) without the 3 pin mini din (e.g. Quadro 370) or with the 3 pin mini din (e.g. Quadro 3700) for Windows. and this too The GeForce cards do not support windowed openGL stereo, so we do not support these series of cards for the NVision 3D solution. For linux, you must have a quadro card that has a 3 pin mini din connector. The cheapest/oldest card that will work with linux is the Quadro 3700.* WARNING*: The Quadro FX1400 does not support 3d vision stereo on Windows7 or Linux. This was posted there a while ago and I was wondering if there has been any update to that which has not been posted. Regarding the passive monitors, I think they are compatible with linux, after all we have been using zalman for long time, which is technically a passive 3D monitor. I also found posts on the ccp4bb from people happily using LG D2342P monitor, though linux or windows was not mentioned. A On Wed, Feb 13, 2013 at 3:21 PM, Harry Mark Greenblatt harry.greenbl...@weizmann.ac.il wrote: BSD Dear Alex, I'm not sure why you think the new Geforce cards will be an issue. Please clarify. As far as stereo is concerned, Geforce cards only give stereo under Windows, not Linux. If you want stereo under Linux you need the Quadro cards with the stereo option (for example, Quadro 4000 or 5000). Not all Quadro cards support this option, and so would only give stereo under Windows, like the Geforce cards. Not sure about the passive type of stereo; I have a feeling that will also only work under Windows. I'm also not sure it works with Pymol and Coot. Perhaps someone can clarify this. As far as I know the stereo under Linux is only the active variety, using the NVidia 3D Vision glasses. Harry From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Alex Kavian [alek6...@gmail.com] Sent: Wednesday, February 13, 2013 9:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] GeForce Graphics cards Hi there, I have an off-toptic question about Graphics card. My searches on pymolwiki and ccp4bb archives resulted in the following conclusion: Coot and pymol are not compatible with the new GeForce graphics cards. Hoewver, most of the posts I found were from 2009 and 2010. Does anyone here have any experience with GeForce 660 or 680 for stereo applications of Coot, Pymol or UCSF chimera? Will quadro cards work equally smooth in the stereo mode of these programs? Do 3D applications put too much pressure on the Graphics card which would justify installing dual Graphics card? (not sure if is relevant, but just for the record, we want to buy passive 3D monitor due to the budget restrictions). Thanks, Alex
Re: [ccp4bb] GeForce Graphics cards
Hi Alex, Thanks for asking before buying. You've avoided a common mistake. If you want to do 120 Hz stereoscopic 3D you must have a Quadro card. GeForce cards, even the really expensive ones, are made for games (and DirectX) not science. I've seen people pay upwards of $1000 for a top-of-the-line GeForce card only to be disappointed to find out it won't do in-window and full-screen OpenGL stereoscopic 3D like a $99 Quadro card will. If you're using passive 3D, like anaglyph or Zalman, then a GeForce card should be capable. I've run both off a MacBook Pro before just fine. Last, here's http://www.pymolwiki.org/index.php/Stereo_3D_Display_Optionsthe discussion on the PyMOLWiki from our users. Cheers, -- Jason On Wed, Feb 13, 2013 at 1:47 PM, Alex Kavian alek6...@gmail.com wrote: Hi there, I have an off-toptic question about Graphics card. My searches on pymolwiki and ccp4bb archives resulted in the following conclusion: Coot and pymol are not compatible with the new GeForce graphics cards. Hoewver, most of the posts I found were from 2009 and 2010. Does anyone here have any experience with GeForce 660 or 680 for stereo applications of Coot, Pymol or UCSF chimera? Will quadro cards work equally smooth in the stereo mode of these programs? Do 3D applications put too much pressure on the Graphics card which would justify installing dual Graphics card? (not sure if is relevant, but just for the record, we want to buy passive 3D monitor due to the budget restrictions). Thanks, Alex -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] GeForce Graphics cards
