[ccp4bb] Announcement: 4th PhD Student Symposium Horizons in Molecular Biology Sept 12th-15th 2007
Dear all, please mark your calendar: You are invited to participate in the 4th Horizons in Molecular Biology Symposium on September 12-15th 2007 in Goettingen, Germany. http://www.horizons.uni-goettingen.de Call for Abstracts: Horizons in Molecular Biology aims to provide deep insights into contemporary life science research and to encourage exchange among people from different biological science branches. We invite distinguished scientists from fields as diverse as structural biology, developmental biology, cell biology and neurobiology. Furthermore, this year's Horizons features a Systems Biology session and a career fair on 12th of September (including company presentations and career workshops). By including a diverse spectrum of topics we hope to broaden horizons and to inspire interdisciplinary discussions. Through the scientific and social events of the meeting we intend to improve the networking of Ph.D. students and young researchers from different parts of the world. The meeting will feature five sessions with invited lectures, two poster sessions, three sessions with student talks and includes an extensive social program. Confirmed invited speakers are: Structural Biology: Hashim Al-Hashimi Nenad Ban Roland Beckmann Kevin Gardner Cell Biology: Jiri Bartek Bernd Bukau Tim Hunt Stefan Müller Phillip Zamore Neuroscience: Jean-Pierre Changeux Joachim Herz Larry Zipursky Developmental Biology: Markus Affolter John Gurdon Andrew McMahon Claudio Stern Systems Biology: Patrick Cramer Friedrich Lottspeich Michael Yaffe Hope to see in September and don't forget to register soon as the number of participants is limited. * Early registration deadline: July 1st, 2007 * Late registration deadline / Abstract Submission deadline: August 1st, 2007 For further details about registration, detailed program, abstract submission and contact information please visit our web page: http://www.horizons.uni-goettingen.de/ Please feel free to download the announcing poster from our website http://www.horizons.uni-goettingen.de/Horizons2007/dl/horizons07.pdf Best regards, Christian Stegmann (On behalf of the the PhD Student Organizing Committee) --- HORIZONS IN MOLECULAR BIOLOGY International PhD Student Symposium PhD Student Organizing Committee Max-Planck-Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Email: [EMAIL PROTECTED] www.horizons.uni-goettingen.de www.gpmolbio.uni-goettingen.de -- -- Christian Stegmann Max-Planck Institute for Biophysical Chemistry Dept. Cellular Biochemistry / X-ray Crystallography Am Fassberg 11 37077 Goettingen, Germany Phone: +49-551-201-1068 Fax: +49-551-201-1197
[ccp4bb] EMBL Grenoble Team Leader: Synchrotron Methods for Structural Biology
*EMBL Grenoble Team Leader: Synchrotron Methods for Structural Biology http://www-db.embl.de/jss/servlet/de.embl.bk.emblGroups.JobsPage/07065.html?EmblGR=x Job Description*: We are looking for a structural biologist who has a focus on advanced crystallographic methods and instrumentation, particularly with relation to synchrotron radiation. The appointed Team Leader will manage, together with the Head of Outstation, the long-term collaboration between the EMBL Grenoble Outstation and the European Synchrotron Radiation Facility (ESRF) concerning the development and operation of the automated protein crystallography beamlines. He/she will oversee the activities of the three existing EMBL beamline scientists currently responsible for the dedicated microfocus beamline ID23-2, the MAD beamline ID14-EH4 and the CRG beamline BM14 (co-operated with MRC-France) as well as a SAXS beamline scientist currently under recruitment. He/she will collaborate in particular with the Outstation Diffraction Instrumentation team led by Florent Cipriani, which has developed state-of-the-art sample handling equipment currently installed on all ESRF MX beamlines (microdiffractometer, sample changer, minikappa) and with the ESRF MX group led by Sean McSweeney. He/she will develop a research programme focused on advanced crystallographic methods and instrumentation coupled to structural biological problems or more generally on new synchrotron techniques that might have an impact in biology and which take advantage of the unique environment at the world-leading 3rd generation synchrotron site in Grenoble. *Commencing date:* As soon as possible following the closing date* *Contract:* An initial contract of 3 years will be offered to the successful candidate. This can be renewed, depending on circumstances at the time of review.* Closing date:* 8 July 2007 * Web page:* http://www.embl-grenoble.fr/ *To apply, please email a curriculum vitae, three references and a concise description of research interests and future plans quoting ref. no. W/07/065 in the subject line, to: [EMAIL PROTECTED] *Informal enquiries to me* *Stephen Cusack* ** Dr. Stephen Cusack, Head of Grenoble Outstation of EMBL Group leader in structural biology of protein-RNA complexes and viral proteins Joint appointment in EMBL Gene Expression Programme ** Email: [EMAIL PROTECTED] Website: http://www.embl-grenoble.fr Tel: (33) 4 76 20 7238 Secretary (33) 4 76 20 7306 Fax: (33) 4 76 20 7786 or (33) 4 76 20 7199 Postal address: EMBL c/o ILL, BP181, 38042 Grenoble Cedex 9, France Delivery address: EMBL c/o ILL, Polygone Scientifique, 6 Rue Jules Horowitz, 38042 Grenoble, France ** -- ** Dr. Stephen Cusack, Head of Grenoble Outstation of EMBL Group leader in structural biology of protein-RNA complexes and viral proteins Joint appointment in EMBL Gene Expression Programme Director of CNRS-UJF-EMBL Mixed Unit (UMR 5233) for Virus Host Cell Interactions (UVHCI) ** Email: [EMAIL PROTECTED] Website: http://www.embl.fr Tel:(33) 4 76 20 7238Secretary (33) 4 76 20 7306 Fax:(33) 4 76 20 7786 or (33) 4 76 20 7199 Postal address: EMBL, 6 Rue Jules Horowitz, BP181, 38042 Grenoble Cedex 9, France Delivery address: EMBL c/o ILL, Polygone Scientifique, 6 Rue Jules Horowitz, 38042 Grenoble, France **
