[ccp4bb] OT: looking for a 3D-beamer that works with nvidia nvision
Dear CCP4ers, sorry for the off-topic mail: We are looking for a 3D-beamer for teaching purposes (structural biology courses). In the teaching rooms we have lots of high-end workstations equipped with 3D-stereo (Nvidia Nvision2, Quadro K5000, ASUS 27 VG278HE) that work perfectly in 3D (Scientific linux). As we have this many Nvidia setups with nvidia glasses it would be nice if we could also use the glasses for presentations done with a 3D-beamer. However, having a look at the Nvidia webpage it seems that the list of compatible projectors is mainly listing products that are not available anymore. Is there anybody out there using a 3D-beamer (linux OS preferred, windows will probably work anyway as the emitter is synced via USB) for COOT/PyMOL presentations using the Nvidia Nvision(1/2) setups? Any recommendation for the beamer? Has anybody tested e.g. the Canon LV-8235UST or the Acer products with PyMOL/Coot? It is probably better to email me directly as this off-topic - I will post a summary to the bb later on. Thanks and cheers from munich! Gregor Dr. Gregor Witte Research Associate Genecenter, University of Munich (LMU) Feodor-Lynen-Str. 25 D-81377 Munich mail: mailto:wi...@genzentrum.lmu.de wi...@genzentrum.lmu.de web: http://grk1721.genzentrum.lmu.de/gregor-witte grk1721.genzentrum.lmu.de/gregor-witte
[ccp4bb] Diamond MX bag training 15-16th July - with registration link working
Sorry I sent the wrong link for the registration... Here is the new one: Registration openhttp://www.diamond.ac.uk/Home/Events/2015/MX-Bag-Training.html until 24th June Pierre Dear all, The Diamond Light Source Macromolecular Crystallography group would like to invite both our academic and industrial users to MX beamline training sessions on the 15th -16th July 2015. The aim is to provide MX users with sufficient training to be able to operate any of the Diamond MX beamlines efficiently and to get the most benefit from their beamtime. The training will involve hands-on sessions on the suite of five operational MX beamlines (http://www.diamond.ac.uk/mx-home/) as well as optional offline software sessions. Sessions include: 15th July, afternoon session and 16th July, morning session on MX beamlines: * MX software: automation in data analysis * Mini-Kappa goniometry / Anomalous data collection * Sample humidity control (HC1) * I24 new end station/ In-situ diffraction * Fragment screening - I04-1/Lab36 * Experiment database: new ISPyB 16th July afternoon optional session Hands on software: Two tutorial sessions: * CCP4: structure solution and model building with CCP4 (CCP4 team) * Manual processing with iMosflm (Harry Powell) Registration is free-of-charge with lunch provided on the 15th and 16th February, and accommodation and dinner for the night of the 15th July. Travelling expenses within the UK will also be provided. The training is targeted at all users, and is not limited to students and post docs. It is essential that each BAG sends at least one representative per calendar year. Registration Places are limited to twenty five participants. The registration deadline is on the 24th June. Registration is now openhttp://www.diamond.ac.uk/Home/Events/2015/MX-Bag-Training.html Pierre Aller, Ph.D. Senior Support Scientist Diamond Light Source Ltd., Diamond House Harwell Science Innovation Campus Didcot, Oxfordshire OX11 0DE +44 (0) 1235 778183 pierre.al...@diamond.ac.uk -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
[ccp4bb] Postdoctoral Position
A postdoctoral position in structural biology is available in the Shamoo Lab at Rice University (http://www.bioc.rice.edu/~shamoo/shamoolab.html ). The successful candidate must have experience in X-ray crystallography as well as biochemistry. Candidates should hold a PhD degree in biophysics or biochemistry. Additional useful experience in one or more of these technical areas is also desirable: . Enzyme kinetics . Ligand (DNA/RNA) binding studies . Molecular biology Our group studies the evolution of antibiotic resistance in clinical pathogens. We use a combination of experimental evolution, genomics and biochemical approaches to understand the biophysical basis for newly evolved resistances. Candidates must also have very good interpersonal skills to work in our highly interdisciplinary research team and be able to assist in the mentoring of students. Interested candidates should send a cover letter, CV and the names of three references to sha...@rice.edu Rice University is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age or protected veteran status. Yousif Shamoo, Ph.D. Rice University Vice Provost for Research Professor, Department of Biosciences MS-603 P.O. Box 1892 Houston, TX. 77251-1892 (Ph) 713-348-5493 (F) 713-348-4105
