Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?
Hello, I'm one of the ARP/wARP developers. Sorry for the slow reply - this is down to time differences. I'll install RHEL6 and try the ARP/wARP install and then report back. This may take a day or so though. My suspicion, based on previous bug reports, is that this problem is related to the TCL installation. The UnpackTaskArchive subroutine is part of the CCP4 API: http://www.ccp4.ac.uk/ccp4bin/viewcvs/*checkout*/ccp4/ccp4i/help/programmers/progdocs/install_utils.html#UnpackTaskArchive We've found that the behaviour of this call is dependent on TCL versions and that we have problems installing on 64bit fink (OSX) because the version of TCL. When I download and install CCP4 onto Ubuntu or SUSE I get a big package (1GB) that contains CCP4 and a compatible version of TCL. The CCP4 installation then adds the following calls to my .bashrc: source /home/saul/ccp4-linux-6.2.0/setup-scripts/sh/ccp4.setup source /home/saul/ccp4-linux-6.2.0/setup-scripts/sh/ccp4-others.setup The ccp4-others.setup pulls in the correct TCL environment. Is your installation of CCP4 similar? Thanks for reporting this problem - it will hopefully improve future versions of ARP/wARP. Saul Hazledine On Jul 28, 2011, at 2:31 AM, Jonathan Kay wrote: Hi all, I have a RHEL 6 x86_64 machine I recently installed CCP4-6.2.0 onto; the install went through fine, but when I went to install the ARP/wARP GUI (via System Administration - Install/uninstall task), I received the following error in the shell window I started ccp4i from: UnpackTaskArchive: uncompress failed to create /tmp/user/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar ExamineTaskArchive: failed to unpack temporary copy of /usr/local/arp_warp_7.1/ARP_wARP_CCP4I6.tar.gz /tmp is not at all full and has plenty of inodes left. (running the install.sh from the arp_warp_7.1 directory doesn't install it either) I have searched around for some solutions, but haven't found anything really relevant. The odd thing I have another x86_64 machine running RHEL 5 that I can do the exact same install method and it works (and using the install.sh from arp_warp_7.1/ works too), so I wonder if something changed with RHEL6 that might be causing problems? Anyone have any suggestions? Thanks! Jonathan
Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?
Hello, My reply is in the text below: On Jul 28, 2011, at 6:00 AM, ccp4 wrote: A plea from West Australia too. I was sitting with someone yesterday who was trying to install it on a Mac , and finding it a nightmare. We're working on improving this. I believe the main issue is that CCP4 has become more user friendly and installs from a DMG, while the ARP/waRP 7.1 install is still showing its Unix command line roots. He finally got it set up as a local installation, whereupon it promtly failed. We use Macs a lot here with few problems (and various versions of CCP4) so my first suspicion is that this might be an install problem. The message said See refmac-last.log but that told us nothing, and indeed refmac seemed to have worked.. Would it be possible to send me the install.log that is created in the ARP/wARP install directory? Also, the refmac-last.log that will be created in the directory where ARP/wARP was working? Its probably best if the remaining communication is done by direct email. I'm sorry for the trouble that you are having. I hope we can fix the problem and prevent it happening to others in future. Saul Hazledine
Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?
