[ccp4bb] Junior research position in Structural Biology
***NB: Posted on behalf of Dr. Macedo-Ribeiro, whom you should contact for further information (e-mail address below).*** The Associate Laboratory IBMC-INEB is recruiting a highly motivated researcher to integrate a multidisciplinary team in the field of the Biochemistry and Structural Biology of enzymes associated with human diseases. A PhD in the appropriate disciplines is mandatory. Previous post-doctoral research experience and demonstrated skills in Biochemistry and Structural Biology are required. Contract: The fixed term contract is limited to 28 months and expected to begin on March 1st 2013. The monthly gross salary amounts to 3.191,82 Euros. Job description: The regulation of biological and pathological processes is achievable through specific inhibition, spatial and temporal compartmentalization, and post-translational modification of the intervening enzymes. Impairment of any of these regulative mechanisms often results in serious pathologies to which specific therapeutic approaches can be conceived by understanding the molecular details of enzyme specificity, as well as of their strict regulation. In order to address the role played by macromolecular interactions and/or regulation by post-translational modifications in enzyme activity and specificity, we use protein X-ray crystallography along with a plethora of complementary biophysical/biochemical techniques. We are especially interested in elucidating the molecular mechanisms of action of proteins associated with neurodegenerative and infectious diseases ( http://www.ibmc.up.pt/research/research-groups/protein-crystallography). Application deadline: 20/01/2013 All details required for application can be found at: http://www.eracareers.pt/opportunities/index.aspx?task=globaljobId=32498 Applications must be submitted online: http://www.ibmc.up.pt/institute/open-positions (position Ciência 2008 Substituição--CONT_DOUT/23/IBMC/316/10253/17/2008). For more information please contact: Dr. Sandra Macedo-Ribeiro Protein Crystallography Group IBMC- Instituto de Biologia Molecular e Celular Rua do Campo Alegre, 823 4150-180 Porto, Portugal (sribeiro_at_ibmc.up.pt) -- Pedro J. B. Pereira, PhD IBMC - Biomolecular Structure Group Rua do Campo Alegre, 823 4150-180 Porto Portugal Tel. +351 226 074 900 Fax +351 226 099 157 E-mail ppere...@ibmc.up.pt
[ccp4bb] Job Opportunity at Rigaku Automation
Hello My colleagues at Rigaku Automation based in Carlsbad, California are looking to recruit a Research Scientist. Please feel free to forward to anyone in your group who may be interested. Information on Rigaku Automation and its products can be found here: http://www.rigakuautomation.com Research Scientist – Protein Crystallization / Protein Crystallography Rigaku Automation is a premier provider of lab automation equipment to structural biology labs worldwide, specializing in protein crystallization. Looking for an equally motivated and experienced protein crystallographer to join our team in Carlsbad, CA USA. Full benefits package. Send resume to raij...@rigaku.commailto:raij...@rigaku.com Essential Duties and Responsibilities (Additional duties may be assigned.) · Contribute to the design, development, and testing of new lab automation products. · Perform experiments that illustrate and exemplify the needs of the scientific community. · Act as a scientific advisor to the company by evaluating novel scientific methods in terms of their potential to define new products or by conducting experiments that drive enhancements of existing ones. Qualifications · Ph.D. in protein crystallography; work experience outside academia strongly preferred. · Proven experience with lab automation and detailed knowledge on lab workflows and research methodologies, especially in relation to protein crystallization. · Demonstrated ability to work in team environments and impact collaborative efforts by independent, creative, scientific thinking. · Excellent communicator and ability to present and document scientific findings and thought processes. Informal enquiries can be made to Alice Sorensen: alice.soren...@rigaku.commailto:alice.soren...@rigaku.com Thanks Mark Rigaku Europe
[ccp4bb] The Institut de Biologie Structurale Jean-Pierre Ebel has a vacancy for a PhD Student
Crystallization with an automated microfluidic pipeline: from crystal screening to crystal mounting A PhD position, funded by the CEA, is available in the Synchrotron Group at the Institut de Biologie Structurale (IBS) at Grenoble, starting in Autumn 2013. IBS is located next to two large European research facilities for X-ray and neutron science: the ILL and the ESRF. The project aims at developing an automated microfluidic pipeline for protein crystallization. The microfluidic chip to be developed will combine the control of temperature and precipitant concentration in a user-friendly setup. It will allow systematic optimization based on the phase diagram, direct in situ X-ray screening and data collection. The pipeline consists of three elements: the microchip for screening, the optimization platform and robotic crystal mounting. This system will be tested with several structure solution projects in which the Synchrotron Group is involved, and where crystal optimization is difficult, including large protein complexes (Cdk cyclins) and membrane proteins. We hope that the new device will help move forward during the course of the thesis on several of these challenging projects. We are looking for an enthusiastic academically qualified biophysicist, physico-chemist or engineer with a strong interest in structural biology and multi-disciplinary problems. Experience in macromolecular crystallization and or crystallography is an advantage. Given the scope of the project and the need for a close collaboration with the other team members as well as with the industrial/external partners excellent communication skills and the ability to work as part of a team of biologists and engineers are prerequisites. More information on the PhD position can be obtained from: Monika Budayova-Spano, PhD Assistant Professor, Faculty of Pharmacy, University Joseph Fourier Synchrotron Group Institut de Biologie Structurale J. P. Ebel CEA-CNRS-UJF UMR 5075 41, Rue Jules Horowitz 38027 Grenoble cedex 1 Tel: + 33 4 38 78 96 13 Fax: + 33 4 38 78 51 22 Email: monika.sp...@ibs.fr Applications including: a detailed resume, a covering letter explaining the applicant’s motivation for the position, detailed exam results and the name and contact details of at least two references should be sent to monika.sp...@ibs.fr and to jean-luc.fer...@ibs.fr.
