[ccp4bb] Postdoc Crystallographer Position at Swiss Light Source
Postdoctoral Fellow Protein Crystallography with PILATUS detector Your tasks After one and a half years of successful operation of the first two- dimensional hybrid pixel array detector (PILATUS 6M) at the beamline X06SA, some of its advantages and outstanding capabilities for macromolecular crystallography have been established. However, there are still great needs to further exploit the potential of the PILATUS detector. In this context, you will work on the improvement of MAD and SAD data collection protocols with focus on long-wavelength phasing as well as room temperature protein crystallography. Furthermore, you are expected to extend the PILATUS applications to other area of crystallography such as charge density and diffuse scattering studies. It is expected that the novel experiments will require the development of appropriate data analysis scripts and software. You will work with experienced synchrotron scientists and will also interact with external user groups as a local contact at the MX-beamlines. Your profile You hold a Ph.D. degree in biology, chemistry or physics, and have substantial experience in protein crystallography. Working knowledge of data processing programs and experience with various phasing and refinement software is a must. Experience in computer programming would be of significant advantage. If you are a good team player with fine communication skills and a sense of responsibility, this position will offer a great opportunity for you to develop your research career in an exciting and highly multidisciplinary environment. For further information please get in touch with: Contact Line: Dr Meitian Wang, Phone +41 (0)56 310 41 75, meitian.w...@psi.ch or Dr Vincent Olieric, Phone +41 (0)56 310 52 33, vincent.olie...@psi.ch Please submit your application to: Paul Scherrer Institut, Human Resources, Elke Baumann, ref. code 6112, 5232 Villigen PSI, Switzerland, elke.baum...@psi.ch More info: http://pa.web.psi.ch/pages/offenestellen/d/index_offenestellen.php?id=2020was=stelle __ Meitian Wang Swiss Light Source at Paul Scherrer Institut CH-5232 Villigen PSI - http://sls.web.psi.ch Phone: +41 56 310 4175 Fax: +41 56 310 5292
Re: [ccp4bb] Ramachandran plot, in a text list
John Pak wrote: Hi, sorry if this was posted earlier. How can I calculate a Ramachandran plot, but output the information to a text file list? i.e. something like Ala51, phi=X, psi=Y. I can't seem to find this information in the ccp4 SFCheck/Procheck log file. I thought PROCHECK listed this? But i see i t is only for residues it thinks are helix.. Eleanor
Re: [ccp4bb] Ramachandran plot, in a text list
However, procheck ramachandran is deprecated these days as it is based on older data than say molprobity. Obviously that won't matter just for a list of phi/psi angles, but might affect selections e.g. what it thinks are in a helix (cf Eleanor's message) m On Wed, 2009-01-14 at 14:39 -0500, Edward A. Berry wrote: John Pak wrote: Hi, sorry if this was posted earlier. How can I calculate a Ramachandran plot, but output the information to a text file list? i.e. something like Ala51, phi=X, psi=Y. I can't seem to find this information in the ccp4 SFCheck/Procheck log file. And lets not forget procheck, since its included with ccp4 and you probably already have it. After you run procheck on your protein (procheck pdbname.pdb 1.8), there is a text file pdbname.rin which lists phi, psi, omega and sidechain dihedrals for each residue: phipsi omega chi1 chi2 chi3chi4 14ASN A 15 E -89.06 141.45-179.73 -63.59 -55.39 999.90 999.90 -2.14 0.00 34.00 89.18 88.838 88.830 8 45 1.980 0.762 15VAL A 16 E-139.67 138.33 177.89-170.03 999.90 999.90 999.90 0.00 0.00 36.23 87.91 86.643 87.253 8 50 0.147 0.499 16THR A 17 E-144.59 139.86-179.12 51.94 999.90 999.90 999.90 -2.64 0.00 34.56 84.27 86.238 85.020 8 40 0.421 0.536 You also have a .ps file pdbname_01.ps with the graphical ramachandran which you can view with gv or gs, or convert to pdf with ps2pdf DSSP also list phi-psi angles, in two columns far to the right. Ed -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
Re: [ccp4bb] Ramachandran plot, in a text list
Hi, How about STAN server at Uppsala? http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl I suppose you can find what you are looking for at MOLEMAN2 main-chain analysis in the output webpage. Takanori From: John Pak john@utoronto.ca Subject: [ccp4bb] Ramachandran plot, in a text list Date: Wed, 14 Jan 2009 13:05:19 -0500 Hi, sorry if this was posted earlier. How can I calculate a Ramachandran plot, but output the information to a text file list? i.e. something like Ala51, phi=X, psi=Y. I can't seem to find this information in the ccp4 SFCheck/Procheck log file. -- MATSUURA Takanori, Ph.D. Visiting Associate Professor Laboratory of Protein Informatics, and Laboratory of Supramolecular Crystallography, Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University 3-2 Yamadaoka, Suita, Osaka 565-0871, JAPAN Tel: +81-6-6879-8635 Fax: +81-6-6879-4313
Re: [ccp4bb] Ligand binding in multiple conformation
An extension of this topic: does anyone know of examples where for complexes between the two proteins A and B, protein A has two different conformations at its interface? thanks chandra -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Aaron Oakley Sent: Tuesday, January 13, 2009 1:19 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Ligand binding in multiple conformation I had a question about flexibility in ligand binding in an enzyme active site. Is it possible for a substrate/product analogue to bind in more than one conformation in the active site. Yes. It is even possible for portions of a ligand to be disordered and not discernable in electron density. Since the ligand/enzyme interactions are very specific I am a little confused about this. Also which program would you use if you have to refine with alternate ligand conformation. REFMAC will do this just fine. Just make sure you have the A, B conformers set in the PDB file. EG: ATOM 72 CA APRO A 7 -2.619 28.983 -0.796 0.62 6.48 C ATOM 73 CA BPRO A 7 -2.226 29.044 -0.847 0.38 5.76 C
