[ccp4bb] P-CUBE workshop on mammalian expression technologies in Oxford
On behalf of the P-cube management team: -Peer Dear All, Don't miss out on the P-CUBE workshop in Oxford in April 2011! Register today under www.p-cube.eu and learn everything about mammalian expression technologies. The registration deadline is March 19, 2011. See you in Oxford! P-CUBE Management Team *** P-CUBE Workshop on Mammalian Expression Technologies Oxford, 3-8 April 2011 The course is designed primarily for structural biologists who have prokaryotic expression experience and would like to use the mammalian expression system for more challenging targets. The goals of the course are to allow participants to have hands-on experience of mammalian cell culture, small and large scale transient gene expression including the use of automated systems, protein purification and crystallization. The course will be structured so as to interleave lectures and practical sessions. The participants will have the opportunity to closely interact with the tutors and to directly discuss their research projects with the experts in small workgroups. PARTICIPANTS Participants will be asked to submit their CV and a letter of motivation. The course will be limited to 12 participants from European structural biology laboratories. • There is no registration fee for the workshop. • Accommodation (5 nights max.) during the workshop will be covered. • Participants are responsible for their own travel costs. TOPICS: 1. Mammalian expression platform overview 2. Mammalian cell lines for protein expression and glycosylation control 3. Mammalian expression constructs design 4. Small scale expression screen with Western Blot 5. Large scale expression and protein purification 6. Protein crystallization 7. Protein structure case studies SPEAKERS: Radu Aricescu (Oxford University, UK), Yuguang Zhao (Oxford University, UK), Joop van den Heuvel (Helmholtz-Zentrum für Infektionsforschung, DE), Veronica Chang (Oxford University, UK), Ben Bishop (Oxford University, UK), Karl Harlos (Oxford University, UK), Tom Walter (Oxford University, UK), Christian Siebold (Oxford University, UK), Joerg Standfuss (Paul Scherrer Institut, CH)
[ccp4bb] Workshop Diffraction Data Collection Using Synchrotron Radiation
After the successful first two workshops on Diffraction Data Collection Using Synchrotron Radiation, which took place in 2007 and 2009, a third edition of the workshop will be held from July 07-09, 2011 at the Helmholtz Zentrum Berlin fuer Materialien und Energie (HZB) in Berlin. The workshop is sponsored by the German Society for Crystallography (DGK) and organised by the DGK Working Group 1 (Biological Structures) in cooperation with Dr. Manfred Weiss and Dr. Uwe Mueller. The workshop comprises a series of basic lectures on the topic and two extended practical sessions. It is aimed at PhD students in Biological Crystallography with little or no experience in diffraction data collection at a synchrotron. The practical sessions will take place at the MX beamlines located at the electron storage ring BESSY II. The workshop fee is 50 EUR for DGK-members and 60 EUR for non-members. This fee covers all conference material as well as board and lodging for two nights on the campus in Berlin-Adlershof. For more information please visit the web page http://www.helmholtz-berlin.de/bessy-mx-workshop/ Registration is now open. Since the number of students will have to be limited to 20 in order to ensure that the practical sessions run efficiently, we expect that the workshop will fill up quickly. Participants are also invited to present a poster. As last time, the best poster will receive an attractive prize. ## Manfred Weiss Uwe Mueller -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin für Materialien und Energie Macromolecular Crystallography (BESSY-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-30-806213149 Fax: +49-30-806214975 Web: http://www.helmholtz-berlin.de/bessy-mx Email: mswe...@helmholtz-berlin.de iHelmholtz-Zentrum Berlin für Materialien und Energie GmbH Hahn-Meitner-Platz 1, 14109 Berlin Vorsitzender des Aufsichtsrats: Prof. Dr. Dr. h.c. mult. Joachim Treusch Stellvertretende Vorsitzende: Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Prof. Dr. Dr. h.c. Wolfgang Eberhardt, Dr. Ulrich Breuer Sitz der Gesellschaft: Berlin Handelsregister: AG Charlottenburg, 89 HRB 5583/i
