[ccp4bb] 2 Research Associate positions at the Membrane Protein Lab, Oxfordshire
Dear All, Two Research Associate positions have become available in the laboratory for crystallisation and crystallographic studies on mammalian transporter in the Membrane Protein Crystallography Laboratory at the Research Complex in Harwell (RCaH) near Didcot, Oxfordshire. The laboratory is headed by Professor So Iwata, who is a world leader in crystallisation and crystallography of membrane proteins. In particular, the group has a proven track record working with respiratory and photosynthetic membrane protein complexes and membrane transporters. The laboratory is an out-house of Imperial College London and is fully equipped for structural studies for membrane proteins. The successful candidate will work on improving the crystals and solving the structure of these important proteins. The Biotechnology and Biological Sciences Research Council (BBSRC) funds the post. The duration of the posts are until 31 December 2014. You must have a PhD in a biological science, or the equivalent in professional qualifications and experience. You must also have experience in molecular cloning, mammalian cell culturing and experience in protein crystallisation and crystallography. Crystallization and X-ray crystallography particularly on membrane proteins or macromolecular complexes, and X-ray diffraction data collection are also essential. Closing date for applications is 13 October 2013. Our preferred method of application is online via this website: https://www4.ad.ic.ac.uk/OA_HTML/OA.jsp?page=/oracle/apps/irc/candidateSelfService/webui/VisVacDispPGOAHP=IRC_EXT_SITE_VISITOR_APPLOASF=IRC_VIS_VAC_DISPLAYakRegionApplicationId=821transactionid=1447932834retainAM=YaddBreadCrumb=RPp_svid=42052p_spid=1633956oapc=21oas=qTAHu7O9l4komvvW1SnQCw Best, Kostas Dr. Konstantinos Beis Lecturer Imperial College London Membrane Protein Lab Research Complex at Harwell Harwell Oxford Didcot Oxfordshire OX11 0FA UK tel: 01235567809 url: http://www3.imperial.ac.uk/people/konstantinos.beis url2: http://www.diamond.ac.uk/Science/MPL/default.htm P Please consider the environment before printing this email
[ccp4bb] postdoc position at the University of Geneva
Dear All, A postdoc position at the University of Geneva to work on lipid kinases is available starting from the 1st of January 2014. We are seeking a highly motivated and independent postdoc to untangle the regulation of PI3Ks lipid kinases using a multidisciplinary approach based on structural biology. Competences in cloning, protein expression, purification, crystallization and X-ray crystallography are essential for this post. Additional expertise in biophysical methods such as fluorescence, SPR, ITC, thermophoresis and in cell-based assays would be desirable. Applicants would integrate a dynamic team within the pharmaceutical biochemistry lab at the school of pharmaceutical sciences, under the supervision of Dr. Oscar Vadas. The project will use structural information obtained from x-ray structures and Hydrogen/deuterium exchange-mass spectrometry (HDX-MS) data to guide biophysical, in vitro activity assays and cellular experiments. The University of Geneva possesses extensive crystallographic resources, including nanoliter-scale liquid-handling robots, in-house X-ray generator and has access to synchrotron beam time. Successful candidate would benefit from the cutting-edge instrumentation in biochemistry, drug discovery and cell biology that is available within the faculty of sciences. Candidates should send a cover letter, CV and contact information of three references to Oscar Vadas at oscar.va...@unige.ch mailto:oscar.va...@unige.ch Best, Oscar Oscar VADAS Maître Assistant University of Geneva Pharmaceutical biochemistry Science II, lab 4-424 Quai Ernest-Ansermet 30 1211 Geneva 4 Tel: +41 22 379 33 76 Mail: oscar.va...@unige.ch
Re: [ccp4bb] Docking models into low-res SAD map
When we have needed to do something like this, the following procedure has worked pretty well for us: 1. Define the volume containing the density into which a model should be docked (most easily as atoms in a PDB file specifying the centres of spheres), then get structure factors corresponding to cut-out density (using cmapcut in CCP4 or phenix.cut_out_density in Phenix). 2. Do a rotation search in Phaser, treating the structure factors from the cut-out density as observed data. 3. Use the phased translation function (program fft in CCP4) to place the oriented model(s) in the cut-out density. With the availability of cmapcut and phenix.cut_out_density, this is much easier than it used to be, but we've still been intending to streamline this process; this is on our very long to-do list. In principle, FFFEAR ought to work for any problem where this works, but I haven't had much luck -- probably I've been doing something wrong! The next time I have a problem like this, I'll have to try Situs colores, which I hadn't heard about until this discussion. Best wishes, Randy Read On 19 Sep 2013, at 16:03, Pete Meyer pame...