[ccp4bb] EMBL Grenoble Staff Scientist : New SAXS Beamline on ID14-EH3 at the ESRF
*EMBL Grenoble Staff Scientist : New SAXS Beamline on ID14-EH3 at the ESRF* http://www-db.embl.de/jss/servlet/de.embl.bk.emblGroups.JobsPage/07069.html?EmblGR=x *Job description:* A scientist is required to join a team within the Partnership for Structural Biology (EMBL, ESRF, ILL and IBS, http://psb.esrf.fr/) which is establishing a unique and integrated SAXS-SANS platform, making use of the intense synchrotron X-ray and neutron beams of respectively the ERSF and ILL. The successful candidate will be responsible for construction, commissioning and user support of a new state-of-the-art SAXS beamline, dedicated to biology, to be built on undulator beamline ID14-EH3 at the ESRF. The beamline will cater to the growing needs of the European structural biology community who wish to combine SAXS studies with crystallography and other techniques. He/She will benefit from strong technical support from the ESRF MX and Soft Condensed Matter groups and other ESRF services as well as the EMBL Grenoble diffraction instrumentation group. In addition there will be a strong collaboration with the SAXS scientists from the EMBL Hamburg Outstation both to transfer expertise and to provide test facilities during the conception and construction phase of the future SAXS beamline at Petra III in Hamburg. *Qualifications and experience:* Applicants for this position are expected to hold a PhD in a related specialization, as well as have postdoctoral experience in instrumentation and software for small-angle scattering in physics, chemistry or biology, preferably at a synchrotron. At least some knowledge of, and demonstrable interest in, biology is required. *Commencing date:* As soon as possible following the closing date *Contract:* An initial contract of 3 years will be offered to the successful candidate. This can be renewed, depending on circumstances at the time of review. *Closing date*: 8 July 2007 *Web page*: http://www.embl-grenoble.fr/ To apply, please email a curriculum vitae, three references and a concise description of research interests and future plans quoting ref. no. W/07/065 in the subject line, to: [EMAIL PROTECTED] Informal enquiries to me Stephen Cusack * * http://www.embl-grenoble.fr/ ** Dr. Stephen Cusack, Head of Grenoble Outstation of EMBL Group leader in structural biology of protein-RNA complexes and viral proteins Joint appointment in EMBL Gene Expression Programme ** Email: [EMAIL PROTECTED] Website: http://www.embl-grenoble.fr Tel:(33) 4 76 20 7238Secretary (33) 4 76 20 7306 Fax:(33) 4 76 20 7786 or (33) 4 76 20 7199 Postal address: EMBL c/o ILL, BP181, 38042 Grenoble Cedex 9, France Delivery address: EMBL c/o ILL, Polygone Scientifique, 6 Rue Jules Horowitz, 38042 Grenoble, France ** -- ** Dr. Stephen Cusack, Head of Grenoble Outstation of EMBL Group leader in structural biology of protein-RNA complexes and viral proteins Joint appointment in EMBL Gene Expression Programme Director of CNRS-UJF-EMBL Mixed Unit (UMR 5233) for Virus Host Cell Interactions (UVHCI) ** Email: [EMAIL PROTECTED] Website: http://www.embl.fr Tel:(33) 4 76 20 7238Secretary (33) 4 76 20 7306 Fax:(33) 4 76 20 7786 or (33) 4 76 20 7199 Postal address: EMBL, 6 Rue Jules Horowitz, BP181, 38042 Grenoble Cedex 9, France Delivery address: EMBL c/o ILL, Polygone Scientifique, 6 Rue Jules Horowitz, 38042 Grenoble, France **
[ccp4bb] Support Scientist: MX Side Station at Diamond
Dear ccp4bb members, There is a permanent position for a Support Scientist open at the Macromolecular Crystallography (MX) Side Station at Diamond Light Source. The MX Side Station - Beam line I04.1 - will be the fifth macromolecular crystallography beam line to be built at Diamond. Its primary use will be for ligand binding studies and for structures that might be expected to be solved by molecular replacement. It is anticipated that this beam line will be extensively used both by the academic community and by pharmaceutical companies. For informal queries please email [EMAIL PROTECTED] The application deadline is 10th July 2007 and further information can be found at: http://www.diamond.ac.uk/Jobs/CurrentVacancies/Scientific/DIA0326SB.htm Regards, Jose Brandao 14 Sep 2007 - Systems Biology Talks at Diamond (SR User Meeting) - Register now! http://www.diamond.ac.uk/ForUsers/SRUser07/Satellites/Satellite2.htm Jose Ribeiro Brandao-Neto Beamline Scientist - I04.1 Macromolecular Crystallography Group Diamond Light Source Ltd Diamond House DR1.78 Harwell Science and Innovation Campus RAL, Chilton, Didcot Oxfordshire OX11 0DE United Kingdom tel: +44 (0)1235 778506/8522 +44 (0)1235 778000 fax: +44 (0)1235 778448 [EMAIL PROTECTED] http://www.diamond.ac.uk Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Diamond Light Source by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. DIVFONT size=1 color=grayThis e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom /FONT/DIV