[ccp4bb] linux flavors
Hello all, Quick question on linux varieties. For years (and years) I have used fedora (after Ultrix of course). In fact, most of my computers are running FC7 (that long ago), it's very stable and works fine. However, since it is no longer supported, I'm toying with upgrading. I upgraded one machine to FC13. However, this nouveau driver thing is killing me, and getting my nvidia drivers installed is hopeless (I have followed every thread on this and I simply give up - it's not worth it). With a Zalman monitor it doesn't matter - nouveau works fine and my stereo is good - so I don't really care (or do I). The question is this - what flavors of linux out there are simplest to install - work instantly with various hardwares, and run stereo seamlessly (either Zalman stereo or hardware stereo with an emitter). For zalman anything works - which is why I'm going that way - but I still need hardware stereo on a few machines. So, for hardware, I need my nvidia drivers to install easily. I'm downloading ubuntu - is that a good choice? Can I run different flavors of linux with nfs and share drives in a local network (so one has fc7, one has fc13, and another has ubuntu)? Thanks Dave
Re: [ccp4bb] linux flavors
I switched from FC8 to Ubuntu 9.04 a few years ago. Ubuntu worked with all of my hardware and peripherals out of the box, even newish motherboards, and I had fewer issues with WINE compatibility for CrysalisPro a WIndows-based X-ray data processing program for our Oxford Diffraction instrument. Ubuntu 10.04 LTS is even better, and I'm scheduling an upgrade of my workstations this summer. Ubuntu will install NVidia drivers for you through a GUI setting with automatic updates, or you can do it manually, too. Each distro has its own specific headaches. For FC, it was SELinux and a few other random driver and package issues, for Ubuntu it's other things, but I'm finding Ubuntu less problematic at the moment for the stuff I want to run. Cheers. On 2/22/2011 10:16 AM, David Roberts wrote: Hello all, Quick question on linux varieties. For years (and years) I have used fedora (after Ultrix of course). In fact, most of my computers are running FC7 (that long ago), it's very stable and works fine. However, since it is no longer supported, I'm toying with upgrading. I upgraded one machine to FC13. However, this nouveau driver thing is killing me, and getting my nvidia drivers installed is hopeless (I have followed every thread on this and I simply give up - it's not worth it). With a Zalman monitor it doesn't matter - nouveau works fine and my stereo is good - so I don't really care (or do I). The question is this - what flavors of linux out there are simplest to install - work instantly with various hardwares, and run stereo seamlessly (either Zalman stereo or hardware stereo with an emitter). For zalman anything works - which is why I'm going that way - but I still need hardware stereo on a few machines. So, for hardware, I need my nvidia drivers to install easily. I'm downloading ubuntu - is that a good choice? Can I run different flavors of linux with nfs and share drives in a local network (so one has fc7, one has fc13, and another has ubuntu)? Thanks Dave -- 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: rrowl...@colgate.edu
Re: [ccp4bb] linux flavors
Installation of the proprietary nVidia driver is easier with Fedora 14; the hassles with removing the Nouveau driver have been greatly simplified. We use Fedora, although I certainly cannot claim that it has been problem free. It does seem better suited for centrally-managed systems, as compared with the most frequently mentioned alternative, Ubuntu, which is perhaps more suitable for a single owner-operator environment. On 02/22/11 10:16, David Roberts wrote: Hello all, Quick question on linux varieties. For years (and years) I have used fedora (after Ultrix of course). In fact, most of my computers are running FC7 (that long ago), it's very stable and works fine. However, since it is no longer supported, I'm toying with upgrading. I upgraded one machine to FC13. However, this nouveau driver thing is killing me, and getting my nvidia drivers installed is hopeless (I have followed every thread on this and I simply give up - it's not worth it). With a Zalman monitor it doesn't matter - nouveau works fine and my stereo is good - so I don't really care (or do I). The question is this - what flavors of linux out there are simplest to install - work instantly with various hardwares, and run stereo seamlessly (either Zalman stereo or hardware stereo with an emitter). For zalman anything works - which is why I'm going that way - but I still need hardware stereo on a few machines. So, for hardware, I need my nvidia drivers to install easily. I'm downloading ubuntu - is that a good choice? Can I run different flavors of linux with nfs and share drives in a local network (so one has fc7, one has fc13, and another has ubuntu)? Thanks Dave -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] linux flavors
