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Invitation to Participate in a NSF-funded workshop/conference
by Sibo Jiang 24 May '13

24 May '13

Invitation to Participate in a NSF-funded workshop/conference Dear Colleagues in Structural Biology, Recently we have received a NSF grant helping to build the community networks and find solutions for the challenging problems. We have also discussed with the program officer of US National Science Foundation on planning for a research conference/workshop series proposal to US NSF. This conference/workshop series will particularly focus on the technical issues and practical challenges in structural biology of nucleic acids, protein-nucleic acid complexes and small molecule-nucleic acid complexes. These challenges include crystallization, derivatization, phasing and high-resolution structure determination. You are invited to participate in this conference/workshop series. If you are interested in our invitation, please reply this email or send your email to huang(a)gsu.edu<mailto:[email protected]>. In your email, please let us know your name, research interests (up to five key words), affiliation and phone number. The details will be announced later. Colleagues in academia are encouraged to forward this email to your friends and colleagues in industry. Colleagues in industry are particularly welcome. Sincerely, The Planning Committee of the NSF-funded Conference/Workshop

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FW: need suggestion
by afshan490＠yahoo.com 24 May '13

24 May '13

<br/><br/><br/>Sent from Yahoo! Mail for iPhone

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From Dmitri Svergun and Matthias Wilmanns: 11th International Conference: Biology and Synchrotron Radiation (BSR)
by Terwilliger, Thomas C 24 May '13

24 May '13

11th International Conference: Biology and Synchrotron Radiation (BSR) 8-11 September 2013, EMBL Hamburg, Germany Abstract submission deadline is approaching – 1st June 2013! Join us in Hamburg, Germany for BSR 2013! Scientists at all possible career levels are invited to this meeting. Check out our preliminary programme to learn more! http://www.bsr2013.org/BSR13-01/programme/index.html Young researchers are highly welcome to apply for a travel grant from the International Union of Crystallography when registering. http://www.bsr2013.org/BSR13-01/info/index.html Present your work! Selected talks and poster sessions provide great opportunities for participants to present their work. Unique networking opportunities are also available to meet colleagues, friends and future collaboration partners from all over the world. Discover the city of Hamburg! BSR 2013 includes a social programme with boat trips and day and night excursions. Accompanying persons will enjoy special rates! http://www.bsr2013.org/BSR13-01/attractions/index.html A tour of DESY’s most impressive research infrastructures - including PETRA, FLASH and the future X-FEL – is included in the registration fee. http://www.bsr2013.org/BSR13-01/desy/index.html Dates at a glance: · Registration and abstract submission: 1 June 2013 · Registration without abstract: 1 August 2013 Take a look at the updated BSR webpage (www.bsr2013.org<http://www.bsr2013.org>) for more information and to register. CONTACT Diah.Yulianti(a)embl.de<mailto:[email protected]> Alternatively, contact us on the event facebook page https://www.facebook.com/events/332259356868854/

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Call for Proposals: IMAGINE, a New Neutron Crystallography Diffractometer
by Meilleur, Flora 23 May '13

23 May '13

IMAGINE, Neutron Crystallography Diffractometer High Flux Isotope Reactor (HFIR), Oak Ridge National Laboratory Call for proposals for experiments anticipated to run from August through December 2013 You are invited to apply for beam time on the neutron quasi-Laue diffractometer IMAGINE, at the High Flux Isotope Reactor. Proposal will be accepted via the web-based proposal system until NOON Wednesday, July 31, 2013. This call is for experiments anticipated to run from August through December 2013. Please see the attached flyer for additional information. For technical information about the capabilities of IMAGINE go to neutrons.ornl.gov/imagine/<http://neutrons.ornl.gov/imagine/> or contact Flora Meilleur, meilleurf(a)ornl.gov, or Andrey Kovalevsky, kovalevskyay(a)ornl.gov. Flora Meilleur, Ph. D Assistant Professor, Molecular and Structural Biochemistry North Carolina State University IMAGINE lead scientist, Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