[ccp4bb] Position: Lab Engineer at SGC-Oxford
The Protein Crystallography (PX) group of the Structural Genomics Consortium (SGC) at Oxford University is recruiting a Laboratory Engineer to take charge of the crystallization and X-ray robotics and drive infrastructure development. The Laboratory Engineer will be responsible for maintenance of robotics, liaison with vendors, hacking existing robotics, integrating them into the LIMS, selection and development of new equipment, and projects to streamline of the SGC pipeline. The SGC-Oxford is a department of Oxford University, and together with SGC sites at Toronto University and Karolinska Institutet, has solved structures of more than 400 novel human protein targets over the 3 years of Phase I funding. The SGC is now entering Phase II funding, with expanded focus on ligand complex structures and membrane proteins. The PX group manages crystallization and structure solution of the SGC-Oxford, in collaboration with the Biology and Biotechnology groups. Therefore, PX runs the crystallization infrastructure, which includes pretty much everything you'd expect in a high-throughput lab that really does do high-throughput. Especially shiny machines with bright lights that go whi. In particular, Mosquito dispensers, MPII liquid handler, Minstrel III inspecting robots, FRE diffractometer with Actor sample changer. For further information, see http://www.sgc.ox.ac.uk/jobs/index.html, or indeed reply to me. Cheers phx
Re: [ccp4bb] Survey on computer usage in crystallography
On Tue, 2007-06-19 at 21:09 -0700, P Hubbard wrote: Hi all, I am doing a survey on computer usage in crystallography. The questionnaire can be found on the following web page: http://www.bioscienceforum.com/survey.html ... I don't care for the way several questions are posed. Examples: 4.What would you consider is a reasonable price to pay for a computer graphics workstation designed with crystallography in mind? A) USD $2000-3000 B) USD $3000-5000 C) USD $5000+ What, no option for I'd be willing to assemble one from parts for under USD $2000? ... If there were a choice, would you prefer stereo graphics displayed using LCD-shuttered glasses or a head mounted display (often referred to as a Virtual Reality headset)? That does not cover all the choices currently available, let alone what I wish were available. -- === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED]
Re: [ccp4bb] Survey on computer usage in crystallography
I don't expect the I'd be willing to assemble one from parts for under USD $2000 crowd will be large but you don't have to do the assembling to get all you need well under the $2000 mark. The times that you needed the fastest computer money could buy and still spent lots of time in the library reading while your rigid body refinement was chewing on the next cycle is long gone. Bart David J. Schuller wrote: On Tue, 2007-06-19 at 21:09 -0700, P Hubbard wrote: Hi all, I am doing a survey on computer usage in crystallography. The questionnaire can be found on the following web page: http://www.bioscienceforum.com/survey.html ... I don't care for the way several questions are posed. Examples: 4.What would you consider is a reasonable price to pay for a computer graphics workstation designed with crystallography in mind? A) USD $2000-3000 B) USD $3000-5000 C) USD $5000+ What, no option for I'd be willing to assemble one from parts for under USD $2000? ... If there were a choice, would you prefer stereo graphics displayed using LCD-shuttered glasses or a head mounted display (often referred to as a Virtual Reality headset)? That does not cover all the choices currently available, let alone what I wish were available. -- == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521 ==
Re: [ccp4bb] Survey on computer usage in crystallography
I am sorry you are unhappy with the questions, David. As I am sure you know, I half-decent system with stereo graphics doesn't come cheap, and if you price things together to make something that performs well I doubt you'll get much change out of $2000. I am aware of other 3D systems (such as those listed on www.stereo3d.com). However, the price of peripherals like a 3D LCD monitor are prohibitively expensive (and the quality of the images is supposed to be poor). Do you know of a relatively inexpensive way of displaying 3D images on PCs? Any other comments would be greatly appreciated. Paul From: David J. Schuller [EMAIL PROTECTED] Reply-To: David J. Schuller [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Survey on computer usage in crystallography Date: Wed, 20 Jun 2007 10:18:44 -0400 On Tue, 2007-06-19 at 21:09 -0700, P Hubbard wrote: Hi all, I am doing a survey on computer usage in crystallography. The questionnaire can be found on the following web page: http://www.bioscienceforum.com/survey.html ... I