[ccp4bb] ESRF Users' Meeting 2013 Associated Structural Biology Workshop
Hello Everybody, The ESRF Users' Meeting, to be held in Grenoble from 4-6 February 2013, will focus on plans for Phase II of the ESRF Upgrade Programe. Current proposals include a major upgrade of the existing ESRF storage ring which will boost brilliance by a factor of 30 or more, providing access to flux densities in excess of 10^14 photon/s/micron^2 . In parallel with this year's Users' Meeting we are organising a workshop 'Seeing is believing: the future of Structural Biology'. The aims of the workshop are to present technical details of the proposed upgrade, to outline ideas for new scientific opportunities that will arise, to explore the limits of Structural Biology at a synchrotron source and to promote meaningful discussions between the ESRF and its User Community that will help formulate the scientific case for the future of Structural Biology at the ESRF. The program for the Workshop along with details of how to register for both the workshop and the Users' Meeting can be found at: http://www.esrf.fr/events/conferences/users-meeting-2013-and-workshops/workshop-seeing-is-believing-the-future-of-structural-biology I encourage as many of our current and future users to attend. With very best wishes for 2013. Yours Gordon
[ccp4bb] Crystallization with acidic bicelles
Hello, Does anyone have any experience working with acidic bicelles for crystallization of membrane proteins? I am working with a small (~100 amino acid), trimeric protein that is not a membrane protein itself but is only fully folded when in the presence of an anionic membrane mimetic, such as PC:PA liposomes or SDS. I would like to try crystallization with DMPC:DHPC bicelles spiked with DMPA but cannot find a good protocol for making this type of bicelle. I have tried adapting the protocol from JOVE by Ujwal and Abramson with no success. Also, what would be a good q value to start with, given that I do not know anything about the footprint of my protein? From what I have read, small q ratios (~1) seem to be good for high resolution structure work, but this comes mostly from the NMR field. Thanks! Jessica Jessica Silverman Molecular Microbiology PhD Candidate Heldwein Laboratory, A611 Tufts University School of Medicine 136 Harrison Ave., Boston, MA phone: 617-636-0474 email: jessica.silver...@tufts.edu
Re: [ccp4bb] Who invented PDB format?
Hi, I appreciate If anybody help me couple of things as follows. (a1) how multiple PDBs (of same or different space groups) can be brought into one frame of coordinates, when dealing with many PDBs? (a2) how does one get scatter plot? (b) how easily can symmetry related units of original PDB (with description of which symmetry element has been used) be made when dealing with many PDBs . Thank you, Teri
[ccp4bb] MX BAG training at Diamond Light Source
To all Diamond MX BAG Users, Diamond Light Source will be holding the next training day for MX BAG Users on Wednesday 27th February 2013. The aim of the day is to provide BAG users with sufficient training to be able to operate any of the Diamond MX beamlines efficiently and get the most benefit from their beamtime. It is essential that each BAG sends at least one representative per calendar year. Sessions include: -Automation In Data Analysis and Remote access -Mini-Kappa Goniometer -Sample Humidity Control (HC1) -Microbeam Crystallography -In Situ Diffraction -New GDA Client and ISPyB Registration is free-of-charge with lunch provided on the 27th February and accommodation and dinner for the night of the 26th February. Travelling expenses within the UK will also be provided. The training is targeted at all BAG members and is not limited to students and post docs. Individuals wishing to register should register here: http://www.diamond.ac.uk/Home/Events/MX-BAG-training.html Early registration is recommended as places are limited to twenty and registration deadline is on 4th February. Best wishes, Jitka Waterman -- 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] Convert cbf to png/tiff?