Dear all, I had no problem with Arp/wARP, but I didn't reinstall. Assume ccp4 sits in /installation/directory/ccp4 and arp in /installation/directory/arp_warp_7.1. The new ccp4 doesn't recognize the existing arp because the task interface is not installed. I run ./install.sh in /installation/directory/arp_warp_7.1, and five seconds later, all is good. I hope this is of help for someone. Andreas On 28/07/2011 4:35, Ethan Merritt wrote: On Wednesday, 27 July 2011, you wrote: Hi Jonathan, seems to be a UW centered day today on the BB (Eric, Jan, you, me). Have the permissions changed ? I assume you are installing as root ? Wouldn't be surprised if Ethan replies soon :-) Sure. I hit the same problem trying to install Arp/wARP on Mandriva. The specific error message you quote comes because the install script fails to create the temp directory before trying to unpack into it. You can fix that by creating the directory by hand first. Unfortunately, that doesn't help very much. The next thing that happens is that the ccp4i installer complains that the tarball is not recognized as a ccp4i install tarball. I gave up at that point. Ethan 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 Jul 27, 2011, at 20:31, Jonathan Kayjp...@u.washington.edu wrote: Hi all, I have a RHEL 6 x86_64 machine I recently installed CCP4-6.2.0 onto; the install went through fine, but when I went to install the ARP/wARP GUI (via System Administration - Install/uninstall task), I received the following error in the shell window I started ccp4i from: UnpackTaskArchive: uncompress failed to create /tmp/user/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar ExamineTaskArchive: failed to unpack temporary copy of /usr/local/arp_warp_7.1/ARP_wARP_CCP4I6.tar.gz /tmp is not at all full and has plenty of inodes left. (running the install.sh from the arp_warp_7.1 directory doesn't install it either) I have searched around for some solutions, but haven't found anything really relevant. The odd thing I have another x86_64 machine running RHEL 5 that I can do the exact same install method and it works (and using the install.sh from arp_warp_7.1/ works too), so I wonder if something changed with RHEL6 that might be causing problems? Anyone have any suggestions? Thanks! Jonathan -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] Fab:antigen complex crystallization!!!
Hi Ivan, you might also want to find out what buffers your particular system likes. Jancarik et al. Optimum solubility (OS) screening: an efficient method to optimize buffer conditions for homogeneity and crystallization of proteins. Acta Crystallogr D Biol Crystallogr (2004) vol. 60 (Pt 9) pp. 1670-3 Andreas On 28/07/2011 4:40, xaravich ivan wrote: Hi everyone, I have been trying to crystallize Fab:antigen complex( 50kda:90kDa) complex and initially got needle clusters which after microseeding gave me single crystals but they are very small and I could not repeat the results. I have been using HEPES buffer at pH 6.8 to do the final SEC purification step of the complex before setting trays. I was wondering whether there are some other buffers (that one could suggest eg tris-hcl etc) which have given decent positive results when crystallizing Fab complexes.Though I have gone through individual papers (case by case) to get some idea, It would be great if anyone could direct me to a comprehensive literature towards studying the crystatllization conditions of Fab complexes. Equally, people who have considerable experience could suggest a list of must do steps for such problems which have routinely been practiced in their lab Also what is a good storage condition for the excess complex that you want to use later? I would really appreciate any suggestion,help, direction. Thanks ivan -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?
Hi, I recently found the problem that after finishing the installation of CCP4-6.2.0 on RHEL5, if the installation destination is not the default path (/usr/local/), the ccp4.setup for csh wouldn't take the customized TCLTK path correctly. No matter if I used sh or csh to install the CCP4 package. This would result in programs using wish failed to start (e.g., ccp4i) from csh. Perhaps it's also related to the issue in this thread. Wei-Chun We've found that the behaviour of this call is dependent on TCL versions and that we have problems installing on 64bit fink (OSX) because the version of TCL. When I download and install CCP4 onto Ubuntu or SUSE I get a big package (1GB) that contains CCP4 and a compatible version of TCL. The CCP4 installation then adds the following calls to my .bashrc: source /home/saul/ccp4-linux-6.2.0/setup-scripts/sh/ccp4.setup source /home/saul/ccp4-linux-6.2.0/setup-scripts/sh/ccp4-others.setup The ccp4-others.setup pulls in the correct TCL environment. Is your installation of CCP4 similar? Thanks for reporting this problem - it will hopefully improve future versions of ARP/wARP. Saul Hazledine
[ccp4bb] PostDoctoral Fellow in Synchrotron Crystallography
A postdoctoral position in synchrotron crystallography is available at EMBL Hamburg in the group of Thomas Schneider. If you would like to join an international team of nice and motivated people to work on interesting projects during the commissioning phase of our new beamlines on PETRA III, please have a look at: http://www.embl-hamburg.de/aboutus/jobs/index.php For informal enquiries, please contact me directly via email. For recent highlights, see http://www.embl-hamburg.de/facilities/petra/highlights --- Dr. Thomas R. Schneider Project Coordinator EMBL@PETRA3 EMBL c/o DESY Notkestr. 85 fax: 0049-(0)40-89902-149 22603 Hamburg phone: 0049-(0)40-89902-190 Germany email:thomas.schnei...@embl-hamburg.de --- EMBL@Petra3: http://www.embl-hamburg.de/services/petra/index.html ---
Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?