The preferred method to get NVIDIA drivers for Fedora is to use the RPM Fusion repositories (http://rpmfusion.org/Howto/nVidia). Drivers installed this way will be automatically updated with the kernel as required. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of David Schuller Sent: February-22-11 9:30 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] linux flavors Installation of the proprietary nVidia driver is easier with Fedora 14; the hassles with removing the Nouveau driver have been greatly simplified. We use Fedora, although I certainly cannot claim that it has been problem free. It does seem better suited for centrally-managed systems, as compared with the most frequently mentioned alternative, Ubuntu, which is perhaps more suitable for a single owner-operator environment. On 02/22/11 10:16, David Roberts wrote: Hello all, Quick question on linux varieties. For years (and years) I have used fedora (after Ultrix of course). In fact, most of my computers are running FC7 (that long ago), it's very stable and works fine. However, since it is no longer supported, I'm toying with upgrading. I upgraded one machine to FC13. However, this nouveau driver thing is killing me, and getting my nvidia drivers installed is hopeless (I have followed every thread on this and I simply give up - it's not worth it). With a Zalman monitor it doesn't matter - nouveau works fine and my stereo is good - so I don't really care (or do I). The question is this - what flavors of linux out there are simplest to install - work instantly with various hardwares, and run stereo seamlessly (either Zalman stereo or hardware stereo with an emitter). For zalman anything works - which is why I'm going that way - but I still need hardware stereo on a few machines. So, for hardware, I need my nvidia drivers to install easily. I'm downloading ubuntu - is that a good choice? Can I run different flavors of linux with nfs and share drives in a local network (so one has fc7, one has fc13, and another has ubuntu)? Thanks Dave -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] linux flavors
Hi, Maybe CentOS 5 or Scientific Linux 5 is another option for you. Because you have experiences of RPM based distributions, I think you can install and maintain software easily. CentOS and Scientific Linux are based on Red Hat Enterprise Linux 5, so actually they are similarly as Fedora Core. You can install the NVIDIA driver from ATrpm (http://atrpms.net/) or http://ftp.scientificlinux.org/linux/scientific/55/i386/contrib/video/ BTW, I think CentOS and Scientific Linux are much more robust than UBUNTU. Xiaoguang On Tue, Feb 22, 2011 at 4:16 PM, David Roberts drobe...@depauw.edu wrote: Hello all, Quick question on linux varieties. For years (and years) I have used fedora (after Ultrix of course). In fact, most of my computers are running FC7 (that long ago), it's very stable and works fine. However, since it is no longer supported, I'm toying with upgrading. I upgraded one machine to FC13. However, this nouveau driver thing is killing me, and getting my nvidia drivers installed is hopeless (I have followed every thread on this and I simply give up - it's not worth it). With a Zalman monitor it doesn't matter - nouveau works fine and my stereo is good - so I don't really care (or do I). The question is this - what flavors of linux out there are simplest to install - work instantly with various hardwares, and run stereo seamlessly (either Zalman stereo or hardware stereo with an emitter). For zalman anything works - which is why I'm going that way - but I still need hardware stereo on a few machines. So, for hardware, I need my nvidia drivers to install easily. I'm downloading ubuntu - is that a good choice? Can I run different flavors of linux with nfs and share drives in a local network (so one has fc7, one has fc13, and another has ubuntu)? Thanks Dave -- Xiaoguang Xue, PhD student Utrecht University Crystal Structural Chemistry Padualaan 8. Room N807 3584 CH Utrecht The Netherlands Tel. +31-30-253-2383
