[ccp4bb] OIST-CCP4 workshop in Okinawa, 5-9 December 2011
Dear Colleagues, we are pleased to announce the first CCP4 structure solution school at the Okinawa Institute of Science and Technology (OIST), Okinawa. All details can be found at http://www.ccp4.ac.uk/schools/OIST-2011/index.php Title: CCP4 school: From data processing to structure refinement and beyond Dates: December 5 to 9. Site: Okinawa Institute of Science and Technology, Okinawa, Japan The school content: Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three Sections - lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets so the problems can be addressed during data collection workshop and/or hands-on sessions. Application: Application deadline is end October. Application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/OIST-2011/index.php Fees: There is no fee for the workshop. The students will be responsible for their transportation costs outside Okinawa. Lodging will be provided at the OIST Guest House Seaside House. The workshop will also cover the expenses for all meals and refreshments. Fadel Samatay, Charles Ballard, Garib Murshudov
[ccp4bb] Hexagonal myoglobin protocol
Dear CCP4BB, I need to grow some myoglobin crystals for testing and ideally they need to be hexagonal. I was wondering if anyone had a protocol which gives these reliably? Thanks in advance for any replies James Hall PhD Student University of Reading
[ccp4bb] Post-doctoral position for structural studies on multifunctional intrinsically disordered actin-binding domains, CNRS, in Paris suburbs, France
*A 2-year post-doctoral position for structural studies on modular proteins containing multifunctional intrinsically disordered actin-binding domains is available at the Laboratory of Structural Enzymology and Biochemistry (LEBS), CNRS, in Paris suburbs, France. Starting date: October/november 2011. European funding - monthly gross salary: ~ 2 500 euros.* *_Project:_*** *Structural basis governing the functional versatility of intrinsically disordered WH2 domains in actin assembly dynamics*** ** *_Job description:_* ***The actin cytoskeleton**relies on the ability of actin ATPase to self-assemble into polarized filaments which provide in all cells mechanical force for cell shape maintenance, traffic or membrane deformation. It forms a dynamic structural network constantly remodeled in non-muscle cells by many actin-binding proteins.* *The postdoctoral research project**study **the structural basis governing the functional versatility of ?-thymosin **(**?T) **and WH2 domains in actin self-assembly dynamics.**These smallubiquitous actin-binding domains are intrinsically disordered but functional with highly variable sequences. Found as single or repeated modules in numerous signalling modular proteins they appear to regulate very versatile functions in **actin assembly dynamics[recent reviews: **Husson**et al. (2010) Annals of the New York Academy of Sciences 1194, 44-52; Carlier et al., (2011) **Int Rev Cell Mol Biol**. 2011;290:55-85**]. * *We try to establish the structure-function relationship of ?T/WH2 domains and the structural basis of their multifunctionality**through a multidisciplinary approachintegratingbiochemical studies(**rapid kinetics **mechanisms ofprotein-protein interactionandself-assemblyof actin**), biophysical **(**hydrodynamic **characterizations**, epi**fluorescence microscopyin reconstitutedmotility medium**) and **structural(small-angleX-ray scatteringin solution andX-ray crystallography**). These techniques are used (**1) to identifyin vitroallexisting activities**in actin assembly found **in differentmodularmodel WH2-containing proteinsregulating massive actin assembly incell migration**, **developmental processes **or**bacterial **pathogen invasion**, **and (2) to understandhow these functionsare regulatedby smallsequence variations**, their **intrinsic flexibility**, some **arrangements**in **repeats or associationswith other**regulatory **adjacentdomains **[Bosch et al. (2007) Molecular Cell 28, 555-68; **Husson et al. (2011) Molecular Cell 43, 464-77]. * *The laboratory LEBS at CNRS provides state-of-the-art equipment for protein expression, purification and characterisations by biochemical and biophysical methods. Crystallization robotics are available in-house and we have regular access to synchrotron sources. * * **_Skills required:_* *The successful candidate should have a PhD in biochemistry/structural biology/biophysics/biology with less than 3-4 years postdoctoral experience and strong practical skills in molecular biology and protein crystallography, with strong interests for multidisciplinary approaches on protein-protein interactions **(**www.lebs.cnrs-gif.fr/carlier/carliereng.html http://www.lebs.cnrs-gif.fr/carlier/carliereng.html**)**.* * **_Location: _**The laboratory is located in a very pleasant green setting within the large CNRS campus of Gif-sur-Yvette which is 45 mn away from **Paris**via local railway (RER B). We benefit from a dynamic scientific surrounding, in close vicinity to Paris labs, Orsay University, the Atomic Energy Commissariat (CEA) center of Saclay and the SOLEIL synchrotron (5 min away by car).* ** *_Contact: _* *Please send a CV, a short summary of your research experience and letters of recommendation of two referees to Louis Renault (renault_at_lebs.cnrs-gif.fr). I will be happy to provide further information to interested candidates.* -- *** Louis RENAULT Laboratoire d'Enzymologie et Biochimie Structurales (LEBS) Bat. 34, CNRS, 1, avenue de la Terrasse 91 198 Gif-sur-Yvette cedex, FRANCE Phone: (+)33-1 69 82 34 89 (inside France: 01 69 82 34 89) Fax: (+)33-1 69 82 31 29 email: louis.rena...@lebs.cnrs-gif.fr ***
[ccp4bb] Vacancy at PDBe for an enthusiastic junior annotator