Hi Jason, aren't the current gaming monitors all (or mostly) 120 Hz? At least companies like alianware sell GeForce together with 120 Hz monitors. A On Wed, Feb 13, 2013 at 4:02 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Alex, Thanks for asking before buying. You've avoided a common mistake. If you want to do 120 Hz stereoscopic 3D you must have a Quadro card. GeForce cards, even the really expensive ones, are made for games (and DirectX) not science. I've seen people pay upwards of $1000 for a top-of-the-line GeForce card only to be disappointed to find out it won't do in-window and full-screen OpenGL stereoscopic 3D like a $99 Quadro card will. If you're using passive 3D, like anaglyph or Zalman, then a GeForce card should be capable. I've run both off a MacBook Pro before just fine. Last, here's http://www.pymolwiki.org/index.php/Stereo_3D_Display_Optionsthe discussion on the PyMOLWiki from our users. Cheers, -- Jason On Wed, Feb 13, 2013 at 1:47 PM, Alex Kavian alek6...@gmail.com wrote: Hi there, I have an off-toptic question about Graphics card. My searches on pymolwiki and ccp4bb archives resulted in the following conclusion: Coot and pymol are not compatible with the new GeForce graphics cards. Hoewver, most of the posts I found were from 2009 and 2010. Does anyone here have any experience with GeForce 660 or 680 for stereo applications of Coot, Pymol or UCSF chimera? Will quadro cards work equally smooth in the stereo mode of these programs? Do 3D applications put too much pressure on the Graphics card which would justify installing dual Graphics card? (not sure if is relevant, but just for the record, we want to buy passive 3D monitor due to the budget restrictions). Thanks, Alex -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] GeForce Graphics cards
Hi, They might be, but please be aware that nearly all scientific applications use OpenGL for drawing and 3D. Many games use DirectX, an MS standard, for that. The capabilities differ by standard (OpenGL vs DirectX), hardware (NVidia GeForce, NVidia Quadro, AMD, Intel, etc) and operating system. Cheers, -- Jason On Wed, Feb 13, 2013 at 3:15 PM, S K alek6...@gmail.com wrote: Hi Jason, aren't the current gaming monitors all (or mostly) 120 Hz? At least companies like alianware sell GeForce together with 120 Hz monitors. A On Wed, Feb 13, 2013 at 4:02 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Alex, Thanks for asking before buying. You've avoided a common mistake. If you want to do 120 Hz stereoscopic 3D you must have a Quadro card. GeForce cards, even the really expensive ones, are made for games (and DirectX) not science. I've seen people pay upwards of $1000 for a top-of-the-line GeForce card only to be disappointed to find out it won't do in-window and full-screen OpenGL stereoscopic 3D like a $99 Quadro card will. If you're using passive 3D, like anaglyph or Zalman, then a GeForce card should be capable. I've run both off a MacBook Pro before just fine. Last, here's http://www.pymolwiki.org/index.php/Stereo_3D_Display_Optionsthe discussion on the PyMOLWiki from our users. Cheers, -- Jason On Wed, Feb 13, 2013 at 1:47 PM, Alex Kavian alek6...@gmail.com wrote: Hi there, I have an off-toptic question about Graphics card. My searches on pymolwiki and ccp4bb archives resulted in the following conclusion: Coot and pymol are not compatible with the new GeForce graphics cards. Hoewver, most of the posts I found were from 2009 and 2010. Does anyone here have any experience with GeForce 660 or 680 for stereo applications of Coot, Pymol or UCSF chimera? Will quadro cards work equally smooth in the stereo mode of these programs? Do 3D applications put too much pressure on the Graphics card which would justify installing dual Graphics card? (not sure if is relevant, but just for the record, we want to buy passive 3D monitor due to the budget restrictions). Thanks, Alex -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
[ccp4bb] UWM is seeking testers for a new protein expression kit
Hi everyone, Dr. M.L.P. Collins at the University of Wisconsin-Milwaukee has developed a new method for making large quantities of active, viable proteins using Rhodospirillum rubrum as a host. R. Rubrum is a bacterium that has traditionally been studied for its simple photosynthetic system, has demonstrated recent success in expressing high-yield protein. To provide a brief overview, R. rubrum possesses the unique characteristic of forming an intracytoplasmic membrane (ICM) in response to membrane protein synthesis. The ICM is non-essential for growth and can incorporate foreign and over-expressed membrane proteins without disrupting normal cellular function. This characteristic has stimulated the expression of active and correctly folded membrane protein where other systems