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conflicting bond_simple restraints
by Jianxun Qi 23 May '13

23 May '13

Hi, I had a phosphoserine (SEP) in my structure that is attached in this message. The data_link file for SEP already exists in the mon_lib (data_link_SEPC-N) and the corresponding cif_link I used is as follow: refinement.pdb_interpretation { apply_cif_link { data_link = "SEPC-N" residue_selection_1 = "chain C and resname PHE and resid 3" residue_selection_2 = "chain C and resname SEP and resid 4" } apply_cif_link { data_link = "SEPC-N" residue_selection_1 = "chain C and resname SEP and resid 4" residue_selection_2 = "chain C and resname ARG and resid 5" } } When I run the phenix.refine (my version is phenix-1.8-1069), it said conflicting bond_simple restraints: Sorry: Conflicting bond_simple restraints: 1. definition from: residues: PHE + SEP 2. definition from: residues: PHE + SEP atoms: "ATOM 3121 C PHE C 3 .*. C " "ATOM 3192 N SEP C 4 .*. N " Has anyone ever experienced this case before? Any hints are welcome. Regards Jianxun Qi May 22,2013

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Ca occupancy in multiple soaked structures
by Daniel Slade 23 May '13

23 May '13

Hi Everyone, I have a complex case of data analysis I would love some opinions on. I have a group of structures of a protein that binds 6 calciums, and we want to know the order/concentration at which they fill. The crystals were soaked with calcium from 0-10 mM and all are 1.6-2.1 A in resolution. I determine the order of the calcium binding, and now I am working on the percent occupancy at each concentration. To do this, I have removed the calciums, and then performed simulated annealing for each structure from 2.1-30A resolution to 'normalize' them. I then look at the omit map and scroll out to find the peak sigma intensity of where the calciums should be. The curves fit very well for each calcium, and the numbers correspond well with other solution studies we have. My thought is that I need to normalize this in another way, so I thought choosing a water molecule that is present in all of the structures and removing it, then performing simulated annealing would be a good idea to normalize the peak intensity for each calcium soak concentration, since this water molecule shouldn't change occupancy. Is this the proper way to do this, or can you guys suggest a better way to go about this. I also looked at B factor and e/A3, but that isn't as consistent as peak sigma. Thanks in advance. Dan Daniel J. Slade, Ph.D. Research Associate Thompson Lab The Scripps Research Institute 130 Scripps Way Jupiter, FL 33458 (561) 228-3213

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43rd Mid-Atlantic Macromolecular Crystallography Meeting -- reminder
by Charles Pemble 22 May '13

22 May '13

*43**rd** Mid-Atlantic Macromolecular Crystallography Meeting* *May 30 – June 1, 2013* *Duke University* *Durham, NC* This is a reminder for the 43rd Mid-Atlantic Macromolecular Crystallography Meeting, which will be held next week, May 30-June 01 at Duke University in Durham, North Carolina. Registration and details can be found at http://www.mid-atlantic.org. We encourage you to submit your abstracts for a poster presentation as the deadline is fast approaching! *DEADLINES (updated):* Abstract submission for poster - Next Monday, May 27th *No deadline for registration With best wishes on behalf of the primary Organizing Committee, Charlie Pemble _____________________________ Charles W. Pemble IV, Ph.D. Duke University Medical Center 308 Research Drive LSRC, A06 Durham, NC 27708 charles.pemble(a)duke.edu We thank our current sponsors for their generous contributions: Rigaku Americas Corporation, Agilent Technologies Inc., GlaxoSmithKline, Art Robbins, Bruker, HKL Research Inc., Molecular Dimensions, Hampton Research, Labcyte, GenScript, Genentech, Emerald BioSystems, TTP LabTech, Oxford Cryosystems, PhD Posters, Duke University School of Medicine, Duke Human Vaccine Institute, and Avanti Polar Lipids Inc.