Hello all - anybody know an easy way to convert CBF images (Pilatus) into something lossless like tiff or png? Ideally *easy* as in r e a l l y e a s y and not requiring extensive installation of dependencies and stuff. Because then I might as well write my own stuff using cbflib and PIL in python. Thanks! phx
Re: [ccp4bb] Convert cbf to png/tiff?
I think ADXV will do the trick. Regards, Dmitry On 2013-01-10, at 3:36 PM, Frank von Delft wrote: Hello all - anybody know an easy way to convert CBF images (Pilatus) into something lossless like tiff or png? Ideally *easy* as in r e a l l y e a s y and not requiring extensive installation of dependencies and stuff. Because then I might as well write my own stuff using cbflib and PIL in python. Thanks! phx
Re: [ccp4bb] Convert cbf to png/tiff?
adxv reads cbf images, and can save them as postscript (actually, it's supposed to be able to save the image as tiff as well, but at least on my version of the program that feature doesn't work). Pat On 10 Jan 2013, at 3:36 PM, Frank von Delft wrote: Hello all - anybody know an easy way to convert CBF images (Pilatus) into something lossless like tiff or png? Ideally *easy* as in r e a l l y e a s y and not requiring extensive installation of dependencies and stuff. Because then I might as well write my own stuff using cbflib and PIL in python. Thanks! phx --- 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
[ccp4bb] Fwd: Re: [ccp4bb] Convert cbf to png/tiff?
Brilliant - thanks Nat!! Easy to work around that feature. And thanks Nick!! Original Message Subject:Re: [ccp4bb] Convert cbf to png/tiff? Date: Thu, 10 Jan 2013 12:47:21 -0800 From: Nat Echols nathaniel.ech...@gmail.com To: Frank von Delft frank.vonde...@sgc.ox.ac.uk Using any recent Phenix distribution: labelit.png file_name For reasons unknown to me, the output is named plain.png - I will bug Nick about this. On Thu, Jan 10, 2013 at 12:36 PM, Frank von Delft frank.vonde...@sgc.ox.ac.uk wrote: Hello all - anybody know an easy way to convert CBF images (Pilatus) into something lossless like tiff or png? Ideally *easy* as in r e a l l y e a s y and not requiring extensive installation of dependencies and stuff. Because then I might as well write my own stuff using cbflib and PIL in python. Thanks! phx
Re: [ccp4bb] Who invented PDB format?
On Jan 10, 2013, at 18:27 , Teri Arman teriar...@gmail.com wrote: Hi, I appreciate If anybody help me couple of things as follows. (a1) how multiple PDBs (of same or different space groups) can be brought into one frame of coordinates, when dealing with many PDBs? You mean that axes of inertia of the same molecule in the different structures(PDB's) - L,M,N are superimposed? You superimpose… :-) (a2) how does one get scatter plot? Scatter of what? :-0 (b) how easily can symmetry related units of original PDB (with description of which symmetry element has been used) be made when dealing with many PDBs . You have to explain better what are you meaning. :-\ Thank you, Teri Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608
[ccp4bb] Symmetry operator
Hi, Which program outputs the symmetry operator (rotation and translation)? I have a dimer in the asymmetric unit and need to know the symmetry operator to get a tetramer, the active molecule. James
Re: [ccp4bb] Symmetry operator
The transformation matrix describing the symmetry is sensitive to the coordinate system origin. You should center the entire tetramer on the origin (0, 0, 0), where the origin coincides with the point symmetry element. If you have a tetramer with true point symmetry, then the center of the tetramer should be the center of mass. Then you can use lsq-expl from O or whatever the equivalent is in pymol, phenix, or coot to get the transformation matrix between any two monomers. Repeated application of that transformation matrix to any monomer of the tetramer should generate the tetramer. James On Jan 10, 2013, at 5:48 PM, james09 pruza wrote: Hi, Which program outputs the symmetry operator (rotation and translation)? I have a dimer in the asymmetric unit and need to know the symmetry operator to get a tetramer, the active molecule. James
Re: [ccp4bb] Symmetry operator
coot: show symmetry molecules, then save symmetry molecule and you have your tetramer most likely Jürgen On Jan 10, 2013, at 7:48 PM, james09 pruza wrote: Hi, Which program outputs the symmetry operator (rotation and translation)? I have a dimer in the asymmetric unit and need to know the symmetry operator to get a tetramer, the active molecule. James .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] Symmetry operator
I need to amend that and make a couple of corrections, after thinking about it. First, the rotation-translations shouldn't be sensitive to the origin. Second, if it has C4 (square) symmetry, then you only need one generator (rotation-translation) to make the tetramer, and the two monomers should be adjacent. If it is T4 (tetrahedral) symmetry, then you need two generators, with one generator made from a pair of monomers opposite and one generator made from a pair adjacent. James On Jan 10, 2013, at 6:05 PM, James Stroud wrote: The transformation matrix describing the symmetry is sensitive to the coordinate system origin. You should center the entire tetramer on the origin (0, 0, 0), where the origin coincides with the point symmetry element. If you have a tetramer with true point symmetry, then the center of the tetramer should be the center of mass. Then you can use lsq-expl from O or whatever the equivalent is in pymol, phenix, or coot to get the transformation matrix between any two monomers. Repeated application of that transformation matrix to any monomer of the tetramer should generate the tetramer. James On Jan 10, 2013, at 5:48 PM, james09 pruza wrote: Hi, Which program outputs the symmetry operator (rotation and translation)? I have a dimer in the asymmetric unit and need to know the symmetry operator to get a tetramer, the active molecule. James
Re: [ccp4bb] Who invented PDB format?