@mcw.edu wrote: Another vote for Situs colores - we've had very good luck with using it to dock domain structures into low resolution multi-crystal SAD maps. Pete Oliver Clarke wrote: Hi all, Can anyone recommend software to dock previously solved domains into a (very) low-resolution experimentally phased map? I am working on a rather marginal case where this would be useful - very large assembly (500kDA per ASU), native goes to 6.9A, and the best derivative goes to 8A with SAD phases from a heavy atom cluster to 11. Unfortunately no NCS is present. The map is (for the resolution!) not too bad - the solvent boundary is clear after SHELXE, and I can manually place a previously solved structure and get a reasonably convincing fit (and the fit I obtain agrees with that previously determined using CryoEM by another group). There are a couple of other domains that I would like to place, and I believe I have some idea of where they are, but manual fitting is somewhat subjective, so I'd like an automated routine for doing the same - something like the functionality that ADP_EM provides when working with CryoEM maps. Does something like this exist? I tried using ADP_EM but it gives a segfault when used with a crystallographic density map. I have tried using MOLREP to look for the model in the map to no avail, and PHASER didn't work either. On another note, if anyone has any tips for density modification/phase extension in this resolution range I would love to hear them - haven't had a whole lot of luck with PARROT, DM, or SOLOMON, the maps seem stuck at ~10A despite data going to 8. I tried using SHARP with the SPHCLUSTER tag on, but it gave no improvement over what I obtain treating the cluster as a super atom in SHELXD. Many thanks in advance! Oliver. -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
[ccp4bb] Post-doctoral position at Diamond Light Source in Experimental Phasing
Dear All, For anyone out there with an interest in methods development for experimental phasing we would like to draw your attention to a post-doctoral position currently available at Diamond Light Source: http://www.diamond.ac.uk/Home/Jobs/Current/DIA0868_SB.html This position is in collaboration with our MX colleagues at Synchrotron Soleil near Paris and hence will involve some international travel. The candidate will be joining a vibrant team of MX developers at Diamond Light Source, working on areas from automated data processing and analysis through to the development of new integration software. For further information please contact Graeme Winter ( graeme.win...@diamond.ac.uk) or Dave Hall (david.h...@diamond.ac.uk) though for applications please use the link above. The closing date is the end of September. Best wishes, Graeme and Dave
Re: [ccp4bb] Docking models into low-res SAD map
Hi Oliver, Use CHIMERA- http://www.cgl.ucsf.edu/chimera/ There are video tutorials for docking- http://www.cgl.ucsf.edu/chimera/videodoc/videodoc.html This is a very good package. While I have used Situs colores, I find this package more versatile and useful. You can also use Pymol (but I think thats not free any more??). Best Dr. Anindito Sen (Ph.D) Structural Biology Graduate School of Medicine University of Tokyo 7-3-1 Hongo. Bunkyo-ku. Tokyo 113-0033. Japan Tel Fax: +81-3-5841-3339 On Sep 20, 2013, at 7:09 PM, Randy Read wrote: When we have needed to do something like this, the following procedure has worked pretty well for us: 1. Define the volume containing the density into which a model should be docked (most easily as atoms in a PDB file specifying the centres of spheres), then get structure factors corresponding to cut-out density (using cmapcut in CCP4 or phenix.cut_out_density in Phenix). 2. Do a rotation search in Phaser, treating the structure factors from the cut-out density as observed data. 3. Use the phased translation function (program fft in CCP4) to place the oriented model(s) in the cut-out density. With the availability of cmapcut and phenix.cut_out_density, this is much easier than it used to be, but we've still been intending to streamline this process; this is on our very long to-do list. In principle, FFFEAR ought to work for any problem where this works, but I haven't had much luck -- probably I've been doing something wrong! The next time I have a problem like this, I'll have to try Situs colores, which I hadn't heard about until this discussion. Best wishes, Randy Read On 19 Sep 2013, at 16:03, Pete Meyer pame...