[ccp4bb] Stereo TFT
Dear all, We had a demo of the ViewSonic® FuHzion(tm) VX2265wm http://www.viewsonic.com/products/desktop-monitors/lcd/x-series/vx2265wm-fuhzion-lcd.htm and Nvidia 3D Vision system yesterday. The stereo quality is equivalent/superior to our Stereographics/CRT setup. We have tested coot and pymol in the normal hardware stereo mode. There are several advantages besides space requirements and availability: integrated recharchable battery and you can work with a second non stereo TFT to expand the desktop as the glasses do not influence other TFTs (unlike Stereographics). On the ViewSonic TFT has a good image quality, however when looking at a plain coloured background a fine grid is visible. In my opinion it does not affect the normal crystallographic work and depending on you background settings you might not even notice it. As far as I understood the key requirements for linux are a quadro graphics card with 3-pin stereo connector and the VESA 3-pin stereo cable that is described in the manual from the Nvidia website but not included in the package in all countries. Best regards, Alexander Mit freundlichen Grüßen / Best regards / Cordialement Dr. Alexander Schiffer Sanofi-Aventis Deutschland GmbH RD CAS Structural Biology FFM Industriepark Hoechst Bldg. G877, Room 029 D-65926 Frankfurt am Main t: +49 69 305 24896 f: +49 69 305 80169 w:www.sanofi-aventis.de * Sanofi-Aventis Deutschland GmbH · Sitz der Gesellschaft: Frankfurt am Main · Handelsregister: Frankfurt am Main, Abt. B Nr. 40661 Vorsitzender des Aufsichtsrats: Hanspeter Spek - Geschäftsführer: Dr. Martin Siewert (Vorsitzender), Ulf Bialojahn, Dr. Matthias Braun, Peter Guenter, Prof. Dr. Dr. Werner Kramer, Dr. Klaus Menken, Dr. Heinz Riederer *
Re: [ccp4bb] Zalman LCD availability / suitability
Hello before you buy a Zalman monitor, check out their list of supported graphics cards carefully. We bought one for a trial and don't have a single computer with a suitable graphics card in our institute... Valerie On Jan 15, 2010, at 7:49 AM, Takaaki Fukami wrote: Hi, Francois We bought it 5 months ago from a supplier in Japan. (and it has been put back in a box under a desk.) Zalman has its own web site in Japan. Model name is the same. http://www.zalman.com/jpn/product/monitors/ZM-M220W.asp You can buy it from many shops through the web. Check the most famous comparison site in Japan, kakaku.com: http://kakaku.com/item/00854312463/ HTH Takaaki Fukami -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Francois Berenger Sent: Friday, January 15, 2010 1:31 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Zalman LCD availability Hello, By the way, does anyone got this LCD in Japan? My team is interested to know the model's exact reference as well as from where you ordered it. Thanks a lot, Francois.
[ccp4bb] Postdoctoral Position studying (epi)genome maintenance complexes in Basel, Switzerland.