have failed. In an attempt to gather additional testing data, the UWM Research Foundation would like to provide FREE protein expression kits to laboratories or universities that are having difficulties with their current method of producing large-scale proteins. Having limited resources, our researchers have only had the ability to test a number of proteins but thus far have seen exceptional promise. We currently have 8 other universities or companies using the new kit and are now ready to distribute to other participants. The link listed below provides a more detailed explanation of the testing process including the specific proteins currently being tested. You may also view Dr. Collin's publication on her findings of using R. rubrum as a host. If you are interested in learning more about this new system or have any additional comments, you may email me at jsilva...@uwmfdn.orgmailto:jsilva...@uwmfdn.org. Testing Kit Link Slides http://www.uwmresearchfoundation.org/getdoc/2a36a544-e47c-442e-baaf-9fb3442694f0/Slides-for-Kit-Testing-2013.aspx Dr. Collin's Publication Butzin, N.C; Owen, H.A.; and M.L.P. Collins. 2010. A new system for heterologous expression of membrane proteins: Rhodospirillum rubrum. Protein Expression and Purification, 70: 88-94. http://www4.uwm.edu/letsci/biologicalsciences/facultystaff/collins/upload/Butzin_et_al_2010.pdf
[ccp4bb] S-nitrosylation protein
Dear All: I plan to use X-ray crystallography method to study the S-nitrosylated protein structure. The native protein crystals diffracted to 2A with synchrontron. I now have the crystals of S-ntrosylated protein. Since S-NO moiety appears to be unstable to synchrotron radiation, could you advice / comments on the stratage on the data collection of S-nitrosylated protein crystals? The protein crystals did not diffract well with in house X-ray. Thank you for your comments. Uma
Re: [ccp4bb] S-nitrosylation protein
Maybe you can try different energies hoping that damage is wavelength dependent. It must be dose dependent though, so you may consider merging short sweeps from multiple crystals. Original message From: Uma Ratu rosiso2...@gmail.com Date: To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] S-nitrosylation protein Dear All: I plan to use X-ray crystallography method to study the S-nitrosylated protein structure. The native protein crystals diffracted to 2A with synchrontron. I now have the crystals of S-ntrosylated protein. Since S-NO moiety appears to be unstable to synchrotron radiation, could you advice / comments on the stratage on the data collection of S-nitrosylated protein crystals? The protein crystals did not diffract well with in house X-ray. Thank you for your comments. Uma
Re: [ccp4bb] GeForce Graphics cards
Hi, Since it is mentioned, I would like to take this chance to clarify: We have used the Zalman and LG 2342P under Linux, Windows(XP and 7) and a VM Windows within a Linux system, on either desktop (with a minimal on-board graphic chip) or laptops. The monitor is quite plug-and-play in all cases we have tested. According to the internet, these monitors also work with Macs for stereo game play and stereo video viewing. In regard to the crystallographic software, the Zalman mode is supported by COOT, Chimera, and the new Pymol (but not the 0.99) - we have tested them all in both Linux and Windows. Passive 3D only requires the graphic program to send out the left and right images in alternating lines. To my understanding this suggests that it is independent of OS or graphic cards. But for Mac users, I think the first thing to check is whether the Mac COOT and Chimera has a Zalman mode option. Here's the link to my previous reply on the BB regarding our experience with the Zalman and LG D2342: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg28113.html Zhijie From: S K Sent: Wednesday, February 13, 2013 3:37 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] GeForce Graphics cards Harry, I found this on pymol wiki NVidia 3D NVision kit only supports DirectX software for GeForce (gaming cards) on Windows; users are reporting that they are not able to run PyMOL with NVision with these cards. Get a newer model low end quadro ( G8x graphics core) without the 3 pin mini din (e.g. Quadro 370) or with the 3 pin mini din (e.g. Quadro 3700) for Windows. and this too The GeForce cards do not support windowed openGL stereo, so we do not support these series of cards for the NVision 3D solution. For linux, you must have a quadro card that has a 3 pin mini din connector. The cheapest/oldest card that will work with linux is the Quadro 3700. WARNING: The Quadro FX1400 does not support 3d vision stereo on Windows7 or Linux. This was posted there a while ago and I was wondering if there has been any update to that which has not been posted. Regarding the passive monitors, I think they are compatible with linux, after all we have been using zalman for long time, which is technically a passive 3D monitor. I also found posts on the ccp4bb from people happily using LG D2342P monitor, though linux or windows was not mentioned. A On Wed, Feb 13, 2013 at 3:21 PM, Harry Mark Greenblatt harry.greenbl...