My two cents: I am installing arp/warp on my Mac since ages and it works ;-) The only thing you need to make sure is that you grab ownership of the /usr/local directory to you as a user, if you installed ccp4 from dmg. If you do this by eg sudo chown -R me.mygroup $CCP4 Then install.sh should work for arp/warp Package type installation for arp/warp is also possible technically, and it can be made available in the next release if it is agreed between developers that from now we will support system-specific installations and not only an all-in-one package as till now. A. Sent from my iPad On 28 Jul 2011, at 10:06, Saul Hazledine s.hazled...@embl-hamburg.de wrote: Hello, My reply is in the text below: On Jul 28, 2011, at 6:00 AM, ccp4 wrote: A plea from West Australia too. I was sitting with someone yesterday who was trying to install it on a Mac , and finding it a nightmare. We're working on improving this. I believe the main issue is that CCP4 has become more user friendly and installs from a DMG, while the ARP/waRP 7.1 install is still showing its Unix command line roots. He finally got it set up as a local installation, whereupon it promtly failed. We use Macs a lot here with few problems (and various versions of CCP4) so my first suspicion is that this might be an install problem. The message said See refmac-last.log but that told us nothing, and indeed refmac seemed to have worked.. Would it be possible to send me the install.log that is created in the ARP/wARP install directory? Also, the refmac-last.log that will be created in the directory where ARP/wARP was working? Its probably best if the remaining communication is done by direct email. I'm sorry for the trouble that you are having. I hope we can fix the problem and prevent it happening to others in future. Saul Hazledine
Re: [ccp4bb] Fab:antigen complex crystallization!!!
Hi Ivan Did you use microseeding with *random *solutions? If not see the following paper by Obmolova and Co about exactly this, microseeding with Fab complexes, http://journals.iucr.org/d/issues/2010/08/00/bw5361/bw5361.pdf For more subtle variations in using microseeding with complexes see http://pubs.acs.org/doi/abs/10.1021/cg2001442 Good luck Patrick On Thu, Jul 28, 2011 at 4:41 AM, xaravich ivan xaravich.i...@gmail.com wrote: Hi everyone, I have been trying to crystallize Fab:antigen complex( 50kda:90kDa) complex and initially got needle clusters which after microseeding gave me single crystals but they are very small and I could not repeat the results. I have been using HEPES buffer at pH 6.8 to do the final SEC purification step of the complex before setting trays. I was wondering whether there are some other buffers (that one could suggest eg tris-hcl etc) which have given decent positive results when crystallizing Fab complexes.Though I have gone through individual papers (case by case) to get some idea, It would be great if anyone could direct me to a comprehensive literature towards studying the crystatllization conditions of Fab complexes. Equally, people who have considerable experience could suggest a list of must do steps for such problems which have routinely been practiced in their lab Also what is a good storage condition for the excess complex that you want to use later? I would really appreciate any suggestion,help, direction. Thanks ivan -- patr...@douglas.co.ukDouglas Instruments Ltd. DouglasHouse, EastGarston, Hungerford, Berkshire, RG177HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
Re: [ccp4bb] Fab:antigen complex crystallization!!!
Hi Ivan, Here is another example of a method to crystallize antibody/antigene complexes. It uses a limited proteolysis step to generate crystals of poor quality, which are then used as seeds for an MMS screening... http://www.ncbi.nlm.nih.gov/pubmed/21536542 Good luck, Alex 2011/7/28 xaravich ivan xaravich.i...@gmail.com Hi everyone, I have been trying to crystallize Fab:antigen complex( 50kda:90kDa) complex and initially got needle clusters which after microseeding gave me single crystals but they are very small and I could not repeat the results. I have been using HEPES buffer at pH 6.8 to do the final SEC purification step of the complex before setting trays. I was wondering whether there are some other buffers (that one could suggest eg tris-hcl etc) which have given decent positive results when crystallizing Fab complexes.Though I have gone through individual papers (case by case) to get some idea, It would be great if anyone could direct me to a comprehensive literature towards studying the crystatllization conditions of Fab complexes. Equally, people who have considerable experience could suggest a list of must do steps for such problems which have routinely been practiced in their lab Also what is a good storage condition for the excess complex that you want to use later? I would really appreciate any suggestion,help, direction. Thanks ivan
Re: [ccp4bb] Fab:antigen complex crystallization!!!