A postdoctoral position in crystallography is available in the group of Dr. Nicolas Thomä at the Friedrich Miescher Institute (FMI) for Biomedical Research in Basel, Switzerland. The group studies macromolecular machines involved in genome maintenance (see Scrima et al, Cell 2008) and protein complexes serving as epigenetic regulators. Training in expression and purification of multi-subunit complexes from insect cells will be provided. Previous experience in crystallography and phasing techniques are essential. State of the art instrumentation for crystallography and high-throughput protein expression is provided in conjunction with the recently established FMI Protein Structure Facility. Salary and benefits will be competitive. We offer an initial 3 year contract, with the possibility of further extension. The FMI is an academic biomedical research centre with 300 members pursuing fundamental research in areas of Neurobiology, Cell Growth and Signaling, and Epigenetics. The institute offers a diverse and stimulating research environment, housing scientist from different nationalities and backgrounds. The working language of the institute is English. The FMI is located in the city of Basel, and has recently been voted as one of the best places to postdoc in the biomedical sciences in Europe (http://www.fmi.ch/downloads/news/FMi_ranks_first.pdf). Please send your CV and three letters of recommendation to thom...@fmi.ch at Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland (http://www.fmi.ch). Review of applications will begin immediately and continue until the position is filled
[ccp4bb] Post-doctoral opening in macromolecular crystallography, Athens Greece
Laboratory of Structural and Supramolecular Chemistry, Institute of Physical Chemistry, National Center for Scientific Research DEMOKRITOS ,Terma Patriarhou Gregoriou, Aghia Paraskevi 15310, Athens-Greece Opening for a position of Experienced Researcher (4-10 years) in production, crystallisation and X-ray crystallography of biological macromolecules TOPIC: TOPCRYST, an academia-industry (IAPP) FP7 Marie Curie project, will use Dual Polarimetric Interferometry, pioneered by Farfield Scientific Ltd., to probe crystallisation at its earliest, most crucial stages. Transfer of knowledge between academia and industry will tackle the problem of detecting crystal nucleation phenomena at the very earliest stages of crystallisation and holds a number of promises that will be investigated in its course. The post doctoral, experienced researcher (4-10 years after the bachelor's degree) will be mainly occupied with production and/or crystallisation of macromolecules (by the method to be developed and by conventional methods), as well as with determination of their molecular structures according to the needs. Additional activity: the structure-based drug design project, specifically on complexes of antibiotics synthesized in-situ with A-site ribosomal RNAs (http://lssc.chem.demokritos.gr/). TYPE OF APPOINTMENT-DURATION-STARTING DATE: Full-time contract - 24 months - Salary, that of an experienced researcher ( 55000/annum gross) according to the Marie Curie projects guidelines - Any time up to March 1st 2010. PROFILE-ELIGIBILITY Applicants should have a PhD degree, experience in production, crystallisation of proteins and X-ray crystallography and 4-10 years research experience at the time of hiring. They can be nationals of any country other than the country of the host organisation (Greece), preferably citizens of EU Member States or Associated Countries, as long as they have not resided or carried out their main activity in Greece for more than 12 months in the last 3 years. Candidates from countries outside the EU are also eligible. Greek citizens who have resided in third countries for at least 3 years in the 4 years prior to this hiring date are also eligible. HOW TO APPLY Applicants should forward electronically (a) their detailed CV (b) copies of published articles, (c) names, e-mails/phone numbers of two referees to: Dr. Emmanuel Saridakis or Dr Irene Mavridis esaridakatchem.demokritos.gr mavridiatchem.demokritos.gr Tel. +30-210-6503658 Tel. +30-210-6503793
Re: [ccp4bb] Zalman LCD availability / suitability