[ccp4bb] Release of iMosflm/Mosflm version 7.2.0
Dear all We are pleased to announce the release of iMosflm/Mosflm 7.2.0; this version includes a number of new features as well as the usual numerous bug fixes - • iMosflm now has a known cell indexing option that can be useful for difficult cases if the cell parameters are known approximately. Thanks to Takanori Nakane for this development. • Removed need for the environment variable MOSFLM_EXEC to be set. iMosflm should now use the executable distributed in the imosflm/bin directory by default; if MOSFLM_EXEC is set it MUST point to a valid executable for the current version of iMosflm. • Missetting angles can be smoothed over several images, useful for processing data from crystals with very small unit cell dimensions. • Summed Pilatus images can be displayed to improve visualization of weak fine-sliced Pilatus data. • Summed Pilatus images can be used when finding spots for detector parameter refinement. • Images can be displayed in reverse video (i.e. light spots on a dark background); this can help to see small spots on Pilatus images. The user's choice is retained on exiting iMosflm. • Mosflm crashing in CENTRS due to too few reflections available for detector parameter refinement is now trapped and a warning message is given. Robustness of refinement improved. • iMosflm now deals correctly with new style Raxis-II images. • iMosflm will now process images collected with the ADSC Pixel Array Detector at APS and with Dectris Eiger 4M images collected at ESRF (detector currently on beamline ID30a3) after extraction from HDF5 container. Images collected on Dectris Eiger 1M at SLS can be processed after extraction from HDF5 container, but the gaps between modules may not be recognised properly. • Since version 7.1.3 iMosflm will deal correctly with images collected using a vertical rotation axis as on station I24 at Diamond Light Source, but it is still necessary to explicitly provide this information to iMosflm as it is not yet stored in the image header. See http://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver720/introduction.html for full details. • iMosflm will check when opening a session file that it is a valid XML file; if not, it will ask the user if they intended to open an image file. • The iMosflm tutorial has been updated and now includes a Tips section. Note that this is the ONLY documentation that has been updated to describe new features. • Many minor bug fixes and some new warnings (including unstable misset angle refinement). Downloads are available from http://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver720/introduction.html or http://www.mrc-lmb.cam.ac.uk/harry/mosflm/index.html (if you just want Mosflm) This is a bug-fix release which has no new features. Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
[ccp4bb] Instruct Call for proposals
Call for proposals utilising Instruct-funded structural biology techniques If you don't have local access to ALL the structural biology instrumentation you need for your research you can access some of the best structural biology facilities in Europe. Instruct has 16 Centres around Europe and in Israel offering access to a full range of advanced technologies for obtaining structural and dynamic information on systems in various dimensions, complexity and resolution. Instruct also ensures expert support at the facility for the best research outcome. Access to the infrastructure at Instruct Centres is provided for all Instruct members and there are no charges for use of the Infrastructure instrumentation or the expert support. Consumable costs, accommodation and travel are supported by Instruct funds up to a maximum of €1500 per visit. In some cases, additional funds may be requested from the user to cover exceptional consumable costs and these should be negotiated between the user and the host Instruct Centre before work commences. Proposals for funded access to the full set of Instruct facilities are now invited. Register at www.structuralbiology.eu and submit your proposal online. The deadline for this round of proposal submission is 5pm CET, 31st August 2015. Best wishes Instruct Operations team Instruct member countries (presently BE, CZ, ES, FR, DE, IL, IT, NL, PT, SE, UK) Dr Claudia Alen Amaro Scientific Project Manager Instruct: An Integrated Structural Biology Infrastructure for Europe, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington OX3 7BN, UK Tel: +44 1865 287808 email: clau...@strubi.ox.ac.uk Follow us on twitter @instructhub