Re: [ccp4bb] linux flavors
Dave, We have used CentOS for years and I am very happy with it. We also use NVIDIA hardware. CentOS does not work out of the box with NVIDIA, but NVIDIA has an installation package for their drivers on their web site that does work out of the box in combination with CentOS. That is, you run it once and the proper drivers get incorporated in the kernel and it works great. You only have to apply this special step when you upgrade your kernel. As far as stereo goes, we use the old-fashioned emitter-based hardware stereo and this works as long as you do as you are supposed to do (properly configure the X-window system). The thing I have most enjoyed is that CentOS is very, very reliable and stable. Hope this helps. Mark van der Woerd -Original Message- From: David Roberts drobe...@depauw.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Tue, Feb 22, 2011 8:16 am Subject: [ccp4bb] linux flavors Hello all, Quick question on linux varieties. For years (and years) I have used fedora (after Ultrix of course). In fact, most of my computers are running FC7 (that long ago), it's very stable and works fine. However, since it is no longer supported, I'm toying with upgrading. I upgraded one machine to FC13. However, this nouveau driver thing is killing me, and getting my nvidia drivers installed is hopeless (I have followed every thread on this and I simply give up - it's not worth it). With a Zalman monitor it doesn't matter - nouveau works fine and my stereo is good - so I don't really care (or do I). The question is this - what flavors of linux out there are simplest to install - work instantly with various hardwares, and run stereo seamlessly (either Zalman stereo or hardware stereo with an emitter). For zalman anything works - which is why I'm going that way - but I still need hardware stereo on a few machines. So, for hardware, I need my nvidia drivers to install easily. I'm downloading ubuntu - is that a good choice? Can I run different flavors of linux with nfs and share drives in a local network (so one has fc7, one has fc13, and another has ubuntu)? Thanks Dave
Re: [ccp4bb] Could someone can help me to explain why EDTA-2Na can formate salt crystals
What other cations are present? Any divalent cations like Mg++ or Ca++? The Ksp of magnesium phosphate is about 10^-24, so even if you have a very small amount present, say as a contaminant with citrate or EDTA, it will crystallize. On Feb 21, 2011, at 1:22 PM, Yibin Lin wrote: Dear all, I got a lot of salt crystals in reservior solution (well solution), which contains 0.1 M phosphate/citrate ph 4.2, PEG200 47%, EDTA-2Na 0-22mM. Reservior solution appears crystals from 12mM EDTA. Could someone help me to explain why? Thank you very much! Yibin William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] Could someone can help me to explain why EDTA-2Na can formate salt crystals
No, there are not any other cations, so I feel very strange. Everything brought from sigma. On Tue, Feb 22, 2011 at 8:58 PM, William Scott wgsc...@ucsc.edu wrote: What other cations are present? Any divalent cations like Mg++ or Ca++? The Ksp of magnesium phosphate is about 10^-24, so even if you have a very small amount present, say as a contaminant with citrate or EDTA, it will crystallize. On Feb 21, 2011, at 1:22 PM, Yibin Lin wrote: Dear all, I got a lot of salt crystals in reservior solution (well solution), which contains 0.1 M phosphate/citrate ph 4.2, PEG200 47%, EDTA-2Na 0-22mM. Reservior solution appears crystals from 12mM EDTA. Could someone help me to explain why? Thank you very much! Yibin William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] Could someone can help me to explain why EDTA-2Na can formate salt crystals