@weizmann.ac.il wrote: BSD Dear Alex, I'm not sure why you think the new Geforce cards will be an issue. Please clarify. As far as stereo is concerned, Geforce cards only give stereo under Windows, not Linux. If you want stereo under Linux you need the Quadro cards with the stereo option (for example, Quadro 4000 or 5000). Not all Quadro cards support this option, and so would only give stereo under Windows, like the Geforce cards. Not sure about the passive type of stereo; I have a feeling that will also only work under Windows. I'm also not sure it works with Pymol and Coot. Perhaps someone can clarify this. As far as I know the stereo under Linux is only the active variety, using the NVidia 3D Vision glasses. Harry From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Alex Kavian [alek6...@gmail.com] Sent: Wednesday, February 13, 2013 9:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] GeForce Graphics cards Hi there, I have an off-toptic question about Graphics card. My searches on pymolwiki and ccp4bb archives resulted in the following conclusion: Coot and pymol are not compatible with the new GeForce graphics cards. Hoewver, most of the posts I found were from 2009 and 2010. Does anyone here have any experience with GeForce 660 or 680 for stereo applications of Coot, Pymol or UCSF chimera? Will quadro cards work equally smooth in the stereo mode of these programs? Do 3D applications put too much pressure on the Graphics card which would justify installing dual Graphics card? (not sure if is relevant, but just for the record, we want to buy passive 3D monitor due to the budget restrictions). Thanks, Alex
Re: [ccp4bb] GeForce Graphics cards
Hi Alex, The graphical computational power of even the lowest-end graphic chips these days will suffice the displaying of our models. To give you some idea: we are still using a Quadro FX 1000 card and an old CRT on one of our stereo systems; my 6-year old laptop has an ATI Radeon X1300, which can still drive the stereo display on Zalman or LG D2342P. You can check the benchmarks of these chips to see why dual card is guaranteed to be a waste. If you are determined to go the passive 3D monitor(Zalman or LG D2342) path, then you actually do not need to worry about the graphic card - even the on-board one will do. Quadro cards are for the use with 120Hz monitors and shutter glasses, whereas the passive 3D monitors are CPL-based and do not need special graphic cards. Having said all the above, UCSF Chimera might become a little demanding when displaying electron densities, so a discrete mainstream Nvidia or ATI chip would probably make life easier in a few cases. Zhijie -- From: Alex Kavian alek6...@gmail.com Sent: Wednesday, February 13, 2013 2:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] GeForce Graphics cards Hi there, I have an off-toptic question about Graphics card. My searches on pymolwiki and ccp4bb archives resulted in the following conclusion: Coot and pymol are not compatible with the new GeForce graphics cards. Hoewver, most of the posts I found were from 2009 and 2010. Does anyone here have any experience with GeForce 660 or 680 for stereo applications of Coot, Pymol or UCSF chimera? Will quadro cards work equally smooth in the stereo mode of these programs? Do 3D applications put too much pressure on the Graphics card which would justify installing dual Graphics card? (not sure if is relevant, but just for the record, we want to buy passive 3D monitor due to the budget restrictions). Thanks, Alex
Re: [ccp4bb] GeForce Graphics cards