Hi Valerie, this is a known issue, exchange the cable with any other cable which you have in the lab. Some of the cables will only work with PC - I had one of them too. I ordered two Zalman's and one was *bad* but changing the cable from one to the other made it clear that something was wrong with the cable. Since then I ordered another two so in total we have four and all are fine. Are you using the DVI or the VGA cable - try both. Good luck, Jürgen On Jan 15, 2010, at 8:03 AM, Valerie Biou wrote: Dear Jurgen, we have many macs but the display says check cable when we plug it in. Neither of our macs has a graphics card listed on their web site. Valerie Le 15 Jan 2010 à 13:09, Jurgen Bosch a écrit : You are saying you don't have any Macs in your institute? We're running the Zalmans on Mac mini, MacPro or Macbookpro as secondary screen. Puzzeled Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Jan 15, 2010, at 3:08, Valerie Biou b...@lebs.cnrs-gif.fr wrote: Hello before you buy a Zalman monitor, check out their list of supported graphics cards carefully. We bought one for a trial and don't have a single computer with a suitable graphics card in our institute... Valerie On Jan 15, 2010, at 7:49 AM, Takaaki Fukami wrote: Hi, Francois We bought it 5 months ago from a supplier in Japan. (and it has been put back in a box under a desk.) Zalman has its own web site in Japan. Model name is the same. http://www.zalman.com/jpn/product/monitors/ZM-M220W.asp You can buy it from many shops through the web. Check the most famous comparison site in Japan, kakaku.com: http://kakaku.com/item/00854312463/ HTH Takaaki Fukami -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Francois Berenger Sent: Friday, January 15, 2010 1:31 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Zalman LCD availability Hello, By the way, does anyone got this LCD in Japan? My team is interested to know the model's exact reference as well as from where you ordered it. Thanks a lot, Francois. - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
Re: [ccp4bb] DSSP server
Hi Jane, the Whatif server lists the secondary structure according to DSSP. http://swift.cmbi.ru.nl/servers/html/index.html - Protein analysis - Secondary Structure, symmetry and accessibility Best regards, Daniel -- Daniel Schlieper email: daniel.schlie...@tuxomania.net Biochemie der Pflanzen phone: +49 211 8115232 Heinrich-Heine-Universitaet fax : +49 211 8113569 40225 Duesseldorf, Germany http://www.biologie.uni-duesseldorf.de
Re: [ccp4bb] 3D monitors
On Fri, 2010-01-15 at 09:11 +0100, alexander.schif...@sanofi-aventis.com wrote: We had a demo of the ViewSonic FuHzion VX2265wm and Nvidia 3D Vision system yesterday. The VX2265wm is a 1680x1050 monitor. Reviews from last year generally pegged it as inferior to the Samsung 2233RZ, another 1680x1050 monitor. Soon a crop of 23.5 1920x1080 120 Hz LCD monitors compatible with active glasses (nVidia 3D vision) will appear on the market. The ViewSonic V3D241wm-LED has been announced as available in April. The Acer GD235HZ and GD245HW were anounced a month ago for january availability, but I haven't seen any for sale yet. These are the only 1920x1080 monitors listed on nVidia's Alienware (Dell) OptX AW2310 - available now? LG W2363D - no date on availability, but since LG is manufacturing the panels which will be used in all of these products, I presume they won't be last to market. I am guessing other manufacturers will follow suit, but I haven't seen anything from Samsung yet. Cheers, -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[ccp4bb] Attached file formats (was Re: [ccp4bb] CCP4i fonts)
I just wanted to point out that since .gif is a compressed image format (and probably uses the same LZW compression as zip?) there is not much point in compressing a gif image. In this case the compressed image is actually larger than the gif. This may be partly because of the mysterious __MACOSX/ empty directory, which was created on unzipping the file, so must have been in .zip archive. -rw-r--r-- 1 berry strbiol 79842 2010-01-14 16:31 Pic.gif drwxrwxr-x 2 berry strbiol 4096 2010-01-14 16:32 __MACOSX/ drwxrwxrwt 32 root root16384 2010-01-15 04:05 ../ -rw--- 1 berry strbiol 96841 2010-01-15 09:21 Pic.gif.zip drwxr-xr-x 3 berry strbiol 4096 2010-01-15 09:21 ./ Also, my mail handler is suspicious of .zip, even when not password protected, so I had to specifically request the release of this. If not compressed, the .gif would have shown up inline with the message in my mail client. Ed Iain Kerr wrote: Dear all, I was wondering if anyone knows the reason for the difference in fonts in the attached (compressed) image. On the left is CCP4i on Mac Tiger and on the right CCP4i on Leopard (my current OS, same version of CCP4 in both). The fonts in the job list on the right are, comparably, pretty grim..at least to me. Both interfaces are set to use adobe helvetica and courier fonts (medium). So, I'm assuming the image on the right lacks one of the fonts or is unable to see it on my system. Any ideas on how to set the interface on the RHS to look like that on the left ? An old post suggested that the lack of the adobe-fonts package on Mac OSX may present a font problem with the GUI but I've been unable to find out how to install the package (if this is indeed the problem). Thanks in advance, Iain