On Thu, 2011-07-28 at 05:07 +0100, Sean Seaver wrote: Spoiler - Fabs like ammonium sulfate. Not really - in my hands the ammonium sulfate was one hit out of 7. While Ivan's question is about Fab complexes with protein antigen, I think it brings up a more general question of protein class-dependent crystallization bias. While some general trends exist for classes of biopolymers (e.g. MPD is number one precipitant for DNA; protein:DNA complexes tend to crystallize in PEG-based conditions), a general idea of assigning a preferred precipitant to a protein class is, imho, pointless. Fabs are a good example - one would think that with half of the protein more or less the same in all instances some general trends should exist. And perhaps they do, as this http://scripts.iucr.org/cgi-bin/paper?S0907444999016224 seems to suggest. But alas, Fab crystallization conditions, once you look into it, appear to be just as diverse as the same for proteins in general. Crystallization conditions may change radically upon point mutation, so why would one expect that a class of proteins sharing some 50% identity will show unusual love for PEG, ammonium sulfate, sodium malonate or any other miracle precipitant? Consider this. Thanks to great engineering at the Douglas Instruments, we can routinely set up ~1000 drops for a given protein. If one of them shows a crystalline shower, we celebrate. To me, the fact that we try wrong crystallization conditions 99.9% of the time, proves that any attempt to predict crystallization conditions beyond vague things like keep pH close to protein pI, sodium malonate is cool, PEG and ammonium sulfate are two most successful precipitants in history of protein crystallography, etc., is futile. Time wasted on looking into what is the most common precipitant for a particular class of proteins is better spent on setting up more trays. Cheers, Ed. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
[ccp4bb] research paper
Dear all, I would appreciate it if anyone could provide me with a copy of this research paper. Thank you very much. A. D'Arcy, F. Villarda, M.Marsh An automated microseed matrix-screening method for protein crystallizationActa Cryst D63 (2007), 550-554. John
Re: [ccp4bb] research paper
On Thu, 2011-07-28 at 14:35 +, Jung-Hoon Lee wrote: Acta Cryst D63 (2007), 550-554. I can't believe Cornell has no access to Acta D. -- Hurry up before we all come back to our senses! Julian, King of Lemurs
Re: [ccp4bb] research paper
The article is available for purchase for $40. Journals cannot survive without funding which can come from many sources - subscriptions, author payment to make the article open-access, etc. But asking someone to provide a 'free' copy without Acta's permission is tantamount to theft. Frances Bernstein = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Thu, 28 Jul 2011, Ed Pozharski wrote: On Thu, 2011-07-28 at 14:35 +, Jung-Hoon Lee wrote: Acta Cryst D63 (2007), 550-554. I can't believe Cornell has no access to Acta D. -- Hurry up before we all come back to our senses! Julian, King of Lemurs
[ccp4bb] Position available: X-ray FEL Crystallography
http://www.desy.de/v2/docs/1310651114-e.pdf DESY, Hamburg location, is seeking a Senior Scientist or Postdoc (m/f) to conduct research in the area of X-ray FEL Crystallography. DESY is one of the world's leading centres for the investigation of the structure of matter. DESY develops,runs and uses accelerators and detectors for photon science and particle physics. The Center for Free-Electron Laser Science (CFEL) is a jointly operated research cooperation between DESY, Max Planck Society and the University of Hamburg. DESY supports three CFEL divisions with leaders jointly appointed with the University of Hamburg. For a joint EU Project with the European XFEL, the Coherent Imaging Division offers the following position. The European X-Ray Free Electron Laser Facility (XFEL) is a multi-national non-profit company. It will make available X-rays of unique quality for studies in physics, chemistry, life sciences, materials research and others. Located in the Hamburg area, Germany, it will comprise scientific instruments for a wide range of experimental techniques. Construction of the European XFEL is underway, its commissioning is scheduled for 2015. The position * Join a team from CFEL and XFEL to design and implement specific algorithms for diffraction analysis and image processing * Development of methods and software to analyse the large amounts of data generated by XFELs * Develop new algorithms for parameterized profile fitting; integrate, optimise and test code on parallel computers and GPUs; and develop advanced user interfaces Requirements * Ph. D. in Physics * Good knowledge of crystallographic theory and programming background * Demonstrated experience with large datasets, broad collaborations, and programming on distributed systems * Experience in the theory of matter/X-ray interactions is desirable * Ability to work in teams and sound communication For further information please contact Henry Chapman, +4940 8998-4155, henry.chap...