Hi Zhijie, thanks for the link. I was actually referring to that post. Can you please tell me what graphics card you are using? Alex On Wed, Feb 13, 2013 at 6:16 PM, Zhijie Li zhijie...@utoronto.ca wrote: ** Hi, Since it is mentioned, I would like to take this chance to clarify: We have used the Zalman and LG 2342P under Linux, Windows(XP and 7) and a VM Windows within a Linux system, on either desktop (with a minimal on-board graphic chip) or laptops. The monitor is quite plug-and-play in all cases we have tested. According to the internet, these monitors also work with Macs for stereo game play and stereo video viewing. In regard to the crystallographic software, the Zalman mode is supported by COOT, Chimera, and the new Pymol (but not the 0.99) - we have tested them all in both Linux and Windows. Passive 3D only requires the graphic program to send out the left and right images in alternating lines. To my understanding this suggests that it is independent of OS or graphic cards. But f or Mac users, I think the first thing to check is whether the Mac COOT and Chimera has a Zalman mode option. Here's the link to my previous reply on the BB regarding our experience with the Zalman and LG D2342: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg28113.html Zhijie *From:* S K alek6...@gmail.com *Sent:* Wednesday, February 13, 2013 3:37 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] GeForce Graphics cards Harry, I found this on pymol wiki NVidia 3D NVision kit only supports DirectX software for GeForce (gaming cards) on Windows; users are reporting that they are not able to run PyMOL with NVision with these cards. Get a newer model low end quadro ( G8x graphics core) without the 3 pin mini din (e.g. Quadro 370) or with the 3 pin mini din (e.g. Quadro 3700) for Windows. and this too The GeForce cards do not support windowed openGL stereo, so we do not support these series of cards for the NVision 3D solution. For linux, you must have a quadro card that has a 3 pin mini din connector. The cheapest/oldest card that will work with linux is the Quadro 3700.*WARNING *: The Quadro FX1400 does not support 3d vision stereo on Windows7 or Linux. This was posted there a while ago and I was wondering if there has been any update to that which has not been posted. Regarding the passive monitors, I think they are compatible with linux, after all we have been using zalman for long time, which is technically a passive 3D monitor. I also found posts on the ccp4bb from people happily using LG D2342P monitor, though linux or windows was not mentioned. A On Wed, Feb 13, 2013 at 3:21 PM, Harry Mark Greenblatt harry.greenbl...@weizmann.ac.il wrote: BSD Dear Alex, I'm not sure why you think the new Geforce cards will be an issue. Please clarify. As far as stereo is concerned, Geforce cards only give stereo under Windows, not Linux. If you want stereo under Linux you need the Quadro cards with the stereo option (for example, Quadro 4000 or 5000). Not all Quadro cards support this option, and so would only give stereo under Windows, like the Geforce cards. Not sure about the passive type of stereo; I have a feeling that will also only work under Windows. I'm also not sure it works with Pymol and Coot. Perhaps someone can clarify this. As far as I know the stereo under Linux is only the active variety, using the NVidia 3D Vision glasses. Harry From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Alex Kavian [alek6...@gmail.com] Sent: Wednesday, February 13, 2013 9:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] GeForce Graphics cards Hi there, I have an off-toptic question about Graphics card. My searches on pymolwiki and ccp4bb archives resulted in the following conclusion: Coot and pymol are not compatible with the new GeForce graphics cards. Hoewver, most of the posts I found were from 2009 and 2010. Does anyone here have any experience with GeForce 660 or 680 for stereo applications of Coot, Pymol or UCSF chimera? Will quadro cards work equally smooth in the stereo mode of these programs? Do 3D applications put too much pressure on the Graphics card which would justify installing dual Graphics card? (not sure if is relevant, but just for the record, we want to buy passive 3D monitor due to the budget restrictions). Thanks, Alex
Re: [ccp4bb] GeForce Graphics cards