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Workshop - The Future of Microfocus Protein Crystallography - 24-25 September, 2013, Lund, Sweden
by Marjolein Thunnissen 22 May '13

22 May '13

Dear all, I would like to announce a workshop on "The Future of Microfocus Protein Crystallography" which will take place at the MAX IV User meeting on the 24th and the 25th of September, 2013, in Lund, Sweden. Recent developments within protein crystallography methods in combination with the possibilities offered by the new upcoming synchrotron sources such as the MAX IV 3 GeV storage ring make possible exciting new ways of carrying out research within structural biology. Small microfocus beamlines with a very high flux and increased coherence will make new types of experimentation possible. The scientific possibilities will be highlighted through a series of talks by experts showing the impact of the new type of X-ray sources and microfocus beamlines on research within structural biology. The new generation of microfocus beamlines will also set a high demand on instrumentation and suitable software. For example, data collection will potentially be very fast (in milliseconds) and radiation damage will allow only a limited amount of data to be collected from each sample. New technical solutions for sample handling and presentation, data processing methods and more will be needed for these types of experiments, and these will also be presented and discussed at the workshop. Confirmed speakers include David Stuart, Daniel Wacker, Simone Weynand, Jens Preben Morth, Tove Sjögren, Richard Neutze, Janet Smith, Alke Meentz, Alexei Soares, Thomas White and Clemens Schulze-Briese The workshop is part of a process to obtain an updated proposal for the possible Phase 2b beam line MicroMAX at the upcoming new 3 GeV storage ring of MAX IV in Lund. This workshop should give the user community an opportunity to explore the scientific possibilities of a new generation of microfocus beam lines, but also it will give them the chance to contribute with specific input on their own experimental demands on the beam line. The workshop is part of the MAX IV laboratory user meeting. Registration will be through the user meeting website which will open for registration soon. Further information on this workshop can be found at https://www.maxlab.lu.se/node/1609 and for the MAX IV user meeting at https://www.maxlab.lu.se/um13 . For the organisers, Richard Neutze, Gunter Schneider and Gregers Rom Andersen Marjolein Thunnissen ________________________________________________________________________ Marjolein Thunnissen Phone +46-(0)76-632 0417 Associate Professor Fax +46-(0)46-22 24692 Dept of Biochemistry and Structural Biology, Lund University http://www.mps.lu.se<http://www.mps.lu.se/> PO-Box 124 S-221 00 Lund, Sweden Scientific coordinator MX (The MAX IV Laboratory): I911 and BioMAX ________________________________________________________________________

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depositing pdb files
by Mengbin Chen 21 May '13

21 May '13

Hi Phenix Users, I am going to deposit some pdb files into RCSB, which requires Luzzati plots and a bunch of other things. I don't know how to get these results from Phenix (actually the main problem is luzzati errors, Phenix does not seem to provide them), although SFcheck from CCP4i provides only some of them. I know CNS can do this by model_stats.inp, but that's too much trouble since I have complicated ligands bound. Any suggestions would be appreciated! Thank you in advance, Mengbin -- Mengbin Chen Department of Chemistry University of Pennsylvania

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mr_rosetta: how to continue from recovered mr_protocols.default run
by Christian Becke 21 May '13

21 May '13

Hi, I am trying mr_rosetta on a complex. At the GROUP_OF_ROSETTA_REBUILD stage, my machine ran out of memory and the mr_protocols.default processes were killed. After adding more swap space, I restarted the mr_protocols.default runs (3 parallel jobs, one for each chain) using the scripts RUN_?/WORK_?/run_rebuild.sh, which appear to have finished correctly (i.e., there are 20 pdb files generated for each of the chains). However, I could not figure out how to restart mr_rosetta so that it picks up these models. Any suggestions? Thanks, Christian

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