Re: [ccp4bb] test data sets part II...
I have put some data sets, and data reductions including crystallographic calculations, into XDSwiki: check out http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Quality_Control This is work in progress, so expect additions/changes! And the best is: anyone may contribute ... HTH, Kay smime.p7s Description: S/MIME Cryptographic Signature
Re: [ccp4bb] test data sets part II...
EMBL-Hamburg and BESSY have put a number of interesting data-sets including tutorial materials for data processing and phase determination made available recently. You can download the data from both locations: http://www.mx.bessy.de/xray_tutorial.shtml http://webapps.embl-hamburg.de/Xray_Tutorial/ Uwe -- ___ Dr. Uwe Mueller AG Makromolekulare Kristallographie BESSY GmbH Albert-Einstein-Straße 15 D-12489 Berlin Phone: +49-(0)30-6392 4974 Fax : +49-(0)30-6392 4975 email: [EMAIL PROTECTED] url : http://www.mx.bessy.de
[ccp4bb] postdoctoral position at the University of Bristol
Dear All, A one year postdoctoral position is available immediately in the lab of Dr. Jim Spencer in the Department of Cellular and Molecular Medicine at the University of Bristol, U.K. The successful applicant will work to biochemically characterise and crystallise a novel metalloprotein involved in antibiotic resistance in Staphylococci. The ideal candidate will have experience in recombinant protein expression and purification, characterisation of metalloproteins (particularly Fe-S proteins) protein crystallisation and structure determination using anomalous scattering methods. However, candidates with a strong background in some of these areas are encouraged to apply. Further details are available online at: http://www.bris.ac.uk/boris/jobs/ads?ID=74286 or feel free to contact me directly. After September 26th (Friday) please send CVs directly to me. Best wishes Jim -- Dr. James Spencer, Lecturer Department of Cellular and Molecular Medicine University of Bristol School of Medical Sciences University Walk Bristol BS8 1TD [EMAIL PROTECTED] http://www.bristol.ac.uk/cellmolmed/staff/spencer.html -- Tel: (44) (0) 117 331 2084 Fax: (44) (0) 117 331 2091
[ccp4bb] Which Linux do you use? Results
Dear BB, Many thanks for the ~100 responses I received - I appreciate the time you have all taken to respond. Here are the results so far, which I will assume represent a statistically valid sample. To be clear though - what follows is not a recommendation for what systems are good! I have also not broken this down into exact numbers, since I was working from fuzzy input. Top rank: Ubuntu 8.x - this was clearly popular with people who maintain their own machines Rank 2: RHEL4 / Centos 4 (~ same thing) and RHEL 5 / Centos 5 (ditto) - combined approximately same as Ubuntu - very popular with large labs, corporate environments. Rank 3: SuSE 10.3 / Fedora 9 / Fedora 8 Rank 4: SuSE 10.1, 11 / Mandriva Last rank: Debian / Fedora = 6 / SuSE 10 / Ubuntu = 7 Ubuntu 8.x + RHEL / Centos 4 + 5 was significantly over half of the responses. SuSE systems may have come out higher if it wasn't for the large numbers of different versions being used out there - this diluted the results a little. All fedora versions and all SuSE versions would give Ubuntu 8.x a run for it's money, but that just indicates how popular ubuntu is. Make of this what you will - it has certainly been an eye opener for me. Best wishes, Graeme
Re: [ccp4bb] recipees for prep of test derivatives
In our protein crystallography course, we succesfully used S-SAD phasing for proteinase K crystals diffracting to 1.58 Å (which is 'low' for these crystals) at our home source. I would highly recommend using proteinase K for heavy atom derivative demonstration purposes as it seems much easier to produce these for proteinase K than for lysozyme. In our hands quick soaks (i.e. a few minutes) in 50 mM stocks of e.g. EuCl3 or SmCl3 (Eu works great because of the strong anomalous signal at the Cu Ka edge) are fine. Our course is based on course material from UCLA: http://www.doe-mbi.ucla.edu/~sawaya/m230d/m230d.html If you are interested, you are welcome to contact me ([EMAIL PROTECTED]) for our teaching material. Cheers, Thomas -- Thomas Boesen Associate Professor, PhD Centre for Structural Biology Department of Molecular Biology University of Aarhus Gustav Wieds Vej 10C 8000 Århus C Phone: +45 8942 5257 (lab: +45 8942 5030) E-mail: [EMAIL PROTECTED] web: http://www.bioxray.au.dk/index_uk.php what is it that you want to demonstrate? If it is just for structure solution, would S-SAD phasing be an option? That way all you need is a crystal, probably diffracting to better than, say, 2A. And a little bit of multiplicity. I assume this is feasible for Lysozyme whereas I don't know the diffraction qualities of proteinase K crystals. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Tue, 23 Sep 2008, Tommi Kajander wrote: Hi, Could anyone give a more or less exact recipee for preparing a derivate for lysozyme or proteinase K? like what used, concentration and soak time. we'd need some data sets for a lab course only thing that really worked so far was lysozyem KI SIRAS (which however doesnt seem to be good enough for demonstration purposes, so we need more) Thanks very much! best, Tommi Tommi Kajander, Ph.D. Structural Biology and Biophysics Institute of Biotechnology University of Helsinki Viikinkaari 1 (P.O. Box 65) 00014 Helsinki Finland p. +358-9-19158903 [EMAIL PROTECTED] This message was sent using IMP, the Internet Messaging Program.