@cfel.de or Adrian Mancuso, +4940 8998-2512, adrian.manc...@xfel.eu The position is limited to 1.5 years for DESY and with prolongation to 1.5 years within the XFEL GmbH Salary and benefits are commensurate with those of public service organisations in Germany. DESY operates flexible work schemes. Handicapped persons will be given preference to other equally qualified applicants. DESY is an equal opportunity, affirmative action employer and encourages applications from women. There is an English-speaking Kindergarten on the DESY site. Please send your application quoting the reference code 119/2011, by post or e-mail to: Deutsches Elektronen-Synchrotron DESY Human Resources Department | Reference code: 119/2011 Notkestraße 85 | 22607 Hamburg | Germany Phone: +49 40 8998-1589 E-Mail: personal.abteil...@desy.de Deadline for applications: 31. August 2011 www.desy.de
Re: [ccp4bb] Fab:antigen complex crystallization!!!
Ed (and Ivan) Peter Sun and colleagues published two papers where they show that crystallization conditions for protein-protein complexes are strongly biased towards PEG-based rather than high-salt or organic-solvent-based conditions. This includes antibody-antigen complexes. http://www.ncbi.nlm.nih.gov/pubmed/16699187 http://scripts.iucr.org/cgi-bin/paper?do0016 I have heard anecdotally that the same is true of protein-peptide and protein-small molecule complexes, although I don't know of any systematic study. Can anyone shed light on this? I guess we can look in the Marseilles database Best wishes to all Patrick On Thu, Jul 28, 2011 at 2:32 PM, Ed Pozharski epozh...@umaryland.edu wrote: On Thu, 2011-07-28 at 05:07 +0100, Sean Seaver wrote: Spoiler - Fabs like ammonium sulfate. Not really - in my hands the ammonium sulfate was one hit out of 7. While Ivan's question is about Fab complexes with protein antigen, I think it brings up a more general question of protein class-dependent crystallization bias. While some general trends exist for classes of biopolymers (e.g. MPD is number one precipitant for DNA; protein:DNA complexes tend to crystallize in PEG-based conditions), a general idea of assigning a preferred precipitant to a protein class is, imho, pointless. Fabs are a good example - one would think that with half of the protein more or less the same in all instances some general trends should exist. And perhaps they do, as this http://scripts.iucr.org/cgi-bin/paper?S0907444999016224 seems to suggest. But alas, Fab crystallization conditions, once you look into it, appear to be just as diverse as the same for proteins in general. Crystallization conditions may change radically upon point mutation, so why would one expect that a class of proteins sharing some 50% identity will show unusual love for PEG, ammonium sulfate, sodium malonate or any other miracle precipitant? Consider this. Thanks to great engineering at the Douglas Instruments, we can routinely set up ~1000 drops for a given protein. If one of them shows a crystalline shower, we celebrate. To me, the fact that we try wrong crystallization conditions 99.9% of the time, proves that any attempt to predict crystallization conditions beyond vague things like keep pH close to protein pI, sodium malonate is cool, PEG and ammonium sulfate are two most successful precipitants in history of protein crystallography, etc., is futile. Time wasted on looking into what is the most common precipitant for a particular class of proteins is better spent on setting up more trays. Cheers, Ed. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs -- patr...@douglas.co.uk Douglas Instruments Ltd. DouglasHouse, EastGarston, Hungerford, Berkshire, RG177HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090 US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
Re: [ccp4bb] OSX Lion
On Jul 27, 2011, at 6:45 AM, Bosch, Juergen wrote: But Bill has updated his webpage http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Lion_upgrade_notes
[ccp4bb] Third issue of Computation Crystallography Newsletter - Volume 2, Number 2
Dear Colleagues, I am pleased to announce the publication of the third issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at nwmoria...@lbl.gov noting that there is a Word Template on the website to streamline production. Articles Improved target weight optimization in phenix.refine Mite-y lysozyme crystal and structure Short communications A lightweight, versatile framework for visualizing reciprocal-space data An extremely fast spotfinder for real-time beamline applications Hints for running phenix.mr_rosetta Cheers Nigel -- Nigel W. Moriarty, PhD Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : nwmoria...@lbl.gov Fax : 510-486-5909 Web : CCI.LBL.gov
Re: [ccp4bb] small lysozyme crystals?