No, there are not any other cations, so I feel very strange. Everything brought from sigma. Nothing's strange. EDTA is very poorly soluble at pH 4.2 and would become even less soluble in the presence of 47% PEG. So it crystallizes. Dima On Tue, Feb 22, 2011 at 8:58 PM, William Scott mailto:wgsc...@ucsc.eduwgsc...@ucsc.edu wrote: What other cations are present? Any divalent cations like Mg++ or Ca++? The Ksp of magnesium phosphate is about 10^-24, so even if you have a very small amount present, say as a contaminant with citrate or EDTA, it will crystallize. On Feb 21, 2011, at 1:22 PM, Yibin Lin wrote: Dear all, I got a lot of salt crystals in reservior solution (well solution), which contains 0.1 M phosphate/citrate ph 4.2, PEG200 47%, EDTA-2Na 0-22mM. Reservior solution appears crystals from 12mM EDTA. Could someone help me to explain why? Thank you very much! Yibin William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/http://chemistry.ucsc.edu/~wgscott/
[ccp4bb] merge and scale high-res and low-res scans with SCALA
I have collected two sets of data, high-res and low-res, with the same crystal and integrated them separately with imosflm. Now I want to merge and scale the two MTZ files with Scala in ccp4i GUI. But I do not know how to input 2 MTZ files through the Scala input GUI window (under Data Reduction module, Scaleand Merge Intensities). Another question on reindexing: The space group for this data set output by imosflm is P21221, which is non-standard. How can I reindex this to P21212, using Sftools or other routine? Thanks for help. Huiying ___ Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: h...@uci.edu
Re: [ccp4bb] merge and scale high-res and low-res scans with SCALA
You can combine them together using the ccp4i task Find or Match Laue group which runs Pointless. This will also try to choose the Laue group and possibly the space group. If the space group is P21 2 21 (not chosen by mosflm which can only choose the Laue group), you can choose in Pointless to reindex to the reference setting P21 21 2 if you want, although the standard setting will be P21 2 21 if this gives you a b c. As far as I know, nearly all programs can use this setting (and those that can't should be changed so that they can). See the documentation for Pointless (and this BB passim) There does seem sometimes to be problems about merging strong and weak data sets (high low resolution) which I don't understand, but it's probably OK Phil On 22 Feb 2011, at 21:53, Huiying Li wrote: I have collected two sets of data, high-res and low-res, with the same crystal and integrated them separately with imosflm. Now I want to merge and scale the two MTZ files with Scala in ccp4i GUI. But I do not know how to input 2 MTZ files through the Scala input GUI window (under Data Reduction module, Scaleand Merge Intensities). Another question on reindexing: The space group for this data set output by imosflm is P21221, which is non-standard. How can I reindex this to P21212, using Sftools or other routine? Thanks for help. Huiying ___ Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: h...@uci.edu
Re: [ccp4bb] Could someone can help me to explain why EDTA-2Na can formate salt crystals
Your 0.1 M Phosphate/citrate can form crystal at high PEG. Deqian From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Yibin Lin [yyb...@gmail.com] Sent: Tuesday, February 22, 2011 2:24 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Could someone can help me to explain why EDTA-2Na can formate salt crystals No, there are not any other cations, so I feel very strange. Everything brought from sigma. On Tue, Feb 22, 2011 at 8:58 PM, William Scott wgsc...@ucsc.edumailto:wgsc...@ucsc.edu wrote: What other cations are present? Any divalent cations like Mg++ or Ca++? The Ksp of magnesium phosphate is about 10^-24, so even if you have a very small amount present, say as a contaminant with citrate or EDTA, it will crystallize. On Feb 21, 2011, at 1:22 PM, Yibin Lin wrote: Dear all, I got a lot of salt crystals in reservior solution (well solution), which contains 0.1 M phosphate/citrate ph 4.2, PEG200 47%, EDTA-2Na 0-22mM. Reservior solution appears crystals from 12mM EDTA. Could someone help me to explain why? Thank you very much! Yibin William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] linux flavors