[ccp4bb] PhD position in the laboratory AFMB, Marseille
Dear all, A PhD position within the Marie-Curie (ITN) network is available in the laboratory AFMB (Marseille, France) to work on the mRNA capping machinery of Alphaviruses. A detailed description of the topic and eligibility can be found at the following link http://hactar.phrmy.cf.ac.uk/antivirals/node/13#overlay-context=node/7 Interested candidates should contact Bruno Coutard (bruno.cout...@afmb.univ-mrs.fr) Best regards, Gerlind -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 491 82 55 66 Fax +33 491 26 67 20 E-mail: gerlind.sulzenbac...@afmb.univ-mrs.fr
Re: [ccp4bb] twinned data refinement
If you have unmerged data try running it through pointless/aimless/ctruncate. That analyses twin fractions very carefully and with that twin law you should see some evidence of 6 fold symmetry but less pronounced than for the 3 and 2 fold symmetry operators.. Eleanor On 11 June 2015 at 01:03, Mengbin Chen mengb...@sas.upenn.edu wrote: Thank you Jacob and Ethan! I haven't put water molecules into the density blob, which aren't many out there, but I fitted the ligands in already. Molbrobity statistics are not yet great, since there are 13.5% rotamer outliers. Will adjust the models manually, and try refmac and TLS refinement. Thanks again for your insightful suggestions! Best, Mengbin On Wed, Jun 10, 2015 at 6:16 PM, Ethan A Merritt merr...@u.washington.edu wrote: On Wednesday, 10 June, 2015 17:35:25 Mengbin Chen wrote: Hello everyone, I am refining a 2.5 angstrom structure whose phase is solved by molecular replacement with a search probe determined by SAD with 3 angstrom resolution. While I am able to see densities of a bunch of water molecules and ligands in the MR solved structure, which means that the phase is correct, the Rfree gets stuck at ~27%. Why do you think this is a problem? It is true that turning on twin refinement is expected to yield lower R factors, and thus 27% in the presence of twin refinement is worse than 27% without twin refinement. But having said that, Rfree = 0.27 is still not so horrible. If the starting point for your MR solution was a 3A model, there may have been errors in sidechain placement or even backbone conformation that can be corrected now that you have higher resolution data. Don't assume that the starting model was perfect. You say that you can see density for a bunch of waters and ligands. Are these in your refinemed model yet? What does Molprobity (or coot or phenix) say about the quality of your sidechain rotamers? Have you tried adding a TLS description? Ethan The crystal belongs to P3221 and has a twinning fraction of 19%, according to Xtriage. Currently I've been sticking to Phenix for refinement, and twin law (-h, -k, l) has been applied. I was wondering if the CCP4 community would have any suggestions of how to refine this twinned structure, such as softwares to use, tricky strategies to choose, etc. I really appreciate any recommendations you would come up with my situation! Thank you in advance! Best, Mengbin -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742 -- Mengbin Chen PhD Candidate Christianson Laboratory Department of Chemistry University of Pennsylvania 231 S. 34th Street, #323 Philadelphia, PA 19104 USA Phone: (215)898-2227 Email: mengb...@sas.upenn.edu
Re: [ccp4bb] OT: looking for a 3D-beamer that works with nvidia nvision