Dear Dr. Frolow Thank you for your mail. I stated again, and hope it is clear now. TA. On Fri, Jan 11, 2013 at 4:11 AM, Felix Frolow mbfro...@post.tau.ac.ilwrote: On Jan 10, 2013, at 18:27 , Teri Arman teriar...@gmail.com wrote: Hi, I appreciate If anybody help me couple of things as follows. (a1) how multiple PDBs (of same or different space groups) can be brought into one frame of coordinates, when dealing with many PDBs? TA: Suppose we have a segment of structure (PDB). That segment carries different co-ordinates in different PDBs. How can that segment from hundreds of PDBs be converted so that we can see all converted segments in one frame/window I like to avoid superimposition of hundreds of times You mean that axes of inertia of the same molecule in the different structures(PDB's) - L,M,N are superimposed? You superimpose… :-) (a2) how does one get scatter plot? Scatter of what? :-0 TA: Suppose a surrounding neighbours of a segment as said above. (b) how easily can symmetry related units of original PDB (with description of which symmetry element has been used) be made when dealing with many PDBs . You have to explain better what are you meaning. :-\ TA: Each PDB (X-ray structures) has its own space group. I like to generate symmetry related whole PDB or a segment of it in hundreds of PDBs of different space groups. Thank you, Teri Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608
Re: [ccp4bb] Who invented PDB format?
On Jan 11, 2013, at 03:47 , Teri Arman teriar...@gmail.com wrote: Dear Dr. Frolow Thank you for your mail. I stated again, and hope it is clear now. TA. On Fri, Jan 11, 2013 at 4:11 AM, Felix Frolow mbfro...@post.tau.ac.il wrote: On Jan 10, 2013, at 18:27 , Teri Arman teriar...@gmail.com wrote: Hi, I appreciate If anybody help me couple of things as follows. (a1) how multiple PDBs (of same or different space groups) can be brought into one frame of coordinates, when dealing with many PDBs? TA: Suppose we have a segment of structure (PDB). That segment carries different co-ordinates in different PDBs. How can that segment from hundreds of PDBs be converted so that we can see all converted segments in one frame/window I like to avoid superimposition of hundreds of times Most probably superposition or any other transformation could not be avoided. Properly written script will do it for you You mean that axes of inertia of the same molecule in the different structures(PDB's) - L,M,N are superimposed? You superimpose… :-) (a2) how does one get scatter plot? Scatter of what? :-0 TA: Suppose a surrounding neighbours of a segment as said above. (b) how easily can symmetry related units of original PDB (with description of which symmetry element has been used) be made when dealing with many PDBs . Knowing mathematical manipulation of a crystalline space (symmetry operations) one can write a script that will do it easy. You have to explain better what are you meaning. :-\ TA: Each PDB (X-ray structures) has its own space group. I like to generate symmetry related whole PDB or a segment of it in hundreds of PDBs of different space groups Again you will need to write or to get a script that will do it for you. Script (little or larger piece of software written using one of the shell syntaxes or by modern popular languages such as Python or JavaScript) may be written to expand each structure by symmetry producing set of coordinates of interacting molecules (you decide to what distance or to what neighbouring unit cells you wish to expand your structure, after that you teach your script to make multiple superposition of all to all (maybe difficult task) or one to one taking one of the structure as a master structure to which you superimpose others. After that you probably will which to clean this set of coordinates from expanded molecules that you do not need for your research. Again you can do it manually or writing script. . Thank you, Teri Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608