Re: [ccp4bb] Stereo TFT
Alexander, What graphics card were you using in the demo system? From my experience, it seems only the high end card (FX3700 and up) can do this (having the 3-pin stereo connector). This is different from the situation for Windows where a low end card like FX380 works fine. The 3-pin stereo cable is part of the 3D Vision kit in our purchase. Yong Yong Wang, Ph.D. Macromolecular Crystallography Eli Lilly and Company, DC 0403 Lilly Corporate Center Indianapolis, IN 46285 Tel: (317) 655-9145 Fax: (317) 651-6333 E-mail: wang_y...@lilly.com alexander.schif...@sanofi-aventis.com Sent by: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK 01/15/2010 03:11 AM Please respond to alexander.schif...@sanofi-aventis.com To CCP4BB@JISCMAIL.AC.UK cc Subject [ccp4bb] Stereo TFT Dear all, We had a demo of the ViewSonic® FuHzion? VX2265wm and Nvidia 3D Vision system yesterday. The stereo quality is equivalent/superior to our Stereographics/CRT setup. We have tested coot and pymol in the normal hardware stereo mode. There are several advantages besides space requirements and availability: integrated recharchable battery and you can work with a second non stereo TFT to expand the desktop as the glasses do not influence other TFTs (unlike Stereographics). On the ViewSonic TFT has a good image quality, however when looking at a plain coloured background a fine grid is visible. In my opinion it does not affect the normal crystallographic work and depending on you background settings you might not even notice it. As far as I understood the key requirements for linux are a quadro graphics card with 3-pin stereo connector and the VESA 3-pin stereo cable that is described in the manual from the Nvidia website but not included in the package in all countries. Best regards, Alexander Mit freundlichen Grüßen / Best regards / Cordialement Dr. Alexander Schiffer Sanofi-Aventis Deutschland GmbH RD CAS Structural Biology FFM Industriepark Hoechst Bldg. G877, Room 029 D-65926 Frankfurt am Main t: +49 69 305 24896 f: +49 69 305 80169 w:www.sanofi-aventis.de * Sanofi-Aventis Deutschland GmbH · Sitz der Gesellschaft: Frankfurt am Main · Handelsregister: Frankfurt am Main, Abt. B Nr. 40661 Vorsitzender des Aufsichtsrats: Hanspeter Spek - Geschäftsführer: Dr. Martin Siewert (Vorsitzender), Ulf Bialojahn, Dr. Matthias Braun, Peter Guenter, Prof. Dr. Dr. Werner Kramer, Dr. Klaus Menken, Dr. Heinz Riederer *
Re: [ccp4bb] off topic: multiple structural sequence alignment
Dear all, Thanks a lot for all the replies and suggestions. I'm currently busy trying out a few of the options, and I'll try to post a brief summary after I've finished the analysis. Cheers, Ronnie On Jan 15, 2010, at 09:12, kuett...@bbz.uni-leipzig.de wrote: Dear Ronnie, have you tried the java program 'indonesia' which also contains a 3D-alignment/sequence comparison tool: http://xray.bmc.uu.se/dennis/ Best regards, Bart Ronnie Berntsson wrote: Dear all, A bit off the topic question perhaps. I am trying to find a program which can do multiple structural sequence alignments. What I would like is a program which can take as input PDB codes (or files), and which will output a multiple sequence alignment in FASTA format with the full sequences of the supplied proteins intact. Preferably said server/program should be able to handle at least 20 input pdbs at once. I've been looking around, but have so far failed to find a program which does this. If anyone knows of a program or server which could handle this, I would be very grateful. Cheers, Ronnie Berntsson
Re: [ccp4bb] Stereo TFT
Yong, We used a HP xw 6600 workstations, with NVIDA FX 3700, RedHat Linux 5.4, 64 Bit version. The driver was from nvidia, version 195.22 (it is a beta version) I was told that indeed in the US the cable is included but not in europe. The situation for Windows is completely different from linux. For Windows the stereo signal is transmitted to the emitter through the driver and the USB port. For Linux the stereo signal is created by the graphics card and directly transmitted through the 3-pin stereo cable to the emitter. Thats why you need the stereo output on the card, but I would asume that any quadro card with stereo output can be used with 3D Vision. Nvidia just seems to increase the price limit for cards with stereo output. Best regards, Alexander -Original Message- From: Yong Y Wang [mailto:wang_yon...