@mcw.edu wrote: Another vote for Situs colores - we've had very good luck with using it to dock domain structures into low resolution multi-crystal SAD maps. Pete Oliver Clarke wrote: Hi all, Can anyone recommend software to dock previously solved domains into a (very) low-resolution experimentally phased map? I am working on a rather marginal case where this would be useful - very large assembly (500kDA per ASU), native goes to 6.9A, and the best derivative goes to 8A with SAD phases from a heavy atom cluster to 11. Unfortunately no NCS is present. The map is (for the resolution!) not too bad - the solvent boundary is clear after SHELXE, and I can manually place a previously solved structure and get a reasonably convincing fit (and the fit I obtain agrees with that previously determined using CryoEM by another group). There are a couple of other domains that I would like to place, and I believe I have some idea of where they are, but manual fitting is somewhat subjective, so I'd like an automated routine for doing the same - something like the functionality that ADP_EM provides when working with CryoEM maps. Does something like this exist? I tried using ADP_EM but it gives a segfault when used with a crystallographic density map. I have tried using MOLREP to look for the model in the map to no avail, and PHASER didn't work either. On another note, if anyone has any tips for density modification/phase extension in this resolution range I would love to hear them - haven't had a whole lot of luck with PARROT, DM, or SOLOMON, the maps seem stuck at ~10A despite data going to 8. I tried using SHARP with the SPHCLUSTER tag on, but it gave no improvement over what I obtain treating the cluster as a super atom in SHELXD. Many thanks in advance! Oliver. -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] Code to handle the syntax of (mm)CIF data correctly.
On Thu, 2013-09-19 at 18:00 +0100, Marcin Wojdyr wrote: On Thu, Sep 19, 2013 at 04:38:12PM +0100, Peter Keller wrote: If there are discrepancies between IUCR website and IT vol.G and it would be worth to list them. It is not a matter of discrepancies: they are rather different, and if you are active in this area, you really need to see the IT ones as well. I'm not active, but after finding and opening IT vol. G on page 28 I see exactly the same lines that you gave as examples. So I'm not convinced. OK - all that means is that the grammar in chapter 2.2 suffers from the same problem as the one on the IUCr's web pages, i.e. if you translate it directly into the input for a parser generator like yacc, bison or ANTLR, that parser won't work properly. The STAR grammar in chapter 2.1 is the accurate one. If you look at page 18, you will see that the productions for quoted text strings are completely different from the ones in chapter 2.2. I accept that it is also more complex than the grammar in chapter 2.2, and unfortunately that complexity has to be catered for correctly in code that reads and writes CIF's. Failure to do this creates dialects of CIF. Where incompatibilities between these dialects are encountered, it is users rather than developers that are first faced with the (massively irritating) task of translating their data from one dialect to another, not developers. This is why it is important that developers get this correct from the start, either by making the effort to understand the formats that they are dealing with fully, or by using code/libraries written by other developers who have made that effort. This, of course, is where this whole thread started :-) Regards, Peter. -- Peter Keller Tel.: +44 (0)1223 353033 Global Phasing Ltd., Fax.: +44 (0)1223 366889 Sheraton House, Castle Park, Cambridge CB3 0AX United Kingdom
Re: [ccp4bb] Docking models into low-res SAD map
Hi Anindito Sen 2013/9/20 Anindito Sen andysen.to...@gmail.com skip . You can also use Pymol (but I think thats not free any more??). /skip I do not know what your definition of free is, but PyMOL is an open-source project. You can download the code from http://sourceforge.net/projects/pymol/ To me, that means free. It is also possible to pay for PyMOL http://www.pymol.org/pymol which will give you an easy installer for windows and support amongst other things. Sorry for the OT post, Folmer -- Folmer Fredslund
Re: [ccp4bb] Docking models into low-res SAD map
Hi Folmer, As I said- I think its not free any more is indicative that I am not sure of its status. In addition to that I do not use Pymol much. Thanks for the correction. Best Dr. Anindito Sen (Ph.D) Department of Cell Biology Anatomy Graduate School of Medicine University of Tokyo Tel fax: +81-3-5841-3339 On Sep 20, 2013, at 8:23 PM, Folmer Fredslund folm...@gmail.com wrote: Hi Anindito Sen 2013/9/20 Anindito Sen andysen.to...@gmail.com skip . You can also use Pymol (but I think thats not free any more??). /skip I do not know what your definition of free is, but PyMOL is an open-source project. You can download the code from http://sourceforge.net/projects/pymol/ To me, that means free. It is also possible to pay for PyMOL http://www.pymol.org/pymol which will give you an easy installer for windows and support amongst other things. Sorry for the OT post, Folmer -- Folmer Fredslund