Re: [ccp4bb] Ramachandran plot, in a text list
Thanks for the replies everyone. I ended up using CNS_SOLVE 1.1 to generate the Ramachandran list. I don't seem to have access to the .rin file you mentioned. The only output I get from Procheck are the log file and the various postscript files. No big deal, perhaps it's because I'm running Procheck through the ccp4i gui, or because I'm using the Windows binaries. Anyways, thanks again. Quoting Edward A. Berry ber...@upstate.edu: John Pak wrote: Hi, sorry if this was posted earlier. How can I calculate a Ramachandran plot, but output the information to a text file list? i.e. something like Ala51, phi=X, psi=Y. I can't seem to find this information in the ccp4 SFCheck/Procheck log file. And lets not forget procheck, since its included with ccp4 and you probably already have it. After you run procheck on your protein (procheck pdbname.pdb 1.8), there is a text file pdbname.rin which lists phi, psi, omega and sidechain dihedrals for each residue: phipsi omega chi1 chi2 chi3chi4 14ASN A 15 E -89.06 141.45-179.73 -63.59 -55.39 999.90 999.90 -2.14 0.00 34.00 89.18 88.838 88.830 8 45 1.980 0.762 15VAL A 16 E-139.67 138.33 177.89-170.03 999.90 999.90 999.90 0.00 0.00 36.23 87.91 86.643 87.253 8 50 0.147 0.499 16THR A 17 E-144.59 139.86-179.12 51.94 999.90 999.90 999.90 -2.64 0.00 34.56 84.27 86.238 85.020 8 40 0.421 0.536 You also have a .ps file pdbname_01.ps with the graphical ramachandran which you can view with gv or gs, or convert to pdf with ps2pdf DSSP also list phi-psi angles, in two columns far to the right. Ed
[ccp4bb] Postdoctoral positions available, Xiamen, China
A structural biology lab has now several openings. This lab conducts two aspects of research using X-ray crystallography and other biochemical approaches. One is to understand how a limited number of transcriptional factors regulate a large amount of genes. Our model is that two or more transcription factors work together and further recruit other protein modification factors to form high-order regulatory assemblies on gene promoters. Another is to study how the extracellular signals transfer to a specific set of transcription factors. This involves ligand-protein and protein-protein interaction and the proteins associated with cell membranes. For some details, please see http://life.xmu.edu.cn/teacher/HTML/1760.html. Those who have Ph.D in any biology or chemistry disciplines are welcome to apply. Experience in protein biochemistry and/or cell biology will be in higher priority. Training in crystallography will be big plus. Xiamen island is the most beautiful city, and Xiamen University has one of few best university campus over China. It is so comfortable to live that it grows a big foreigner community. Please see www.xmu.edu.cn/english for university and http://www.amoymagic.com for Xiamen. Successful candidates will be provided with a standard package from Xiamen University including convenient low-cost apartment, medical insurance and family assistance. If interested, please send your CV and contacts of 3 referees to Dr. Aidong Han through a...@xmu.edu.cn. Thank your attention.
[ccp4bb] Crystallography plates, hanging drop but templated sealing film.
Does such a thing exist? A 24-well microplate configuration where in substitution of glass cover slips, you have a roll of tape templated such that there are circular areas where you can add your protein where there is no adhesive, but there is adhesive everywhere else? This may be a nightmare for plate manufacturers, but to reuse the plate, you just throw away the film and tear a new one. Thanks! FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Re: [ccp4bb] Crystallography plates, hanging drop but templated sealing film.
This sounds very similar to a nifty little device the folks in Buffalo came up with: J. Appl. Cryst. (1992). 25, 324-325[ doi:10.1107/S0021889891011354 ] HANGMAN: a macromolecular hanging-drop vapor-diffusion technique J. R. Luft and G. T. DeTitta On 15 Jan 2009, at 4:34 PM, Francis E Reyes wrote: Does such a thing exist? A 24-well microplate configuration where in substitution of glass cover slips, you have a roll of tape templated such that there are circular areas where you can add your protein where there is no adhesive, but there is adhesive everywhere else? This may be a nightmare for plate manufacturers, but to reuse the plate, you just throw away the film and tear a new one. Thanks! FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu
Re: [ccp4bb] Crystallography plates, hanging drop but templated sealing film.
Why not just use a 96 well plate. Should be able to do this by hand with a large enough drop. You can get them from either TTP Labtech or Grace Biosystems, I think that is the name. Cheers, Len Leonard Thomas Ph. D. Macromolecular Crystallography Laboratory Manager University of Oklahoma Department of Chemistry and Biochemistry 620 Parrington Oval Norman, OK 73032 lmtho...@ou.edu Office: 405-325-1126 Lab: 405-325-7571 On Jan 15, 2009, at 3:34 PM, Francis E Reyes wrote: Does such a thing exist? A 24-well microplate configuration where in substitution of glass cover slips, you have a roll of tape templated such that there are circular areas where you can add your protein where there is no adhesive, but there is adhesive everywhere else? This may be a nightmare for plate manufacturers, but to reuse the plate, you just throw away the film and tear a new one. Thanks! FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