don't care for the way several questions are posed. Examples: 4.What would you consider is a reasonable price to pay for a computer graphics workstation designed with crystallography in mind? A) USD $2000-3000 B) USD $3000-5000 C) USD $5000+ What, no option for I'd be willing to assemble one from parts for under USD $2000? ... If there were a choice, would you prefer stereo graphics displayed using LCD-shuttered glasses or a head mounted display (often referred to as a Virtual Reality headset)? That does not cover all the choices currently available, let alone what I wish were available. -- === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED] _ Need a break? Find your escape route with Live Search Maps. http://maps.live.com/default.aspx?ss=Restaurants~Hotels~Amusement%20Parkcp=33.832922~-117.915659style=rlvl=13tilt=-90dir=0alt=-1000scene=1118863encType=1FORM=MGAC01
Re: [ccp4bb] Survey on computer usage in crystallography
Hi, If you build a system without stereo graphics, and use a standard monitor, I agree. In-fact it can be done for for under ~$1000. However, stereo systems are rather expensive (LCD stereo systems are VERY expensive). I was just curious to see how popular stereo graphics is for crystallographers. I personally think its a wonderful teaching tool which is currently under-utilized. Paul From: Bart Hazes [EMAIL PROTECTED] Reply-To: [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Survey on computer usage in crystallography Date: Wed, 20 Jun 2007 09:28:25 -0600 I don't expect the I'd be willing to assemble one from parts for under USD $2000 crowd will be large but you don't have to do the assembling to get all you need well under the $2000 mark. The times that you needed the fastest computer money could buy and still spent lots of time in the library reading while your rigid body refinement was chewing on the next cycle is long gone. Bart David J. Schuller wrote: On Tue, 2007-06-19 at 21:09 -0700, P Hubbard wrote: Hi all, I am doing a survey on computer usage in crystallography. The questionnaire can be found on the following web page: http://www.bioscienceforum.com/survey.html ... I don't care for the way several questions are posed. Examples: 4.What would you consider is a reasonable price to pay for a computer graphics workstation designed with crystallography in mind? A) USD $2000-3000 B) USD $3000-5000 C) USD $5000+ What, no option for I'd be willing to assemble one from parts for under USD $2000? ... If there were a choice, would you prefer stereo graphics displayed using LCD-shuttered glasses or a head mounted display (often referred to as a Virtual Reality headset)? That does not cover all the choices currently available, let alone what I wish were available. -- == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521 == _ Like puzzles? Play free games earn great prizes. Play Clink now. http://club.live.com/clink.aspx?icid=clink_hotmailtextlink2
Re: [ccp4bb] Survey on computer usage in crystallography
More likely the issue is that some of us do not find stereo to be necessary of beneficial for crystallographic model building. In which case, given the power of modern PCs and graphics cards, a basic off-the-shelf PC costing $1000/£500 is completely adaquate for typical structure solution and model building problems. I use coot a lot and I haven't even bothered installing the graphics drivers for my graphics card. All the 3D stuff gets gone in software, and most of the graphics hardware sits around doing nothing. If I needed the performance, it would be a 5 minute job to install the drivers, but I haven't needed it. Kevin P Hubbard wrote: I am sorry you are unhappy with the questions, David. As I am sure you know, I half-decent system with stereo graphics doesn't come cheap, and if you price things together to make something that performs well I doubt you'll get much change out of $2000. I am aware of other 3D systems (such as those listed on www.stereo3d.com). However, the price of peripherals like a 3D LCD monitor are prohibitively expensive (and the quality of the images is supposed to be poor). Do you know of a relatively inexpensive way of displaying 3D images on PCs? Any other comments would be greatly appreciated. Paul
Re: [ccp4bb] Survey on computer usage in crystallography
Hi Paul, I didn't intend to criticise the survey, I actually filled it out immediately, and am interested in the outcome. Perhaps more so for the issue of easing crystallographic software installation and updating than the stereographics part. Wrt stereographics; I bought three sets of NuVision stereographics units with glasses when I started up my lab. I personally prefer to use side-by-side stereo and cross my eyes and most of my trainees don't appear to be interested in using the hardware stereo option. So the glasses mostly get used to impress high-school students and other visitors. In hind-sight I would have gotten one stereo-ready setup with 2 or 3 sets of glasses. Similarly, I think it is effective to have one (or a few depending on size of lab) higher-end number cruncher with large memmory and disk storage and pretty basic PC's for individual users. Bart P Hubbard wrote: Hi, If you build a system without stereo graphics, and use a standard monitor, I agree. In-fact it can be done for for under ~$1000. However, stereo systems are rather expensive (LCD stereo systems are VERY expensive). I was just curious to see how popular stereo graphics is for crystallographers. I personally think its a wonderful teaching tool which is currently under-utilized. Paul From: Bart Hazes [EMAIL PROTECTED] Reply-To: [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Survey on computer usage in crystallography Date: Wed, 20 Jun 2007 09:28:25 -0600 I don't expect the I'd be willing to assemble one from parts for under USD $2000 crowd will be large but you don't have to do the assembling to get all you need well under the $2000 mark. The times that you needed the fastest computer money could buy and still spent lots of time in the library reading while your rigid body refinement was chewing on the next cycle is long gone. Bart David J. Schuller wrote: On Tue, 2007-06-19 at 21:09 -0700, P Hubbard wrote: Hi all, I am doing a survey on computer usage in crystallography. The questionnaire can be found on the following web page: http://www.bioscienceforum.com/survey.html ... I don't care for the way several questions are posed. Examples: 4.What would you consider is a reasonable price to pay for a computer graphics workstation designed with crystallography in mind? A) USD $2000-3000 B) USD $3000-5000 C) USD $5000+ What, no option for I'd be willing to assemble one from parts for under USD $2000? ... If there were a choice, would you prefer stereo graphics displayed using LCD-shuttered glasses or a head mounted display (often referred to as a Virtual Reality headset)? That does not cover all the choices currently available, let alone what I wish were available. == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521 ==
Re: [ccp4bb] Popularity of Stereo graphics in crystallography
Hello, Personally I don't really care if I have a stereo setup or not. I have not really used stereo to build in probably 3-4 years. The majority of the users of my facility on the other hand really want stereo. Usually in the initial and final stages of building and analysis. It is becoming harder to maintain stereo systems overall. You are tied in to a very limited number of graphics cards and as seen on the BB setup of the drivers/libraries can sometimes lead to the urge to pitch the systems out of highest window possible. It would be nice to have some sort of 'standard' 3D system for crystallography, but with the rapid change in computers and graphics hardware it probably is not a really viable possibility. We are currently looking to upgrade our systems and the biggest problems I have encountered in building a system is the on the graphics end. Just my 1/2 a cent worth. Len On Jun 20, 2007, at 9:45 AM, P Hubbard wrote: Hi, Thanks for the e-mail. The current results of the survey would certainly put you in the minority! Stereo graphics are not dead after all. I have used systems with and without stereo graphics. I personally prefer them, and think they are great for helping newbies refine, and for non-structural biologists and students to look at molecular architecture. It seems a lot of other people, for whatever reason, like them too. Paul From: Kevin Cowtan [EMAIL PROTECTED] Reply-To: Kevin Cowtan [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Survey on computer usage in crystallography Date: Wed, 20 Jun 2007 17:27:04 +0100 More likely the issue is that some of us do not find stereo to be necessary of beneficial for crystallographic model building. In which case, given the power of modern PCs and graphics cards, a basic off-the-shelf PC costing $1000/£500 is completely adaquate for typical structure solution and model building problems. I use coot a lot and I haven't even bothered installing the graphics drivers for my graphics card. All the 3D stuff gets gone in software, and most of the graphics hardware sits around doing nothing. If I needed the performance, it would be a 5 minute job to install the drivers, but I haven't needed it. Kevin P Hubbard wrote: I am sorry you are unhappy with the questions, David. As I am sure you know, I half-decent system with stereo graphics doesn't come cheap, and if you price things together to make something that performs well I doubt you'll get much change out of $2000. I am aware of other 3D systems (such as those listed on www.stereo3d.com). However, the price of peripherals like a 3D LCD monitor are prohibitively expensive (and the quality of the images is supposed to be poor). Do you know of a relatively inexpensive way of displaying 3D images on PCs? Any other comments would be greatly appreciated. Paul _ Get a preview of Live Earth, the hottest event this summer - only on MSN http://liveearth.msn.com?source=msntaglineliveearthhm Leonard M. Thomas Ph.D. Director, Macromolecular Crystallography Laboratory Howard Hughes Medical Institute California Institute of Technology Division of Biology 1200 E. California Blvd. MC 114-96 Pasadena, CA 91125 626-395-2453 [EMAIL PROTECTED] http://www.br.caltech.edu/cmclab
Re: [ccp4bb] Popularity of Stereo graphics in crystallography