Hi Alex, We actually didn't invest on a discrete video card for the LG-D2342P system. The one we are using on the LG-D2342P desktop is the integrated Intel HD graphic 2000 chip, which is physically located in the CPU. The CPU is i7-2600. We installed a Linux OS on this desktop and also run a VirtualBoxed Windows XP inside the Linux for office jobs. Due to some limitations of the Virtualbox, the VM Windows system does not get hardware 3D acceleration, but still the speed of rendering is fine in most cases even for UCSF Chimera. In Linux there is no issue on speed. Zhijie From: A K Sent: Wednesday, February 13, 2013 6:51 PM To: Zhijie Li Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] GeForce Graphics cards Hi Zhijie, thanks for the link. I was actually referring to that post. Can you please tell me what graphics card you are using? Alex On Wed, Feb 13, 2013 at 6:16 PM, Zhijie Li zhijie...@utoronto.ca wrote: Hi, Since it is mentioned, I would like to take this chance to clarify: We have used the Zalman and LG 2342P under Linux, Windows(XP and 7) and a VM Windows within a Linux system, on either desktop (with a minimal on-board graphic chip) or laptops. The monitor is quite plug-and-play in all cases we have tested. According to the internet, these monitors also work with Macs for stereo game play and stereo video viewing. In regard to the crystallographic software, the Zalman mode is supported by COOT, Chimera, and the new Pymol (but not the 0.99) - we have tested them all in both Linux and Windows. Passive 3D only requires the graphic program to send out the left and right images in alternating lines. To my understanding this suggests that it is independent of OS or graphic cards. But f or Mac users, I think the first thing to check is whether the Mac COOT and Chimera has a Zalman mode option. Here's the link to my previous reply on the BB regarding our experience with the Zalman and LG D2342: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg28113.html Zhijie From: S K Sent: Wednesday, February 13, 2013 3:37 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] GeForce Graphics cards Harry, I found this on pymol wiki NVidia 3D NVision kit only supports DirectX software for GeForce (gaming cards) on Windows; users are reporting that they are not able to run PyMOL with NVision with these cards. Get a newer model low end quadro ( G8x graphics core) without the 3 pin mini din (e.g. Quadro 370) or with the 3 pin mini din (e.g. Quadro 3700) for Windows. and this too The GeForce cards do not support windowed openGL stereo, so we do not support these series of cards for the NVision 3D solution. For linux, you must have a quadro card that has a 3 pin mini din connector. The cheapest/oldest card that will work with linux is the Quadro 3700. WARNING: The Quadro FX1400 does not support 3d vision stereo on Windows7 or Linux. This was posted there a while ago and I was wondering if there has been any update to that which has not been posted. Regarding the passive monitors, I think they are compatible with linux, after all we have been using zalman for long time, which is technically a passive 3D monitor. I also found posts on the ccp4bb from people happily using LG D2342P monitor, though linux or windows was not mentioned. A On Wed, Feb 13, 2013 at 3:21 PM, Harry Mark Greenblatt harry.greenbl...@weizmann.ac.il wrote: BSD Dear Alex, I'm not sure why you think the new Geforce cards will be an issue. Please clarify. As far as stereo is concerned, Geforce cards only give stereo under Windows, not Linux. If you want stereo under Linux you need the Quadro cards with the stereo option (for example, Quadro 4000 or 5000). Not all Quadro cards support this option, and so would only give stereo under Windows, like the Geforce cards. Not sure about the passive type of stereo; I have a feeling that will also only work under Windows. I'm also not sure it works with Pymol and Coot. Perhaps someone can clarify this. As far as I know the stereo under Linux is only the active variety, using the NVidia 3D Vision glasses. Harry From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Alex Kavian [alek6...@gmail.com] Sent: Wednesday, February 13, 2013 9:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] GeForce Graphics cards Hi there, I have an off-toptic question about Graphics card. My searches on pymolwiki and ccp4bb archives resulted in the following conclusion: Coot and pymol are not compatible with the new GeForce graphics cards. Hoewver, most of the posts I found were from 2009 and 2010. Does anyone here have any experience with GeForce 660 or 680 for stereo applications of Coot, Pymol or UCSF chimera? Will quadro cards work equally smooth in the stereo mode of these programs? Do 3D
[ccp4bb] observed reflections
Dear ccp4 I apologise for the straightforward question. I'm just a bit confused about the observed reflections quoted in tables. What exactly is this and should it include outer shell separately? Best Careina