@lilly.com] Sent: Friday, January 15, 2010 4:40 PM To: Schiffer, Alexander RD/DE Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Stereo TFT Alexander, What graphics card were you using in the demo system? From my experience, it seems only the high end card (FX3700 and up) can do this (having the 3-pin stereo connector). This is different from the situation for Windows where a low end card like FX380 works fine. The 3-pin stereo cable is part of the 3D Vision kit in our purchase. Yong Yong Wang, Ph.D. Macromolecular Crystallography Eli Lilly and Company, DC 0403 Lilly Corporate Center Indianapolis, IN 46285 Tel: (317) 655-9145 Fax: (317) 651-6333 E-mail: wang_y...@lilly.com alexander.schif...@sanofi-aventis.com Sent by: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK 01/15/2010 03:11 AM Please respond to alexander.schif...@sanofi-aventis.com To CCP4BB@JISCMAIL.AC.UK cc Subject [ccp4bb] Stereo TFT Dear all, We had a demo of the ViewSonic® FuHzion? VX2265wm and Nvidia 3D Vision system yesterday. The stereo quality is equivalent/superior to our Stereographics/CRT setup. We have tested coot and pymol in the normal hardware stereo mode. There are several advantages besides space requirements and availability: integrated recharchable battery and you can work with a second non stereo TFT to expand the desktop as the glasses do not influence other TFTs (unlike Stereographics). On the ViewSonic TFT has a good image quality, however when looking at a plain coloured background a fine grid is visible. In my opinion it does not affect the normal crystallographic work and depending on you background settings you might not even notice it. As far as I understood the key requirements for linux are a quadro graphics card with 3-pin stereo connector and the VESA 3-pin stereo cable that is described in the manual from the Nvidia website but not included in the package in all countries. Best regards, Alexander Mit freundlichen Grüßen / Best regards / Cordialement Dr. Alexander Schiffer Sanofi-Aventis Deutschland GmbH RD CAS Structural Biology FFM Industriepark Hoechst Bldg. G877, Room 029 D-65926 Frankfurt am Main t: +49 69 305 24896 f: +49 69 305 80169 w:www.sanofi-aventis.de * Sanofi-Aventis Deutschland GmbH · Sitz der Gesellschaft: Frankfurt am Main · Handelsregister: Frankfurt am Main, Abt. B Nr. 40661 Vorsitzender des Aufsichtsrats: Hanspeter Spek - Geschäftsführer: Dr. Martin Siewert (Vorsitzender), Ulf Bialojahn, Dr. Matthias Braun, Peter Guenter, Prof. Dr. Dr. Werner Kramer, Dr. Klaus Menken, Dr. Heinz Riederer *
Re: [ccp4bb] Stereo TFT
Alexander, I thought FX3700 would work. Good to hear confirmation from you. It would be nice a Linux driver is available to allow USB based stereo sync. No, not any Quadro card with stereo output will work. The old FX1400 does not work. Even the relatively new FX3500 does not work. The nVidia website has a list of cards that support 3D Vision. That should be consulted before purchasing even though the list was created for Windows. Regards, Yong alexander.schif...@sanofi-aventis.com 01/15/2010 11:04 AM To wang_yon...@lilly.com cc CCP4BB@JISCMAIL.AC.UK Subject RE: [ccp4bb] Stereo TFT Yong, We used a HP xw 6600 workstations, with NVIDA FX 3700, RedHat Linux 5.4, 64 Bit version. The driver was from nvidia, version 195.22 (it is a beta version) I was told that indeed in the US the cable is included but not in europe. The situation for Windows is completely different from linux. For Windows the stereo signal is transmitted to the emitter through the driver and the USB port. For Linux the stereo signal is created by the graphics card and directly transmitted through the 3-pin stereo cable to the emitter. Thats why you need the stereo output on the card, but I would asume that any quadro card with stereo output can be used with 3D Vision. Nvidia just seems to increase the price limit for cards with stereo output. Best regards, Alexander -Original Message- From: Yong Y Wang [mailto:wang_yon...@lilly.com] Sent: Friday, January 15, 2010 4:40 PM To: Schiffer, Alexander RD/DE Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Stereo TFT Alexander, What graphics card were you using in the demo system? From my experience, it seems only the high end card (FX3700 and up) can do this (having the 3-pin stereo connector). This is different from the situation for Windows where a low end card like FX380 works fine. The 3-pin stereo cable is part of the 3D Vision kit in our purchase. Yong Yong Wang, Ph.D. Macromolecular Crystallography Eli Lilly and Company, DC 0403 Lilly Corporate Center Indianapolis, IN 46285 Tel: (317) 655-9145 Fax: (317) 651-6333 E-mail: wang_y...@lilly.com alexander.schif...@sanofi-aventis.com Sent by: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK 01/15/2010 03:11 AM Please respond to alexander.schif...