I agree with Kevin. We have stereo on about half of our workstations, and no one has used them in about three years. We typically use O. Also, we have three large servers which are relatively fast. So the main purpose of a workstation is building, not computing here. That way you can easily work on multiple structures on a workstation at the same time, while you're refining and building them. We have a few people that use PC's and Coot as well. Bernie On Wed, June 20, 2007 11:45 am, P Hubbard wrote: Hi, Thanks for the e-mail. The current results of the survey would certainly put you in the minority! Stereo graphics are not dead after all. I have used systems with and without stereo graphics. I personally prefer them, and think they are great for helping newbies refine, and for non-structural biologists and students to look at molecular architecture. It seems a lot of other people, for whatever reason, like them too. Paul From: Kevin Cowtan [EMAIL PROTECTED] Reply-To: Kevin Cowtan [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Survey on computer usage in crystallography Date: Wed, 20 Jun 2007 17:27:04 +0100 More likely the issue is that some of us do not find stereo to be necessary of beneficial for crystallographic model building. In which case, given the power of modern PCs and graphics cards, a basic off-the-shelf PC costing $1000/£500 is completely adaquate for typical structure solution and model building problems. I use coot a lot and I haven't even bothered installing the graphics drivers for my graphics card. All the 3D stuff gets gone in software, and most of the graphics hardware sits around doing nothing. If I needed the performance, it would be a 5 minute job to install the drivers, but I haven't needed it. Kevin P Hubbard wrote: I am sorry you are unhappy with the questions, David. As I am sure you know, I half-decent system with stereo graphics doesn't come cheap, and if you price things together to make something that performs well I doubt you'll get much change out of $2000. I am aware of other 3D systems (such as those listed on www.stereo3d.com). However, the price of peripherals like a 3D LCD monitor are prohibitively expensive (and the quality of the images is supposed to be poor). Do you know of a relatively inexpensive way of displaying 3D images on PCs? Any other comments would be greatly appreciated. Paul _ Get a preview of Live Earth, the hottest event this summer - only on MSN http://liveearth.msn.com?source=msntaglineliveearthhm
Re: [ccp4bb] Survey on computer usage in crystallography
Hello All- Regarding the expense of stereo graphics, I use a Nuvision 60GX-NSR (non-stereo ready) driven by a GeForce FX5200 card to build in Xtalview and have no complaints regarding the stereo performance. I believe the Nuvision setup was around $600 USD and today the FX500 costs the staggering sum of $31.70 compared to the Quadro-based cards which seem to be running $900-$1200 and, I believe, are required for stereo in programs such as O and Coot. Since it works with Xtalview/Xfit, what is the reason that other graphics programs are unable to use the less expensive graphics cards? Thanks, Tim Fritz Timothy A. Fritz, Ph.D. NIH/NIDDK Section on Biological Chemistry 9000 Rockville Pike/MSC 8029 Bldg 50 Rm 4120 Bethesda, MD 20892 [EMAIL PROTECTED] -Original Message- From: P Hubbard [mailto:[EMAIL PROTECTED] Sent: Wednesday, June 20, 2007 12:25 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Survey on computer usage in crystallography Hi, If you build a system without stereo graphics, and use a standard monitor, I agree. In-fact it can be done for for under ~$1000. However, stereo systems are rather expensive (LCD stereo systems are VERY expensive). I was just curious to see how popular stereo graphics is for crystallographers. I personally think its a wonderful teaching tool which is currently under-utilized. Paul From: Bart Hazes [EMAIL PROTECTED] Reply-To: [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Survey on computer usage in crystallography Date: Wed, 20 Jun 2007 09:28:25 -0600 I don't expect the I'd be willing to assemble one from parts for under USD $2000 crowd will be large but you don't have to do the assembling to get all you need well under the $2000 mark. The times that you needed the fastest computer money could buy and still spent lots of time in the library reading while your rigid body refinement was chewing on the next cycle is long gone. Bart David J. Schuller wrote: On Tue, 2007-06-19 at 21:09 -0700, P Hubbard wrote: Hi all, I am doing a survey on computer usage in crystallography. The questionnaire can be found on the following web page: http://www.bioscienceforum.com/survey.html ... I don't care for the way several questions are posed. Examples: 4.What would you consider is a reasonable price to pay for a computer graphics workstation designed with crystallography in mind? A) USD $2000-3000 B) USD $3000-5000 C) USD $5000+ What, no option for I'd be willing to assemble one from parts for under USD $2000? ... If there were a choice, would you prefer stereo graphics displayed using LCD-shuttered glasses or a head mounted display (often referred to as a Virtual Reality headset)? That does not cover all the choices currently available, let alone what I wish were available. -- === === Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521 === === _ Like puzzles? Play free games earn great prizes. Play Clink now. http://club.live.com/clink.aspx?icid=clink_hotmailtextlink2