[ccp4bb] Is anyone interested in sponsoring a Master’s student research in the US
Hi All, Sorry for the non-CCP4 issue. A student I am mentoring asked me for a favor to post this information. A German master student is looking for a research opportunity for half a year in the US. He has experience with chromatography and has some research work at Roche. Please either email me or the student at sergest...@mytum.demailto:sergest...@mytum.de for his CV if you are interested. Thank you and I apologize again for the non-ccp4 post. Zhen From: Sachnik, Thomas Sent: Thursday, September 19, 2013 5:00 PM To: Zhang, Zhen Subject: Just in case... Hi Zhen, In case you know somebody, who is working a lot with chromatography and needs some help, I attached the resume of a friend, who has quite a lot experience for a student in downstream processing. He would like to do his Master’s research project in the US too. He is a very dependable person. We studied together in Munich and he also did his Bachelor’s research project at Roche in Basel, Switzerland. He is seeking for a 6 months project beginning in February 2014. Just in case... Thanks, Thomas The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [ccp4bb] Code to handle the syntax of (mm)CIF data correctly.
On Fri, Sep 20, 2013 at 11:51:57AM +0100, Peter Keller wrote: The STAR grammar in chapter 2.1 is the accurate one. If you look at page 18, you will see that the productions for quoted text strings are completely different from the ones in chapter 2.2. Different, but look equivalent to me. But clearly there are differences between STAR and CIF grammars. I'm not interested enough in these format to continue this thread much longer. When I was writing CIF parser 5 years ago I also had impression that there are mistakes in the CIF spec. If that's true, IMO listing (and then fixing) these mistakes can prevent different CIF dialects. Recommending STAR spec as extra reading can't. Regards Marcin -- Scanned by iCritical.
Re: [ccp4bb] Code to handle the syntax of (mm)CIF data correctly.
On Fri, 2013-09-20 at 17:30 +0100, Marcin Wojdyr wrote: On Fri, Sep 20, 2013 at 11:51:57AM +0100, Peter Keller wrote: The STAR grammar in chapter 2.1 is the accurate one. If you look at page 18, you will see that the productions for quoted text strings are completely different from the ones in chapter 2.2. Different, but look equivalent to me. In principle, they should be equivalent, but in practice as I explained the CIF grammar has at least one ambiguity that doesn't exist in the STAR grammar But clearly there are differences between STAR and CIF grammars. I'm not interested enough in these format to continue this thread much longer. When I was writing CIF parser 5 years ago I also had impression that there are mistakes in the CIF spec. and probably errors too, as you have noticed. If that's true, IMO listing (and then fixing) these mistakes can prevent different CIF dialects. Well, by itself that is not sufficient, but it would certainly help. I'm not sure that there is anyone around who has both sufficient clout and also the interest to make sure that those fixes become authoritative, although I have no objection to being proved wrong about that of course. CIF has been around a long time, and the fact that ambiguities and errors in the specification can still form a subject for discussion seems unfortunate to me. Recommending STAR spec as extra reading can't. Like you I think that this thread is becoming unproductive, but I have to close by insisting that the STAR spec has an important role to play in the (mm)CIF developers' world at the present time, because: * All CIF data has to conform to the STAR syntax (Int Tab G, section 2.2.1). * The STAR specification as far as I can see is free of errors and ambiguities. Therefore, the STAR spec is authoritative as far as the lexical and syntactical aspects of CIF are concerned (although clearly not for semantic issues). Regards, Peter. -- Peter Keller Tel.: +44 (0)1223 353033 Global Phasing Ltd., Fax.: +44 (0)1223 366889 Sheraton House, Castle Park, Cambridge CB3 0AX United Kingdom
[ccp4bb] acetylated methionine
I am trying to include a N-terminal acetylated methionine in my model. I replaced my methionine with a AME residue from the pdb data bank and included a link command to connect the C from AME with the N of the second residue. The AME is defined as HETATM. When I try to regularize this structure in Coot it doesn't recognize that the 1. and 2. residue should stay connected. What or how do I need to define this residue or the connection so that I can model in Coot and refine in Phenix? -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220