@sanofi-aventis.com To CCP4BB@JISCMAIL.AC.UK cc Subject [ccp4bb] Stereo TFT Dear all, We had a demo of the ViewSonic® FuHzion? VX2265wm and Nvidia 3D Vision system yesterday. The stereo quality is equivalent/superior to our Stereographics/CRT setup. We have tested coot and pymol in the normal hardware stereo mode. There are several advantages besides space requirements and availability: integrated recharchable battery and you can work with a second non stereo TFT to expand the desktop as the glasses do not influence other TFTs (unlike Stereographics). On the ViewSonic TFT has a good image quality, however when looking at a plain coloured background a fine grid is visible. In my opinion it does not affect the normal crystallographic work and depending on you background settings you might not even notice it. As far as I understood the key requirements for linux are a quadro graphics card with 3-pin stereo connector and the VESA 3-pin stereo cable that is described in the manual from the Nvidia website but not included in the package in all countries. Best regards, Alexander Mit freundlichen Grüßen / Best regards / Cordialement Dr. Alexander Schiffer Sanofi-Aventis Deutschland GmbH RD CAS Structural Biology FFM Industriepark Hoechst Bldg. G877, Room 029 D-65926 Frankfurt am Main t: +49 69 305 24896 f: +49 69 305 80169 w:www.sanofi-aventis.de * Sanofi-Aventis Deutschland GmbH · Sitz der Gesellschaft: Frankfurt am Main · Handelsregister: Frankfurt am Main, Abt. B Nr. 40661 Vorsitzender des Aufsichtsrats: Hanspeter Spek - Geschäftsführer: Dr. Martin Siewert (Vorsitzender), Ulf Bialojahn, Dr. Matthias Braun, Peter Guenter, Prof. Dr. Dr. Werner Kramer, Dr. Klaus Menken, Dr. Heinz Riederer *
Re: [ccp4bb] Picking a given bond in RASMOL
Hi Try this select MET1A.CA in the terminal and then display it with wire frame or sticks. Hope it helps. Abhik On Fri 15/01/10 16:19 , Rex Palmer rex.pal...@btinternet.com sent: I want to pick a bond or series of bonds in RASMOL and display with wireframe or sticks. Any ideas please? Rex Palmer
[ccp4bb] Protein Biochemist/Crystallographer Position available at Genentech in San Francisco
For more than 30 years, Genentech has been at the forefront of the biotechnology industry, using human genetic information to develop novel medicines for serious and life-threatening diseases. Today, Genentech is among the world's leading biotech companies, with multiple therapies on the market for cancer and other serious medical conditions. Please take this opportunity to learn about Genentech, where we believe that our employees are our most important asset. The following opportunity exists in our South San Francisco, CA, headquarters: Scientist - Protein Biochemist/Crystallographer Responsibilities: The position will play a key role in exploring the structure and functional properties of proteins of therapeutic interest and their interactions with ligands. He/she will purify, characterize, crystallize and determine the structure of proteins and protein-ligand complexes, with a focus on developing and implementing automated higher-throughput methods while contributing to small molecule discovery programs, basic research projects and participating in multi-disciplinary drug discovery teams. In this position, the candidate will work within a group that encompasses protein expression, purification, crystallography and NMR spectroscopy. He/she will collaborate with scientists throughout the Research organization. Requirements: A PhD in Structural Biology, Biophysics, Biochemistry or a related discipline is required, in addition to relevant postdoctoral experience. The candidate will show evidence of sustained productivity and independent contributions in science, as demonstrated by a strong publication record. He/she should be a technical expert in protein purification, characterization and crystallization with demonstrated expertise in handling challenging proteins for structural studies. Strong analytical, organizational and communication skills are essential, as well as the ability to work independently and in a collaborative team-oriented setting. Experience in solving X-ray crystal structures of proteins and protein complexes and familiarity with techniques such as ITC, surface plasmon resonance, ELISAs and/or immunoprecipitation to characterize proteins in support of structural biology is highly desired. Genentech is dedicated to fostering an environment that is inclusive and encourages diversity of thought, style, skills and perspective. To learn more about our current opportunities, please visit: http://careers.gene.com and reference Req. #130878. Please use Web - CCP4 when a source is requested. Genentech is an equal opportunity employer. -- Scanned by iCritical.