Re: [ccp4bb] Popularity of Stereo graphics in crystallography
I've found that many of my undergraduates like the stereo capability, although I personally rarely use it. So I guess it's worth the pain of getting the stereo hardware to play nice with the OS and specialized applications. We put the cheapest stereo-ready cards available at the time(Quadro 980XGL) in our Linux workstations, along with NuVision 60GX glasses, and none of the workstations cost more than $2000 to build. If you don't need stereo, clearly almost any reasonable PC will do. Even the lowliest of Nvidia or ATI graphics cards are more than ample for running O, Coot, Pymol, etc. Cheers, ___ Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED] -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Santarsiero, Bernard D. Sent: Wednesday, June 20, 2007 1:24 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Popularity of Stereo graphics in crystallography I agree with Kevin. We have stereo on about half of our workstations, and no one has used them in about three years. We typically use O. Also, we have three large servers which are relatively fast. So the main purpose of a workstation is building, not computing here. That way you can easily work on multiple structures on a workstation at the same time, while you're refining and building them. We have a few people that use PC's and Coot as well. Bernie On Wed, June 20, 2007 11:45 am, P Hubbard wrote: Hi, Thanks for the e-mail. The current results of the survey would certainly put you in the minority! Stereo graphics are not dead after all. I have used systems with and without stereo graphics. I personally prefer them, and think they are great for helping newbies refine, and for non-structural biologists and students to look at molecular architecture. It seems a lot of other people, for whatever reason, like them too. Paul From: Kevin Cowtan [EMAIL PROTECTED] Reply-To: Kevin Cowtan [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Survey on computer usage in crystallography Date: Wed, 20 Jun 2007 17:27:04 +0100 More likely the issue is that some of us do not find stereo to be necessary of beneficial for crystallographic model building. In which case, given the power of modern PCs and graphics cards, a basic off-the-shelf PC costing $1000/£500 is completely adaquate for typical structure solution and model building problems. I use coot a lot and I haven't even bothered installing the graphics drivers for my graphics card. All the 3D stuff gets gone in software, and most of the graphics hardware sits around doing nothing. If I needed the performance, it would be a 5 minute job to install the drivers, but I haven't needed it. Kevin P Hubbard wrote: I am sorry you are unhappy with the questions, David. As I am sure you know, I half-decent system with stereo graphics doesn't come cheap, and if you price things together to make something that performs well I doubt you'll get much change out of $2000. I am aware of other 3D systems (such as those listed on www.stereo3d.com). However, the price of peripherals like a 3D LCD monitor are prohibitively expensive (and the quality of the images is supposed to be poor). Do you know of a relatively inexpensive way of displaying 3D images on PCs? Any other comments would be greatly appreciated. Paul _ Get a preview of Live Earth, the hottest event this summer - only on MSN http://liveearth.msn.com?source=msntaglineliveearthhm
Re: [ccp4bb] The CRT is dead, long live the ?
Hi, I recently bought CRT monitors for the 3D workstations in our lab. I bought the Viewsonic G225fB and I can really recommend them. You find them here: http://www.viewsonic.com/products/desktopdisplays/crtmonitors/graphicseries/g225fb/ We bought them from CDW (http://www.cdw.ca in Canada or http://www.cdw.com in the USA) And concerning the 3D stereo discussion, I really do not want to miss stereo for model building. Cheers, Markus DeLano Scientific wrote: Note that is a parallel thread running simultaneously on ccp4bb. Indeed, the future of stereo 3D is uncertain to bleak. Lack of demand for and availability of high-refresh CRTs is a serious problem, and as of yet, I have not seen a replacement technology capable of matching the price-point and usability of CRT-based quadbuffer stereo 3D. One way to obtain CRTs nowadays is to buy used equipment through the online sites. In terms of models to look for, see http://pymol.sourceforge.net/stereo3d.html. Note however that high-refresh CRTs do have a finite useful life, so this workaround won't last forever. Cheers, Warren -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Esben Jannik Bjerrum Sent: Wednesday, June 20, 2007 9:18 AM To: [EMAIL PROTECTED] Subject: [PyMOL] The CRT is dead, long live the ? Hi Everyone I know it might be a bit off-topic, but 3D stereo is an issue which I think many pymol-users care about. We need to equip some workstations with stereo capable CRT monitors. We have long used quadro cards on linux with emitters and stereo glasses, using CRT's capable of 130-140 kHz, but now its not possible to find CRTs anymore. Do anyone know a company which still sells quality CRTs? What else do people do in those TFT and LCD ages? The autostereoscopic displays I've seen have just not been good enough, either visually or with support for quad-buffered stereo under linux. Best Regards Esben __ __ Expecting? Get great news right away with email Auto-Check. Try the Yahoo! Mail Beta. http://advision.webevents.yahoo.com/mailbeta/newmail_tools.html -- --- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ PyMOL-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/pymol-users - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ PyMOL-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/pymol-users -- Markus Meier, Ph.D. University of Manitoba Department of Chemistry 144 Dysart Road Winnipeg, MB, R3T 2N2, Canada Phone: +1 204 474 9731 Fax:+1 204 474 7608 E-mail: [EMAIL PROTECTED]