Hi James, Not as many responses on lysozyme crystallization as I would have expected. Or may be people thought you were joking (were you?). Anyhow, higher concentrations of lyso gives smaller crystals but if you let them grow on their own, you may get few huge ones instead. What worked for me was following streak-seeding: An acupuncture needle of 5- to 10-μm diameter was loaded with microcrystals by plunging it into a large crystal. Excess seeds were washed off by passing the needle through the well solution. Then, the crystallization drops were seeded by streaking the needle through the drops. Twelve drops were seeded successively with a single needle-load to achieve gradual dilution of seeds, resulting in a varying number and size of crystals. Happy seeding! N. Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James Holton Sent: Tuesday, July 26, 2011 12:56 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] small lysozyme crystals? Does anyone out there have a protocol of growing HEWL crystals that are all 50-100 microns wide? I gave this project to a summer student recently, thinking it would be easy, but it is turning out to be more difficult than I thought. Keep getting sphereulites instead of small crystals. Yes, I know you can smash a large lysozyme crystal with a hammer, but that is not exactly what I was going for. What I was hoping for was a well-defined protocol for growing reference crystals that stay evenly illuminated in our x-ray beams as they rotate. The beam is 100 um wide. I'm sure someone has done this before? -James Holton MAD Scientist
[ccp4bb] Postdoc position available
SUMMARY DESCRIPTION: Structural biology of virus-host interactions The Kvansakul Laboratory is seeking a postdoctoral fellow to investigate the structural basis of inhibition of programmed cell death during viral infection (e.g. Kvansakul et al 2007 Mol. Cell 25: 933 942, Kvansakul et al Cell Death Differ 2008 15: 1564 1571, Kvansakul et al 2010 PLoS Pathogens Dec 23;6(12):e1001236). This position offers the opportunity to work in a highly collaborative and stimulating environment. The Kvansakul Lab is part of the recently established La Trobe Institute for Molecular Sciences (LIMS) at La Trobe University, Melbourne, Australia. LIMS is a multidisciplinary institute that brings together the Departments of Biochemistry, Chemistry, Genetics and Pharmacy. The successful candidate will have the opportunity to: 1.Express and purify viral and host proteins and their complexes 2.Investigate different host binding partners for viral effector proteins and their affinities 3. Crystallize and determine the macromolecular structure of these proteins and their complexes with ligands START DATE: The position is available immediately for 2 years in the first instance. REQUIREMENTS: Ph.D. in biochemistry, biophysics or structural biology. Experience with expression of recombinant proteins in a variety of hosts (bacteria, yeast, insects) and purification of proteins to a high degree of homogeneity are required. Prior experience with protein crystallization and structure determination is strongly desirable. Experience with biochemical assays and analyzing protein-protein interactions is also highly desirable. For more details see http://jobs.latrobe.edu.au/jobDetails.asp?sJobIDs=545338lWorkTypeID=lLoca tionID=lCategoryID=stp=AWsLanguage=en For informal enquiries please email m.kvansa...@latrobe.edu.au or come to the IUCr 2011 in Madrid. APPLICATION: Closing date is September 11th. Please apply online at http://jobs.latrobe.edu.au/jobDetails.asp?sJobIDs=545338lWorkTypeID=lLoca tionID=lCategoryID=stp=AWsLanguage=en