David, I'm a big fan of SuSE. the nuveau problem exists, too, but blacklisting fixed it for me. For older hardware I love ultimate linux. The way I understand Zalman stereo it works with everything, given the program you use supports it. I'm sure you are aware of the problem with nVidia and emitters under Linux: you need the DIN pin on the card; USB emitters won't work. As far as I can tell, you also need the new nVidia DIN emitter, I had bad results with nuVision emitters and the new nVidia driver. Cheers, Jens linux.On Tue, 2011-02-22 at 10:16 -0500, David Roberts wrote: Hello all, Quick question on linux varieties. For years (and years) I have used fedora (after Ultrix of course). In fact, most of my computers are running FC7 (that long ago), it's very stable and works fine. However, since it is no longer supported, I'm toying with upgrading. I upgraded one machine to FC13. However, this nouveau driver thing is killing me, and getting my nvidia drivers installed is hopeless (I have followed every thread on this and I simply give up - it's not worth it). With a Zalman monitor it doesn't matter - nouveau works fine and my stereo is good - so I don't really care (or do I). The question is this - what flavors of linux out there are simplest to install - work instantly with various hardwares, and run stereo seamlessly (either Zalman stereo or hardware stereo with an emitter). For zalman anything works - which is why I'm going that way - but I still need hardware stereo on a few machines. So, for hardware, I need my nvidia drivers to install easily. I'm downloading ubuntu - is that a good choice? Can I run different flavors of linux with nfs and share drives in a local network (so one has fc7, one has fc13, and another has ubuntu)? Thanks Dave
Re: [ccp4bb] linux flavors
I vouch for Ubuntu too. FC always has the stability problem for me and I am too tired to find right drivers and compile the programs. I switched after FC8. Ubuntu's repositories seems to be much more reliable and it worked with every program that I am using, including 3D imaging (I am using Nvidia shuttle glass though). You can easily retrieve the Nvidia driver from the repository if Ubuntu hasn't already done it for you. But the bad side is that you are going lose your computation skill since you have less problem to handle. Nian Huang, Ph.D. UT Southwestern Medical Center On Tue, Feb 22, 2011 at 9:16 AM, David Roberts drobe...@depauw.edu wrote: Hello all, Quick question on linux varieties. For years (and years) I have used fedora (after Ultrix of course). In fact, most of my computers are running FC7 (that long ago), it's very stable and works fine. However, since it is no longer supported, I'm toying with upgrading. I upgraded one machine to FC13. However, this nouveau driver thing is killing me, and getting my nvidia drivers installed is hopeless (I have followed every thread on this and I simply give up - it's not worth it). With a Zalman monitor it doesn't matter - nouveau works fine and my stereo is good - so I don't really care (or do I). The question is this - what flavors of linux out there are simplest to install - work instantly with various hardwares, and run stereo seamlessly (either Zalman stereo or hardware stereo with an emitter). For zalman anything works - which is why I'm going that way - but I still need hardware stereo on a few machines. So, for hardware, I need my nvidia drivers to install easily. I'm downloading ubuntu - is that a good choice? Can I run different flavors of linux with nfs and share drives in a local network (so one has fc7, one has fc13, and another has ubuntu)? Thanks Dave
Re: [ccp4bb] linux flavors
On Tue, Feb 22, 2011 at 9:16 AM, David Roberts drobe...@depauw.edu wrote: Hello all, Quick question on linux varieties. For years (and years) I have used fedora (after Ultrix of course). In fact, most of my computers are running FC7 (that long ago), it's very stable and works fine. However, since it is no longer supported, I'm toying with upgrading. I upgraded one machine to FC13. However, this nouveau driver thing is killing me, and getting my nvidia drivers installed is hopeless (I have followed every thread on this and I simply give up - it's not worth it). With a Zalman monitor it doesn't matter - nouveau works fine and my stereo is good - so I don't really care (or do I). I've been running Mandriva for years on both my lab and home machines. I think its configuration out of the box is more suitable than anything of Redhat's for both lab and home use. Fedora is too bleeding edge and broken. RHEL is too crufty and locked down. Besides, the gnome desktop environment is too awful for words :-) Mandriva has automated installation and update support for nvidia's drivers; just make sure you that if you later upgrade the