Hi, if you plan to use the IR emitter and work in groups ( 10 people), you are probably going to need a stronger IR emitter. If people are sitting in rows, the IR emitter signal can get lost in the backrows. Better to have a short throw beamer so nobody gets in the way (at a distance of 1 meter from the wall I get a 2 meters wide picture). You need a beamer with _at least_ 3000 ANSI (absolut minimum as the glasses filter out light). A resolution of ±720p more than enough. Nividia glasses are expensive (100$). I purchased the optoma gt750-xl a few years ago because of the 3-pin stereo connector on the beamer (no need for high end cards with 3-pin). It can be used with the IR-emitter connected to the beamer (and a cheap quadro or gtx card) and Nvidia glasses or with cheap DLP-link 3D glasses. The 3-pin option on beamers is disappearing because of the cheap DLP-link 3D glasses (white-flash in between right and left picture). We purchased 20 XPAND DLP-link 3D glasses (more rigid, professional cinema glasses but still cheaper than Nvidia glasses) and the set-up works great. Since you are based (German but I think intuitive to many for selecting a beamer based on different options): selection of 3000 ANSI short throw 3D beamers http://www.beamershop24.net/filterresult.php?fromappareaprojectorfilter=1application=kurzdistanz-beameroptansi=3000chkresolution_13=1280%2Bx%2B720_WXGAchkresolution_14=1280%2Bx%2B800_WXGAoptprice=2 selection of 3000 ANSI class room beamers http://www.beamershop24.net/filterresult.php?fromappareaprojectorfilter=1application=schulbeameroptansi=3000optprice=chkfeature_486=3D%2Bready and selection of 3000 ANSI Home Cinema / Gamer beamers http://www.beamershop24.net/filterresult.php?fromappareaprojectorfilter=1application=heimkino-hd-beameroptansi=3000chkresolution_13=1280%2Bx%2B720_WXGAchkresolution_14=1280%2Bx%2B800_WXGAoptprice=chkfeature_486=3D%2Bready Jeroen Am 11.06.15 um 12:04 schrieb Gregor Witte: Dear CCP4ers, sorry for the off-topic mail: We are looking for a 3D-beamer for teaching purposes (structural biology courses). In the “teaching rooms” we have lots of high-end workstations equipped with 3D-stereo (Nvidia Nvision2, Quadro K5000, ASUS 27” VG278HE) that work perfectly in 3D (Scientific linux). As we have this many Nvidia setups with nvidia glasses it would be nice if we could also use the glasses for presentations done with a 3D-beamer. However, having a look at the Nvidia webpage it seems that the list of compatible projectors is mainly listing products that are not available anymore. Is there anybody out there using a 3D-beamer (linux OS preferred, windows will probably work anyway as the emitter is synced via USB) for COOT/PyMOL presentations using the Nvidia Nvision(1/2) setups? Any recommendation for the beamer? Has anybody tested e.g. the Canon LV-8235UST or the Acer products with PyMOL/Coot? It is probably better to email me directly as this off-topic – I will post a summary to the bb later on. Thanks and cheers from munich! Gregor Dr. Gregor Witte Research Associate Genecenter, University of Munich (LMU) Feodor-Lynen-Str. 25 D-81377 Munich mail: wi...@genzentrum.lmu.de mailto:wi...@genzentrum.lmu.de web: grk1721.genzentrum.lmu.de/gregor-witte http://grk1721.genzentrum.lmu.de/gregor-witte -- Dr.math. et dis. nat. Jeroen R. Mesters Deputy, Senior Researcher Lecturer Program Coordinator /Infection Biology/ http://www.uni-luebeck.de/studium/studiengaenge/infection-biology/introduction.html Institute of Biochemistry, University of Lübeck Ratzeburger Allee 160, 23538 Lübeck, Germany phone: +49-451-5004065 (secretariate -5004061) fax: +49-451-5004068 http://www.biochem.uni-luebeck.de Http://www.biochem.uni-luebeck.de http://www.uni-luebeck.de/studium/studiengaenge/infection-biology http://www.iobcr.org Http://www.iobcr.org -- If you can look into the seeds of time and tell which grain will grow and which will not, speak then to me who neither beg nor fear (Shakespeare's Macbeth, Act I, Scene 3) -- Disclaimer * This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. * E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. If verification is required please request a hard-copy version. Please send us by fax any message containing deadlines as incoming e-mails are not screened for response deadlines. * Employees of the Institute are expressly required
[ccp4bb] Peltier cooled incubators
Little off topic and after a quick search I could not find much on the BB already. We are looking at purchasing a larger Peltier cooled incubator for crystal trays. They are designed to go down to 15 C. I know people have had pretty good luck with the bench top models but we are looking at a 19 cu. ft, 546 L model. These are designed for BOD experiments. So I would like to hear if we are wasting our money and should look at a more expensive compressor based incubator for crystal growth or will this work just fine. Thanks in advance, Len Leonard M. Thomas Ph.D. Macromolecular Crystallography Laboratory Manager University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019 405-325-1126 lmtho...@ou.edu http://barlywine.chem.ou.edu http://structuralbiology.ou.edu
