[ccp4bb] Postdoctoral position, Karolinska Institute, Stockholm, Sweden
*Postdoctoral position in structural biology of protein complexes in nerve development and disease* Dept. of Medical Biochemistry and Biophysics, Karolinska Institute A postdoctoral position is available immediately in the Molecular Structural Biology group at the Karolinska Institute in Stockholm (http://phillips.mbb.ki.se/ https://udcf.gla.ac.uk/horde/services/go.php?url=http%3A%2F%2Fphillips.mbb.ki.se%2F). The position is initially available for 1 year with the possibility of extension to three years. We are seeking a motivated scientist to join a new research project on structural and functional studies of protein-protein complexes involved in nerve cell development and disease. The project focuses on the characterization of the complexes and their function in the cell. The experiments will involve a broad range of techniques, such as protein expression/purification, site-directed mutagenesis, enzyme kinetics, and various methods of structure determination (X-ray crystallography, EM, SAXS). Applicants should have a background in biochemistry or molecular biology, and possess experience with cloning, protein expression/purification techniques. Biochemists and molecular biologists who would like to learn structural biology are encouraged to apply. Experience in mammalian cell culturing is a plus. Interested candidates should send a cover letter including CV and names and e-mail addresses of three references to: Dr. Bernhard Lohkamp Div. of Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics Karolinska Institutet SE-17177 Stockholm Sweden e-mail: Bernhard.Lohkamp(at)ki.se, phone: +46 8 5248 7673, fax: +46 8 32 7626
[ccp4bb] Postdoctoral Research Scientist, Cambridge, UK.
Job Title Postdoctoral Research Scientist Description Vernalis is a specialist bio-pharmaceutical company with a marketed product, frovatriptan, several product candidates in clinical trials and a research capability based on structure-based drug discovery technologies. We are seeking a macromolecular crystallographer with a keen interest in fragment-based drug design and high-throughput crystallography. You'll be part of a multi-disciplinary team that includes macro-molecular biologists, NMR spectroscopists, medicinal chemists and computational chemists. Your knowledge of crystallization, data collection, data analysis, structure solution and structure validation will play a pivotal role in the success of our drug-design efforts. Find out more about us by visiting www.vernalis.com http://www.vernalis.com/ . Duties * Participation in all in-house research programmes, including presentation and publication of the results; * Rapid data collection and structure solution of protein-ligand complex structures; * Assist in crystallisation trials; * Assist in the development of new technologies within the company. Education / Work Experience * PhD in relevant discipline; * Demonstratable experience or knowledge of macromolecular crystallography; * Experience with Windows/Linux/Unix and appropriate crystallographic software suites; * Experience of data collection at synchrotrons; * Experience or knowledge in molecular biology and protein crystallization; * Experimental research experience; * Must be available to travel occasionally within the UK and abroad, including overnight stay. Personal Qualities * Good problem solving; * Good interpersonal, communication and presentational skills; * Good organisational and planning skills; * Ability to interact effectively with staff at all levels; * Ability to work as part of a multi-disciplinary team; * Self motivation. Post details Full time, initial one year fixed term contract (maternity cover). Start date August 2009 Salary information Negotiable, depending upon skills, qualifications and previous experience. Location Granta Park, Cambridge, UK. Application deadline Friday 8th May 2009 Application details Applications should include a covering letter describing relevant research experience to date, a CV, and the names and addresses of two referees. These should be sent by email to h...@vernalis.com. Any informal enquiries can be sent via email to l.ba...@vernalis.com. __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies Oakdene Court 613 Reading Road Winnersh, Berkshire RG41 5UA. Tel: +44 118 977 3133 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the Company address and registration details link at the bottom of the page.. __
Re: [ccp4bb] soaking with Samarium chloride
Hi Amit, I wouldn't worry about acetate depleting the Sm3+. I have tried to make a derivative of a kinase by soaking ions of lanthanoid series but in the presence of phosphate buffer and ADP. In this case, lanthanoid ions are *known* to precipitate with phosphate (and phosphoryl moiety). I simply spun down the precipitate and took the clear but colorful supernatant for soaking. A successful ADP-2Ho derivative for phasing is reported in Acta D 2007 63:493-9. (Failed cases were rejected by JFCE on April 2.) Shao-Yang Quoting amit sharma 3112a...@gmail.com: Dear All, I have a crystal growing in the presence of 0.1M Sodium Acetate pH 5.0, 10% PEG4000, 7.5% Dioxane and 10% Ethylene Glycol. I wanted to know if it would be alright to use Samarium chloride for derivatization. I am worried about the leaching of samarium by acetate. Also, what soak times can I use and what conc. of Samarium chloride? My protein is 10 kDa , has no cysteines/methionines and pI for the molecule is 4.6. Also, could somebody suggest what other heavy atom soaks could be performed in this case? Any suggestions would be appreciated. Many thanks in advance -- Amit Sharma
[ccp4bb] Recompiling getax for large maps
Dear All, I am trying to use getax for finding NCS in a map radius of 100A and get the error 'ERROR: more than MAXPTS points in sphere - please recompile'. I am running CCP4 6.0.2 on my intel macbook pro. I am not sure which parameter to change in the getax.f file and how to exactly recompile getax with the existing CCP4 installation. Any advice would be really appreciated. Thanks, Vidya
