[ccp4bb] Fwd: [ccp4bb] Calculate dipole moment of ligands from their coordinates
Hi all, For those interested, this script can be downloaded from: http://www.ysbl.york.ac.uk/~mol/scripts.htmlhttp://www.ysbl.york.ac.uk/%7Emol/scripts.html There is a short description as well. It works with proteins and molecules for which you can generate partial charges in a force field supported by pd2pqr. It produces a bild object that can be loaded in the program Chimera from the UCSF. But it can be easily re-written to produce output for other graphic programs. Feel free to do it! Cheers, Miguel 2008/1/26, Miguel Ortiz-Lombardía [EMAIL PROTECTED]: Hi Zheng, I have python script that does so if you have the program 'pdb2pqr' installed (http://pdb2pqr.sourceforge.net/) Let me know if you're interested. Cheers, Miguel 2008/1/19, Zheng Zhou [EMAIL PROTECTED]: Hi, All Sorry about non-CCP4 questions. It is the best board I find so far to learn stuff related to structure biology. Could anyone suggest me any program that calculates dipole moment of a ligand from its coordinates? Thanks, sorry to bother others. Zheng -- http://www.pangea.org/mol/spip.php?rubrique2 ~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens -- http://www.pangea.org/mol/spip.php?rubrique2 ~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens -- http://www.pangea.org/mol/spip.php?rubrique2 ~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens
[ccp4bb] Post-Doc Available in Ion Channel Structural Biology - Oxford UK
Post Doctoral Research Assistant in Ion Channel Biochemistry Structural Biology Grade 7: £26,666 - £32,796 pa An experienced post doctoral research assistant is required to work on structural studies of an exciting new class of prokaryotic ion channels. The successful applicant will join the Potassium Channel Research Group headed by Dr Stephen J. Tucker which will shortly be transferring to new custom built laboratories in the Biological Physics Unit, based in the Department of Physics. The ideal candidate will have significant experience of protein expression and purification, protein crystallisation and a particular interest in membrane proteins. The project is at a relatively advanced stage and therefore additional experience in X-ray structure determination would be an advantage. The position would ideally suit graduates with a PhD degree in biochemistry, crystallography, biophysics, or related subjects, and with relevant research experience. This post is available immediately and is funded by the BBSRC for a maximum of three years. Letters of application including a CV and names and addresses of 2 referees should be sent to The Personnel Officer, Department of Physics, Clarendon Laboratory, Parks Road, Oxford OX1 3PU or by email: [EMAIL PROTECTED] by 12th February, 2008, quoting reference number DK08-002. Informal enquiries may be addressed to Dr Tucker. Further Particulars are available from www.physics.ox.ac.uk/cm/vacancies.htm or www.physiol.ox.ac.uk/~sjt -- Dr Stephen J. Tucker Oxford Centre for Gene Function Department of Physiology, Anatomy and Genetics, Sherrington Building, Parks Road Oxford, OX1 3PT, United Kingdom Tel: +44-1865-285835 (Office) -285836 (Laboratory) Fax: +44-1865-285813 Email: [EMAIL PROTECTED] Tucker Lab Webpage: http://www.physiol.ox.ac.uk/~sjt PLEASE USE MY NEW EMAIL ADDRESS: [EMAIL PROTECTED] My lab will physically relocate to the Dept Physics during Summer 2008 **
[ccp4bb] Format convertion ccp4 to spider
Goodmorning. I need to convert a file form ccp4 to spider or situs format. The only programs I found to do this task are em2em and map2map (in the situs package). But both of them seems not to work. Do someone knows if any other program exists for converting files? Thak you very much. Francesco
[ccp4bb] Postdoctoral positions in Protein Crystallography, Glasgow
Postdoctoral Positions in Protein Crystallography at the Beatson Institute for Cancer Research, Glasgow We are seeking several highly motivated postdoctoral researchers to investigate the structure of cancer related proteins and drug targets. We are a newly established group at the Beatson Institute for Cancer Research in Glasgow, UK. Our group is interested in proteins of the kinesin superfamily, and their associated proteins, with a focus on human mitotic kinesins. Many of these proteins are good candidates for drug development in cancer chemotherapy. In addition, we will also determine the structures of other cancer-related proteins in collaboration with other groups in the Institute. We have a new, fully equipped and state-of-the-art structural biology laboratory including ÄKTA protein purification systems, nano- and micro-drop robots for automated protein crystallization, a Rigaku HighFlux Homelab microfocus diffraction system and comprehensive data processing facilities. In addition, we are well equipped to characterise the biochemistry of protein - inhibitor complexes towards the optimisation of lead compounds in collaboration with our chemist colleagues. The Beatson Institute has a large range of core service facilities including DNA sequencing, protein production and mass spectrometry. A number of positions are available (3 year contract in the first instance): 1) We require researchers with significant experience in protein crystallisation and structure determination and who are fully familiar with all the major software packages for x-ray crystallography. 2) An additional post is available for a biochemist with experience of characterising protein-inhibitor complexes. Experience in data processing, structure solution and model building is required. 3) The third position requires experience in cloning, expression and purification of proteins. The successful candidate is expected to actively participate in structure determination. Experience of crystallisation robots is an advantage but not essential. Closing date for applications is 22nd Feb 2008. Applications, with CV and names of three referees, should be sent by email to: Prof. Frank Kozielski The Beatson Institute for Cancer Research Switchback Road, Bearsden Glasgow G61 1BD Scotland Email: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] http://www.beatson.gla.ac.uk/research/index.html?topic_id=544
Re: [ccp4bb] Format convertion ccp4 to spider