[ccp4bb] Post-doc available on membrane protein structure determination at Columbia University
A postdoctoral position is available in the laboratory of Dr. Filippo Mancia in the Department of Physiology and Cellular Biophysics at Columbia University in New York, USA. The labs primary interest is in unraveling the structure and function of eukaryotic and prokaryotic membrane proteins, with a focus on membrane embedded enzymes involved in lipid metabolism. The ideal candidate should have a PhD in structural biology and extensive experience in all aspects of protein X-ray crystallography or electron microscopy, including protein expression and purification, crystallization, structure determination and refinement. Experience with protein expression in insect or mammalian cells is a plus. Interested candidates should send their CV, brief description of prior research accomplishments and contact information for three references to: fm...@cumc.columbia.edu For further information see: 1) Structural basis for catalysis in a CDP-alcohol phosphotransferase. Sciara G, Clarke OB, Tomasek D, Kloss B, Tabuso S, Byfield R, Cohn R, Banerjee S, Rajashankar KR, Slavkovic V, Graziano JH, Shapiro L, Mancia F. Nat Commun. 2014 Jun 13;5:4068. 2) Structure of a mammalian ryanodyne receptor. Zalk R, Clarke OB, des Georges A, Grassucci RA, Reiken S, Mancia F, Hendrickson WA, Frank J, Marks AR. Nature. 2015 Jan 1;517(7532):44-9. Lab web site: http://www.physiology.columbia.edu/mancia.html
Re: [ccp4bb] Ligand relevance for bioinformaticians using PDB files
Firslty, there is credo http://marid.bioc.cam.ac.uk/credo a database set up in the Blundell lab, that deals with protein ligand interactions. That might be of interest. Second, as more general points. I see your point Shane, I'd argue there is no great value in trying to distinguish artefacts from relevant ligands. Whether or not the crystallographer perceives something as biologically relevant any binding informs the community about the protein in some way. For his use case, might it be better to consider what the student wants to achieve with this work? For example using a minimum number of heavy atoms would remove a lot of buffer molecules and all metals. The advantage of this being you are now looking at all ligand like substances that a chemist might consider working with. If you then felt the need to get rid of say MES, then I think you would need to justify that. Is it because it's too high concentration? Then I'd ban any component above a certain concentration, if it's given to the PDB, but then I think you're missing valuable data. Or is it because it doesn't bind with any potency? Then I'd pick only ligands above a certain ligand efficiency, but that again would miss lots of data. It might be interesting however, to compare the interactions found from those two subsets, with that of the broader ligand world. Hope this helps! Best wishes, Anthony On 11 Jun 2015, at 20:55, Shane Caldwell shane.caldwel...@gmail.commailto:shane.caldwel...@gmail.com wrote: Hmm, this makes me think of how upon deposition to the PDB, we describe the expected biological assembly that a crystal structure represents. This is a judgement call, but can be backed up with experimental data. A similar flag for physiological ligands as opposed to components of the crystallization solution (with just as much subjectivity) could be very useful for differentiating physiological versus artifactual ligands. Of course, much easier said than done. Shane Caldwell McGill University On Thu, Jun 11, 2015 at 3:14 PM, Lucas lucasbleic...@gmail.commailto:lucasbleic...@gmail.com wrote: This week a bioinformatics PhD candidate was talking about his PDB analysis tool which was aimed at studying protein-ligand statistics and asked for some advice on what should he consider as biologically relevant or not. I told him many of the most common molecules he found were buffers, cryoprotectants, metals used for phasing, etc., and also said that some cases could be more complicated (e.g., PO4 is very common because of its use as a buffer, but in the same time it could be biologically relevant in many cases such as kinases or phosphatases). Well, I tried my best to list most usually biologically irrelevant I could remember, but now I wonder if that is something someone has probably thought about doing before and there's some article/database dealing with it somewhere. Any suggestions? Lucas