Re: [ccp4bb] Stereo TFT
On Fri, 2010-01-15 at 11:17 -0500, Yong Y Wang wrote: Alexander, I thought FX3700 would work. Good to hear confirmation from you. It would be nice a Linux driver is available to allow USB based stereo sync. No, not any Quadro card with stereo output will work. The old FX1400 does not work. Even the relatively new FX3500 does not work. The nVidia website has a list of cards that support 3D Vision. That should be consulted before purchasing even though the list was created for Windows. Here is nVidia's list http://www.nvidia.com/object/quadro_pro_graphics_boards.html This details which cards are supported for 3D vision and which have a 3 pin mini-DIN stereo connector. That page says cards without the connector can be used via USB, but I am not sure if that applies to Linux or just to Windows. FX1400 and FX3500 not working - are you just saying that because they do not appear on the list, or have you personally verified it? Those happen to be the cards I currently have. The FX3800 card can use a mini-DIN stereo plug on a separate PCI blank, which is sold separately. See for example: http://www.bhphotovideo.com/c/product/652465-REG/PNY_Technologies_900_50762__000_QUADRO_FX_3800_STEREO.html PNY Technologies Stereo Bracket for Quadro FX 3800 Someone posted a link for the release notes of the 195.30 beta driver last week. I can't find the link right now, but I believe it said that to be supported for 3D vision, the card has to be G82XL or newer. The Core designations for Quadro cards can be found at Wikipedia: http://en.wikipedia.org/wiki/Nvidia_Quadro -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Stereo TFT
I personally verified that FX1400 and FX3500 do not work with 3D Vision (stereo mode 10). I was using the beta 195.30 driver. Here is the link http://www.nvidia.com/object/linux_display_ia32_195.30.html Yong David J. Schuller dj...@cornell.edu Sent by: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK 01/15/2010 01:41 PM Please respond to schul...@cornell.edu To CCP4BB@JISCMAIL.AC.UK cc Subject Re: [ccp4bb] Stereo TFT On Fri, 2010-01-15 at 11:17 -0500, Yong Y Wang wrote: Alexander, I thought FX3700 would work. Good to hear confirmation from you. It would be nice a Linux driver is available to allow USB based stereo sync. No, not any Quadro card with stereo output will work. The old FX1400 does not work. Even the relatively new FX3500 does not work. The nVidia website has a list of cards that support 3D Vision. That should be consulted before purchasing even though the list was created for Windows. Here is nVidia's list http://www.nvidia.com/object/quadro_pro_graphics_boards.html This details which cards are supported for 3D vision and which have a 3 pin mini-DIN stereo connector. That page says cards without the connector can be used via USB, but I am not sure if that applies to Linux or just to Windows. FX1400 and FX3500 not working - are you just saying that because they do not appear on the list, or have you personally verified it? Those happen to be the cards I currently have. The FX3800 card can use a mini-DIN stereo plug on a separate PCI blank, which is sold separately. See for example: http://www.bhphotovideo.com/c/product/652465-REG/PNY_Technologies_900_50762__000_QUADRO_FX_3800_STEREO.html PNY Technologies Stereo Bracket for Quadro FX 3800 Someone posted a link for the release notes of the 195.30 beta driver last week. I can't find the link right now, but I believe it said that to be supported for 3D vision, the card has to be G82XL or newer. The Core designations for Quadro cards can be found at Wikipedia: http://en.wikipedia.org/wiki/Nvidia_Quadro -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Stereo TFT