kernel manually you pick the nvidia version of the kernel package. I tried a Ubuntu live disk recently, but it didn't manage to load working wifi or graphics drivers for my laptop so for me it fails on the hardware detection criterion. Also that would mean choosing gnome (which I hate) or Kubuntu (which is widely rumoured to be an unsupported orphan although I have never tried it myself). I'm not entirely sure what I'd pick if Mandriva weren't available. Probably Suse or PLD. The PLD rpms are cross-compatible with Mandriva's; Suse not so much. cheers, Ethan The question is this - what flavors of linux out there are simplest to install - work instantly with various hardwares, and run stereo seamlessly (either Zalman stereo or hardware stereo with an emitter). For zalman anything works - which is why I'm going that way - but I still need hardware stereo on a few machines. So, for hardware, I need my nvidia drivers to install easily. I'm downloading ubuntu - is that a good choice? Can I run different flavors of linux with nfs and share drives in a local network (so one has fc7, one has fc13, and another has ubuntu)? I can't think of any reason you'd have nfs problems per se. Be aware that to make shared nfs work well you should set each user's UID to match on all the machines with nfs access. Thanks Dave
Re: [ccp4bb] linux flavors
I'm downloading ubuntu - is that a good choice? Can I run different flavors of linux with nfs and share drives in a local network (so one has fc7, one has fc13, and another has ubuntu)? Replied too fast and didn't finish your message. I have Ubuntu and most of other machines in NFS are running Redhat. So it shouldn't be a problem. Nian On Tue, Feb 22, 2011 at 9:16 AM, David Roberts drobe...@depauw.edu wrote: Hello all, Quick question on linux varieties. For years (and years) I have used fedora (after Ultrix of course). In fact, most of my computers are running FC7 (that long ago), it's very stable and works fine. However, since it is no longer supported, I'm toying with upgrading. I upgraded one machine to FC13. However, this nouveau driver thing is killing me, and getting my nvidia drivers installed is hopeless (I have followed every thread on this and I simply give up - it's not worth it). With a Zalman monitor it doesn't matter - nouveau works fine and my stereo is good - so I don't really care (or do I). The question is this - what flavors of linux out there are simplest to install - work instantly with various hardwares, and run stereo seamlessly (either Zalman stereo or hardware stereo with an emitter). For zalman anything works - which is why I'm going that way - but I still need hardware stereo on a few machines. So, for hardware, I need my nvidia drivers to install easily. I'm downloading ubuntu - is that a good choice? Can I run different flavors of linux with nfs and share drives in a local network (so one has fc7, one has fc13, and another has ubuntu)? Thanks Dave
Re: [ccp4bb] merge and scale high-res and low-res scans with SCALA
Hi, you first need to be sure that both datasets are indexed the same way (this depends on your spacegroup). During the processing step, you have to give each dataset different batch numbers (directly from imosflm) or you can rebatch them after processing (Data Reduction/Utilities/Sort-Modify-Combine MTZ task in ccp4i). Then you can sort (Data Reduction/Utilities/Sort-Modify-Combine MTZ task in ccp4i) your files in a single run in order to get a merged sorted file that you can feed to scala. hope this helps laurent Le 22/02/2011 22:53, Huiying Li a écrit : I have collected two sets of data, high-res and low-res, with the same crystal and integrated them separately with imosflm. Now I want to merge and scale the two MTZ files with Scala in ccp4i GUI. But I do not know how to input 2 MTZ files through the Scala input GUI window (under Data Reduction module, Scaleand Merge Intensities). Another question on reindexing: The space group for this data set output by imosflm is P21221, which is non-standard. How can I reindex this to P21212, using Sftools or other routine? Thanks for help. Huiying ___ Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: h...@uci.edu -- -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 Département BiologieStructurale et Biophysique 205 route de Narbonne 31077 TOULOUSE Cedex FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 --