Re: [ccp4bb] Recompiling getax for large maps
Dear Vidya, On Tue, Apr 07, 2009 at 02:20:42PM +0100, Vidya Chandran wrote: Dear All, I am trying to use getax for finding NCS in a map radius of 100A and get the error 'ERROR: more than MAXPTS points in sphere - please recompile'. I guess you're using a sphere of radius 100A for searching for the NCS? The error you're getting isn't directly related to the map/grid size, but to the generated simple description for the region following your NCS. Some information: 1. you usually don't need to use a map calculated at high resolution - most of the time something at 6A is good enough. This already reduces the grid size of your map and has a direct effect on the number of points used for that simple description 2. what are you trying to search for? Have you got some idea what the multimer should look like? Is it a 2-fold, 3-fold etc (i.e. Cn symmetry) or a more complex multimer (Dn symmetry)? I would first start looking for the low-order symmetry axes (2-fold, 3-fold). 3. what shape do you expect the multimer to be? How large do you expect the volume to be that follows the n-fold symmetry? With a radius (not diameter) of 100A this would be a VERY large dimer. But maybe you have something really big that that looks more like a cage (like in the FAS case)? Then you would have a 'shell' of protein with a large cavity in the middle: in which case you could use something like SPHERE 100.0 80.0 to create such a shell (outer and inner radius given). This will also reduce the number of points needed to describe the multimer. 4. instead of a large shell/sphere: just use a small SLICE with the desired radius but a smaller height (e.g. 20A high). This will also reduce the number of points needed. In any case: if you run searches for Cn symmetry (i.e. proper n-folds) make sure to visually inspect the resulting correlation maps. You'd expect long stretches of 'density' showing you the location of the n-fold rotation axis. I am running CCP4 6.0.2 on my intel macbook pro. I am not sure which parameter to change in the getax.f file and how to exactly recompile getax with the existing CCP4 installation. Any advice would be really appreciated. If you really want/need to recompile: change the line parameter (maxpts=2) in $CCP4/src/getax.f and then % cd $CCP4/src % make getax Note: this will only work if you did the compilation of CCP4 yourself _and_ you left all files in place afterwards. Cheers Clemens Thanks, Vidya -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
[ccp4bb] ccp4mg colours
Hi all I've got a quick question regarding ccp4mg which hopefully isn't rtfm. I'm making some pictures at the moment and the inner artist in me is feeling slightly limited by the 17 colours on offer. Is there any way of adding RGB definitions. I've had a little play with the colours.def and colour.py files but adding extras makes no difference so I'm a bit stumped. Any help gratefully received Ambrose Cole CRUK This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a charity registered under number 1089464 and a company limited by guarantee registered in England Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.
[ccp4bb] ccp4mg question
I've found out how to do it on ccp4mg but I was working with the new QtMG, still can't find where to do it there though. Ambrose This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a charity registered under number 1089464 and a company limited by guarantee registered in England Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.
[ccp4bb] temporary files in CCP4i/Refmac
Greetings, I have a feeling that this is a stupid question. But I am baffled here and I need some help: I am working with a solid 3.0 Angstrom native data set. Processed in HKL2000. I created the mtz file and used a homemade poly-Ala model as a probe for molecular replacement. Both PHASER and AMORE give similar solutions with good packing, so I think that I am ready to go. BUT, when I attempt refinement with any .pdb file and the original .mtz in REFMAC5 I get an error message that my xxx.refmac file does not exist in its designated DepositFiles directory and that temporary xxx.pdb and xxx.mtz files cannot be found in the Temporary directory. I checked and, sure enough, those files are not being created in those directories. Now I am left scratching my head as this has never been a problem before. CCP4i has always been a bit black boxish for me (though addictingly convenient). This has been keeping me up the last couple of nights. Please offer any trouble shooting suggestions. Then feel free to hit me up for a plate of fish tacos the next time you come through San Diego. Details: I am using CCP4i v. 6.0.0 interface 1.4.3 installed on a RedHat Enterprise Dell Workstation. Thank you, Tom Huxford. Department of Chemistry Biochemistry San Diego State University
Re: [ccp4bb] Second coordination sphere of a metal ion
Hi Nick, Have you checked the web services provided by Marjorie Harding? http://tanna.bch.ed.ac.uk/index.html http://eduliss.bch.ed.ac.uk/MESPEUS/ Maybe, you can also find information about water mediated contacts over there. The first web site gives also some links to other interesting web pages. Of course, higher resolution data or another crystal form would help... Best regards, christian Nicholas Keep wrote: I have a 3.0 A structure which has a Mg liganded by a His NE and a substrate carboxylate at around 2.1 -2.3 A. There are a number of other potential liganding amino acid atoms at between 3.2 and 4.5 A. This is clearly longer than the direct bonding distances found by Harding http://journals.iucr.org/d/issues/1999/08/00/ad0073/index.html but these could conceively be coordinating via a water not visible at this resolution. I wondered if anyone knew of a tabulation of amino-acid to ion via water distances (ie second coordination sphere distances). I have not been able to google one so far. Thanks nick ___ Dr. Christian Biertümpfel Laboratory of Molecular Biology NIDDK/National Institutes of Health phone: +1 301 402 4647 9000 Rockville Pike, Bldg. 5, Rm. B1-03 fax: +1 301 496 0201 Bethesda, MD 20892-0580 USA ___