Hi, I thought FX3700 would work. Good to hear confirmation from you. It would be nice a Linux driver is available to allow USB based stereo sync. Yeah, it won't happen anytime soon. This details which cards are supported for 3D vision and which have a 3 pin mini-DIN stereo connector. That page says cards without the connector can be used via USB, but I am not sure if that applies to Linux or just to Windows. Again, USB stereo only works with Windows. They did not put the USB stereo code into the Linux binary driver :( . FX1400 and FX3500 not working - are you just saying that because they do not appear on the list, or have you personally verified it? Those happen to be the cards I currently have. We have also verified that both the 1400 and 3500 do not work and also that the Quadro 370 works with Windows using the USB stereo but does not work with Linux. Thus, the cheapest way to go on Linux for hardware stereo is with the Quadro 3700. Someone posted a link for the release notes of the 195.30 beta driver last week. I can't find the link right now, but I believe it said that to be supported for 3D vision, the card has to be G82XL or newer. The Core designations for Quadro cards can be found at Wikipedia: http://en.wikipedia.org/wiki/Nvidia_Quadro It only works with a G8x based card or better (see stereo option 10 in the 195.22 driver readme ftp://download.nvidia.com/XFree86/Linux-x86/195.22/README/README.txt). We've been using 195.22 with Stereo 10 without problems, here's an xorg.conf for Centos5: http://forums.nvidia.com/index.php?showtopic=91072st=0p=968627#entry968627 HTH, Sabuj Pattanayek
[ccp4bb] Coot segmentation fault
I am running Coot prerelease dated Feb 2009 on a macbook, OS 10.6 (snow leopard). Prior to installing Reduce and Probe I had no problems, but I have been getting segmentation faults whenever I try to download a pdb and map from the EDS. Errors look something like: CCP4MTZfile: open_read - File missing or corrupted: coot-download/foo.mtz /usr/local/xtal/coot/bin/coot: line 7: 4056 Segmentation fault /usr/local/xtal/coot/bin/coot-real $@ The fault number changes with each run, but the ultimate result is that it aborts Coot and closes. I also cannot run rotamer picking on longer residues (K or R), as it terminates after a runtime_error. It looks like something to do with the torsion restraints of various terminal atoms: Can't fill atom_quad with indices [torsion-restraint: hh1 NE CZ NH1 HH12 O 20 2] line 7: Abort trap Interestingly, Coot as run from PHENIX works fine. Does anyone have any suggestions as to what it may be or should I try installing a newer version? Thanks, Regina Kettering University of Pittsburgh
Re: [ccp4bb] Coot segmentation fault
Regina Kettering wrote: I am running Coot prerelease dated Feb 2009 on a macbook, OS 10.6 (snow leopard). Prior to installing Reduce and Probe I had no problems, but I have been getting segmentation faults whenever I try to download a pdb and map from the EDS. Errors look something like: CCP4MTZfile: open_read - File missing or corrupted: coot-download/foo.mtz /usr/local/xtal/coot/bin/coot: line 7: 4056 Segmentation fault /usr/local/xtal/coot/bin/coot-real $@ The fault number changes with each run, but the ultimate result is that it aborts Coot and closes. I also cannot run rotamer picking on longer residues (K or R), as it terminates after a runtime_error. It looks like something to do with the torsion restraints of various terminal atoms: Can't fill atom_quad with indices [torsion-restraint: hh1 NE CZ NH1 HH12 O 20 2] line 7: Abort trap Does anyone have any suggestions as to what it may be or should I try installing a newer version? Dear Regina, These issues have been fixed in 0.6.1-pre. If you want to try a pre-release: http://www.biop.ox.ac.uk/coot/devel/build-info.html If you can wait a couple of weeks, the 0.6.1 should be out soon. I recently (2 days ago) installed fink (converted to unstable) and built coot from scratch - it took a while (226 packages) but works fine and I recommend it. Paul.
Re: [ccp4bb] Zalman LCD availability
Hi Francois, Zalman LCD (21) is available in Japan. We already bought 2 sets one month ago and both are working perfectly with mac pro, windows and Linux. For William: I think the best way to get extra glasses is to go, in the weekend (or late night show if you like), to the nearest movie theater with 3D projection. Personally I did this way, and I got two pairs of glasses just for ~3US$ extra/pair and of course enjoyed the 3D movie. Youssef Francois Berenger wrote: Hello, By the way, does anyone got this LCD in Japan? My team is interested to know the model's exact reference as well as from where you ordered it. Thanks a lot, Francois.