Re: [ccp4bb] PyMol bulletin Board
Greetings Fred, Links to both the PyMOL bulletin board and source code can be found on the pymol home page: http://pymol.org Seek Mailing List and Source Code. Please do note that Subversion is the sole means for accessing current PyMOL source code, given that our main intent in releasing source code is to enable open-source development, and given that collaborative open-source software development requires use of a revision control system. To pull the latest release (1.1): svn co https://pymol.svn.sourceforge.net/svnroot/pymol/branches/b11/pymol pymol-1.1 To pull the development code (1.2b): svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol-1.2b Cheers, Warren -Original Message- From: CCP4 bulletin board on behalf of Vellieux Frederic Sent: Wed 9/24/2008 6:00 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] PyMol bulletin Board Dear All, I am looking for the web site where to register for the PyMol bulletin board (if there is one). A search with google did not return that. The aim of this is for a colleague of mine who does not wish to become a subscriber to obtain the source files for PyMol (I think they are located on sourceforge.net), apparently this colleague went to sourceforge but failed to locate where the source file(s) reside. Any help would be appreciated. Regards, Fred.
[ccp4bb] Post-doctoral position available with Phaser team
We are looking to expand the team developing our program Phaser, for use within both the CCP4 and Phenix packages. Our goals include expanding the functionality to new phasing experiments (in addition to the options for molecular replacement and SAD that exist in the current version), and enhancing the automation of Phaser runs. The ideal applicant would be someone with experience solving macromolecular crystal structures and programming in both C++ and Python. However, if you only have experience in one of those areas, but a strong desire to expand your skills, then you might be the right person. If you're interested, please look at the formal advertisement (http://www.admin.cam.ac.uk/offices/hr/jobs/vacancies.cgi?job=4017), and submit an application as described there. I'm also happy to answer any informal enquiries. The position is funded by a grant from the Wellcome Trust, which extends to May 2013. Please note that the closing date for applications is 2 October 2008. Regards, Randy Read
[ccp4bb] Off topic: Art Robbins Hydra +1 original software?
We have an old Hydra +1 that I'm trying to get running to set up crystallization plates. The unit has an automated wash station and a plate positioner. The original laptop that used to run it has long since disappeared, along with any software. Although Art Robbins no longer actively supports the Hydra, their lead Engineer Dave Wright sent me what looked like the files I needed. Unfortunately, they're for a software upgrade and need to be installed over the original software. Does anyone have the Hydra+1 installation disks, or know of anyone who might? Thanks for your help, Jeff P.S. If you're concerned about sharing the software you can contact Dave Wright at Robbins: [EMAIL PROTECTED] Jeff Christensen Research Scientist deCODE biostructures 7869 NE Day Rd. W. Bainbridge Island, WA 98110 phone (206) 780-8933 fax (206) 780-8547 [EMAIL PROTECTED]
Re: [ccp4bb] Off topic: Art Robbins Hydra +1 original software?
Dave Wright of Robbins Instruments has just gently reminded me that: 1) It's very bad form to include someones email address in a post without their consent, and 2)The software he was kind enough to send me was for the Hydra, not the Hydra +1. I apologize for any misunderstanding. Jeff Christensen