Hi all, The Protein Data Bank in Europe (PDBe; pdbe.org) is looking to recruit an expert structural biologist to join the PDBe curation team at the EBI near Cambridge, UK. Applicants should be computer-literate and possess a recent PhD in some area of structural biology or structural chemistry as well as a broad knowledge in molecular biology or biochemistry. An in-depth knowledge of protein structure (including structure determination, analysis and validation) is essential. A few years of post-doctoral research experience in structural biology, as well as hands-on experience in the determination of protein structure is highly desirable. The ideal candidate will be familiar with Linux/Unix operating systems and molecular graphics software. Basic programming skills, e.g. with Perl, Python or Java, would be an advantage. Given the extensive interactions with colleagues in the PDBe team as well as with international collaborators, depositors and users, excellent written and oral communication skills, fluency in English, ability to work in a team and attention to detail are required. More details and a link to the electronic application procedure can be found here: http://ig14.i-grasp.com/fe/tpl_embl01.asp?s=MbkMjPUrEcTFkHhTczjobid=46332,8998483234 Feel free to pass this on to suitable candidates! --Gerard PS: Some hints for prospective applicants: it doesn't hurt to add a nice cover letter in which you explain why you would love to be a PDB annotator and why PDBe strikes you as a brilliant place to work. Also, if you should get invited for an interview and we ask you what the main colour of our website is, please don't answer blue... --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
Re: [ccp4bb] map file specification
Hi Pascal, This document makes an attempt at an explanation, but in a somewhat obtuse way: http://conventions.cnb.uam.es/References/maplib.html. The important point is that the machine stamp is 4 bytes that are specific for the architecture that wrote the file. For little endian hardware the stamp is 0x44, 0x41, 0x00, 0x00 while the big endian stamp is 0x11, 0x11, 0x00, 0x00. Cheers -- David On 20 September 2011 16:06, Pascal pascal...@parois.net wrote: On 09/15/2011 09:30 AM, Pascal wrote: I am looking at the specifications of the ccp4 map file format and I am confused with the number of columns and the number of intervals. Thanks for all the answers. I can almost write a map file. Only one problem remain: what is the machine stamp (element 54)? What should I put there? A small fortran program is used to write the file. Pascal
[ccp4bb] Beamline Scientist position available for macromolecular crystallography beamlines at NSLS-II
The Photon Sciences Directorate at Brookhaven National Laboratory is seeking an experienced scientist to lead the effort in the development of a pair of canted macromolecular crystallography beamlines at NSLS-II, which is a new third-generation synchrotron facility being constructed on Long Island, New York, with extremely high brightness and exceptional beam stability over a wide spectral range. As the Group Leader, the selected candidate will lead a group of scientific and engineering staff to design, build, and commission a pair of state-of-the-art macromolecular crystallography beamlines, known as (1) the Frontier Macromolecular Crystallography (FMX) beamline and (2) the Highly Automated Beamline for Macromolecular Crystallography (AMX) beamline. Please see http://www.bnl.gov/nsls2/beamlines/2010BeamlineProposal-Approved.asp for more information. Responsibilities include interacting with the scientific user community to define the mission and technical scope of the beamline and managing all aspects of the beamline design, construction, and commissioning, including aspects associated with work planning and execution and cost and schedule performance reporting. For more information and to apply, go to: http://www.bnl.gov/HR/careers/
[ccp4bb] Beamline Scientist position available for small- and wide- angle x-ray scattering beamline at NSLS-II
The Photon Sciences Directorate at Brookhaven National Laboratory is seeking an experienced scientist to lead the effort in the development of a small- and wide-angle x-ray scattering (SAXS/WAXS) beamline at NSLS-II, which is a new third-generation synchrotron facility being constructed on Long Island, New York, with extremely high brightness and exceptional beam stability over a wide spectral range. As the Group Leader, the selected candidate will lead a group of scientific and engineering staff to design, build, and commission a state of the art SAXS/WAXS beam line, known as High Brilliance X-ray Scattering for Life Sciences (LIX), and it’s associated scientific programs at NSLS-II; please see http://www.bnl.gov/nsls2/beamlines/2010BeamlineProposal-Approved.asp for more information. Responsibilities include interacting with the scientific user community to define the mission and technical scope of the beamline and managing all aspects of the beamline design, construction, and commissioning, including aspects associated with work planning and execution and cost and schedule performance reporting. For more information and to apply, go to: http://www.bnl.gov/HR/careers/
[ccp4bb] Setup pymol in Mac OS X 10.7
Dear members, I want to setup pymol in Mac OS X 10.7, but I didn't do this before. Who can tell me how to setup and tell me the detail setup procedure. and if need other programs to setup this. Thank you very much!
[ccp4bb] off topic: Another protein forming gel
Hi all I am working with a human protein (not membrane protein) which is forming gel at higher concentration. I am not able to concentrate the protein even more than 7 mg/ml. It become like jelly which is hard to pipette out. I have gone through all the suggestions which you guys proposed very recently for another member. what i mean that i already have tried different temperature, pH, salt concentration, reducing agents (DTT, TCEF, in different concentration), stability analysis. But unfortunately nothing is working. One think i want to try to add some detergent to it. If you guys have any experience about it then please suggest the name and/or kind of detergent for the protein. Any other suggestion also appreciated which might help. cheers M. Obayed Ullah E.mail: obayed.o...@yahoo.com obayed.o...@gmail.com
[ccp4bb] off topic: Another protein forming gel
Hi all I am working with a human protein (not membrane protein) which is forming gel at higher concentration. I am not able to concentrate the protein even more than 7 mg/ml. It become like jelly which is hard to pipette out. I have gone through all the suggestions which you guys proposed very recently for another member. what i mean that i already have tried different temperature, pH, salt concentration, reducing agents (DTT, TCEF, in different concentration), stability analysis. But unfortunately nothing is working. One think i want to try to add some detergent to it. If you guys have any experience about it then please suggest the name and/or kind of detergent for the protein. Any other suggestion also appreciated which might help. cheers M. Obayed Ullah E.mail: obayed.o...@yahoo.com obayed.o...@gmail.com