Re: [ccp4bb] mac pro configuration for crystallographic computing
Gretchen Meinke wrote: Hi-- I last saw some entries on the Mac Pro Xeon dated ~ April 2007. Were they purchased? Are you happy with them? Does ccp4, mosflm, hkl2000, coot run seamlessly on them? If so, what was the final cost and configuration (we would like stereo). How much memory should one get? Assuming Nuvision glasses for stereo, A CRT monitor (either NEC or Viewsonic) Based on previous readings, it still looks like the FX4500 is the only graphics card to support stereo for macs, correct? Thanks for any and all input. Gretchen Meinke I don't have one of those beast in my hands unfortunately. But I can verify that all except of HKL2000 (which I don't use, so I don't care/bother to check if there is an OS X version there) of the programs you mentioned run without any troubles. There's one more program I know that has not been ported to OS X and that is Grasp but there are other options to draw nice electrostatics. Regarding memory I would go for 1 GB per CPU and not less, otherwise you have a nice 4 core CPU but you are putting the brakes on if say 4 solve jobs run in parallel because they all need 500 MB or perhaps if you have larger problems to solve even larger than that. I'm running all my stuff from data processing to paper submission on my MacBook Pro 1.83 GHz with 2 GB of RAM. The only reason I leave my Mac is to sit in front of a Linux box running Coot in stereo. If you google for Stereo on Macintosh you will find a list of more than 1 graphics card which are stereo enabled on the Mac. the FX4500 is just the turbo card, there are also some from ATI which seem to work. But I'm not an expert in stereo graphics cards. Hope that helps. If you have further questions regarding Mac OS X don't hesitate to ask. I assume you are aware of the following web page: http://xanana.ucsc.edu/xtal/ Juergen -- Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002
Re: [ccp4bb] Survey on computer usage in crystallography
aol Me too. /aol I use coot quite a lot too. In my case though, I don't have hardware rendering because I don't know how to enable it and can't be bothered to find out. It's fine as it it - spending more than 1000 GBP on a computer to run CCP4 and Coot seems excessive (I don't use stereo in any of its forms). Paul. On Wed, Jun 20, 2007 at 05:27:04PM +0100, Kevin Cowtan wrote: More likely the issue is that some of us do not find stereo to be necessary of beneficial for crystallographic model building. In which case, given the power of modern PCs and graphics cards, a basic off-the-shelf PC costing $1000/?500 is completely adaquate for typical structure solution and model building problems. I use coot a lot and I haven't even bothered installing the graphics drivers for my graphics card. All the 3D stuff gets gone in software, and most of the graphics hardware sits around doing nothing. If I needed the performance, it would be a 5 minute job to install the drivers, but I haven't needed it. Kevin P Hubbard wrote: I am sorry you are unhappy with the questions, David. As I am sure you know, I half-decent system with stereo graphics doesn't come cheap, and if you price things together to make something that performs well I doubt you'll get much change out of $2000. I am aware of other 3D systems (such as those listed on www.stereo3d.com). However, the price of peripherals like a 3D LCD monitor are prohibitively expensive (and the quality of the images is supposed to be poor). Do you know of a relatively inexpensive way of displaying 3D images on PCs? Any other comments would be greatly appreciated. Paul
Re: [ccp4bb] mac pro configuration for crystallographic computing
On Thursday 21 June 2007 06:50, Juergen Bosch wrote: I don't have one of those beast in my hands unfortunately. But I can verify that all except of HKL2000 (which I don't use, so I don't care/bother to check if there is an OS X version there) of the programs you mentioned run without any troubles. There's one more program I know that has not been ported to OS X and that is Grasp but there are other options to draw nice electrostatics. Grasp2 runs nicely in a Windows XP installation within Virtualbox under Linux. Since Virtualbox is also available for Mac (even though only as beta1-Version) one might get it to run under MacOSX And I think one can run Windows within MacOSX anyhow? (even though in my opinion one might as well use the gimp to paint your protein red-blue and still have about the same information content, but that's only my very personal opinion). Tim -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia pgpFhY3yeObxL.pgp Description: PGP signature