What sort of file? Coordinates or reflections or map? Look at the GUI - reflection utilities or coordinate utilities and see if it offers what you want? Eleanor francesco zonta wrote: Goodmorning. I need to convert a file form ccp4 to spider or situs format. The only programs I found to do this task are em2em and map2map (in the situs package). But both of them seems not to work. Do someone knows if any other program exists for converting files? Thak you very much. Francesco
[ccp4bb] New versions of Mosflm and iMosflm
Hi folks We are pleased to announce updated versions of Mosflm (version 7.0.2) and iMosflm (0.6.0). If you upgrade iMosflm, you should certainly upgrade Mosflm at the same time; there are many changes which depend on both parts being in sync. The main change is that we have a new developer for iMosflm; Luke Kontogiannis ([EMAIL PROTECTED]) has been with us since October and has been very busy implementing improvements to iMosflm, so that it is now more robust and even easier to use. Most of the changes to Mosflm itself are involved with bug fixing and improved communications with iMosflm, so you shouldn't notice a lot of difference. Changes to Mosflm since 7.0.1 * New detectors - Mar555 Flat Panel. Pilatus miniCBF images added. * Better support for Bruker 100 Format images (converted with frm2frm). * Change IP address for communication with iMosflm to the loopback address (127.0.0.1 or localhost). * Rectangular non-square detectors added for output to iMosflm display. * Bug involving R-Axis detectors writing d*Trek style headers fixed. * Many small bugs fixed - many thanks to all those who gave us feedback, especially Clemens Vonrhein Jim Pflugrath. Changes to iMosflm since 0.5.3 * Resizeable image display by dragging the window edges * Ability to delete sectors in the image selection panel by right-clicking on selected sector * iMosflm correctly deals with datasets where the first image has an index of zero. The batch number is offset to 1000 and the processing and writing out of the mtz file proceed normally * The spotfinding summary pane in the indexing panel now shows the number of spots with an intensity greater than the I/sigI threshold * Ability to stop the log file view autoscrolling with Control-UpArrow key combination. Resume autoscrolling with Control-DownArrow * Search the log file by bringing up the search panel with Control-F key combination. Control-F searches forward and Control-G searches backwards Harry Luke -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH
[ccp4bb] Crystal Screening and Analysis web server
Hi All, I've rewitten the code for the Crystal Screen Wizard web server. The original aim of this home project was to analyze drop appearance patterns from initial screening in order to find ideal storage buffers for unstable proteins; however, I've modified it to include other useful features for things such as cataloging crystal optimization trays. The new server can do the following: 1) Using simple point-and-click options, produce extensively annotated graphics of your crystal trays (screens and optimizations) which can be cut and pasted into your lab book/computer file. 2) Handle 24 and 96 well plates. 3) Allow one to select multiple drop appearance types for each condition for analysis. 4) Analyze all possible drop appearance types for common agents simultaneously. 5) Using a crystal screen, analysis now gives the user a quick summary of what general salt and pH conditions the protein appears to like/dislike. I will include a simple salt crystal predictor and ionic strength estimator in the near future. Please feel free to e-mail me any comments, report bugs, or suggest improvements. URL: http://www.pageforaday.com/xtalwizard/ P.S: Old users, please note the change of the domain name. Cheers, AGS _ Climb to the top of the charts! Play the word scramble challenge with star power. http://club.live.com/star_shuffle.aspx?icid=starshuffle_wlmailtextlink_jan
[ccp4bb] Protein RNA interactions: Positions available.
RESEARCH FELLOW POSITIONS CURRENTLY AVAILABLE FOR JOINT BIOCHEMISTRY MOLECULAR BIOLOGY, MONASH UNIVERSITY/ MONASH INSTITUTE FOR MEDICAL RESEARCH PROJECTS The Wilce Laboratory at Monash University, headed by Jackie and Matthew Wilce, seeks highly motivated and talented scientists to join their research team. A number of Research Fellow positions for protein chemists/structural biologists are currently available to work in the field of protein/RNA interactions. Positions are available in two research streams: 1) Characterisation of RNA recognition by RNA-binding proteins involved in innate immunity – in collaboration with Professor Bryan Williams (Monash Institute for Medical Research), and, 2) The molecular basis of protein-RNA interactions underlying mRNA stability and translational control of inflammatory mediators - in collaboration with Dr Myriam Gorospe (NIH) Dr Paul Anderson (Harvard) and Professor Bryan Williams (Monash Institute for Medical Research). Monash University is literally across the road from Australia’s first and only Synchrotron. The Wilce laboratory has access to high- throughput protein production facilities as well as crystallisation robotics. Research Fellow applicants are expected to have a PhD and track record in a molecular science and a background in the following: protein chemistry, molecular biology, biochemistry, recombinant protein production and structural biology. Applicants with a very strong computational background, ie. molecular dynamics, computational estimation of Free Energy of binding are also encouraged to apply. Salary range: RF Level A $60, 019 - $64,427 RF Level B $67, 818 - $80,535 Appointments will be made at a level appropriate to the successful applicant’s qualifications, experience and in accordance with classification standards for each level. The positions are available immediately. Contact: Dr Jackie Wilce, tel. 613 9902 0121 email: [EMAIL PROTECTED] Applications: By mail addressed to Mrs Reenu Johnson, Department of Biochemistry and Molecular Biology, Monash University, 3800 or email [EMAIL PROTECTED] by 4th February 2008. Location: Clayton Campus, Melbourne, Australia. Position information, selection criteria and application details can be viewed on our website at www.monash.edu.au/opportunities, Position Number A088559. Or go directly to http://sssd.adm.monash.edu.au/employ/job.asp?refnumber=A088559work=staff=Academicfaculty=keyword=whichpage=2pagesize=5 Applications must address the selection criteria, quote the reference number and include curriculum vitae and the names and contact details of three referees. Monash respects the privacy of your personal information. For more details visit www.privacy.monash.edu.au