[ccp4bb] ppGpp purification and concentrate
Dear ccp4bb members, Sorry for asking a non-crystallographic question where google search cannot provide any valuable answer. pppGpp was synthesized by relQ enzyme using ATP and GTP, the product was purified by anion exchange chromatography. The problem is that the concentration of pppGpp is too low for crystal soaking. My question is that using volatile buffer, how can I concentrate my substrate, and how can I desalt it? Should I need a freeze dried machine? Best wishes! Lu Zuokun
Re: [ccp4bb] ppGpp purification and concentrate
desiccator with P2O5 in the freezer should do the trick... Artem - Cosmic Cats approve of this message On Thu, Jun 11, 2015 at 11:12 PM, luzuok luzuo...@126.com wrote: Dear ccp4bb members, Sorry for asking a non-crystallographic question where google search cannot provide any valuable answer. pppGpp was synthesized by relQ enzyme using ATP and GTP, the product was purified by anion exchange chromatography. The problem is that the concentration of pppGpp is too low for crystal soaking. My question is that using volatile buffer, how can I concentrate my substrate, and how can I desalt it? Should I need a freeze dried machine? Best wishes! Lu Zuokun
Re: [ccp4bb] ppGpp purification and concentrate
Can you elute from AE with NH4HCO3? It's volatile, so you could just evaporate it off afterwards. JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of luzuok Sent: Friday, June 12, 2015 7:13 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] ppGpp purification and concentrate Dear ccp4bb members, Sorry for asking a non-crystallographic question where google search cannot provide any valuable answer. pppGpp was synthesized by relQ enzyme using ATP and GTP, the product was purified by anion exchange chromatography. The problem is that the concentration of pppGpp is too low for crystal soaking. My question is that using volatile buffer, how can I concentrate my substrate, and how can I desalt it? Should I need a freeze dried machine? Best wishes! Lu Zuokun
[ccp4bb] PREDOCTORAL POSITION IN STRUCTURAL BIOLOGY (BARCELONA)
PREDOCTORAL POSITION IN STRUCTURAL BIOLOGY Applications are invited for a predoctoral position in the group headed by Prof. Miquel Coll at the Institute for Research in Biomedicine (IRB Barcelona) / Institute of Molecular Biology of Barcelona (IBMB-CSIC) to work on the project Structure of DNA-binding proteins, complexes and molecular machines. IRB Barcelona has been recognized as a Severo-Ochoa Centre of Excellence and the IBMB Structural Biology Unit as a Maria de Maeztu Unit of Excellence. The laboratory is located in the stimulating scientific and cultural environment of the Barcelona Science Park. The 4-year position is funded by the MINECO (Ministerio de Economía y Competitividad, project-associated predoctoral contract). Candidates should have an outstanding CV, high motivation for scientific research, and the ability to work in a competitive research team. Previous experience in a molecular biology or structural biology laboratory would be desirable. Applicants should send a CV, a copy of their academic records with the average grade, and the names and addresses of 2 researchers or professors for references no later than 19th of June 2015. Interviews for short-listed candidates will be held during the week 22-26 June 2015. Those interested should contact: Ms. Esther Fernández Structural and Computational Biology Programme Secretary Email: mailto:esther.fernandez.rodrig...@irbbarcelona.org esther.fernandez.rodrig...@irbbarcelona.org Tel.: +34 40349953
[ccp4bb] Ligand relevance for bioinformaticians using PDB files
This week a bioinformatics PhD candidate was talking about his PDB analysis tool which was aimed at studying protein-ligand statistics and asked for some advice on what should he consider as biologically relevant or not. I told him many of the most common molecules he found were buffers, cryoprotectants, metals used for phasing, etc., and also said that some cases could be more complicated (e.g., PO4 is very common because of its use as a buffer, but in the same time it could be biologically relevant in many cases such as kinases or phosphatases). Well, I tried my best to list most usually biologically irrelevant I could remember, but now I wonder if that is something someone has probably thought about doing before and there's some article/database dealing with it somewhere. Any suggestions? Lucas
