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Submissions to the Computational Crystallography Newsletter – 15 NOV 19
by Nigel Moriarty 10 Sep '19

10 Sep '19

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission for the January 202-0 issue is 15 November 2019. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.phenix-2Donline.org…>. As a reminder, the last issue is detailed here. July 2019 <http://phenix-online.org/newsletter/CCN_2019_07.pdf> Articles - Processing serial crystallographic data from XFELs or synchrotrons using the cctbx.xfel GUI <http://phenix-online.org/newsletter/CCN_2019_07.pdf#page=11> Short Communications - Automatic β-peptide linking in Phenix <http://phenix-online.org/newsletter/CCN_2019_07.pdf#page=5> - phenix.hbond: a new tool for annotation hydrogen bonds <http://phenix-online.org/newsletter/CCN_2019_07.pdf#page=7> - Bytes and Bobs : Accelerating python code with Numba <http://phenix-online.org/newsletter/CCN_2019_07.pdf#page=8> Fitting tips #18 – A subversive kind of misfit “water” <http://phenix-online.org/newsletter/CCN_2019_07.pdf#page=2> FAQ - Can I submit my X-ray model to the Protein Data Bank in PDB format? <http://phenix-online.org/newsletter/CCN_2019_07.pdf#page=4> Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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General interest
by John R Helliwell 09 Sep '19

09 Sep '19

Dear Colleagues, The recent IUCr Committee on Data Satellite Workshop at ECM32 Vienna on “Data science skills in publishing” speaker presentations, overall report and photos from the day are now available via the IUCr CommDat Public Forum weblink:- https://forums.iucr.org/viewtopic.php?f=39&t=422&sid=f14add194ce5e9c146b51b… Best wishes, John Emeritus Professor John R Helliwell DSc Chairman of IUCr Committee on Data

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Post-doctoral position for structure determination of large RNAs and RNP
by Sunandan Mukherjee 08 Sep '19

08 Sep '19

Hi everyone, Laboratory of Bioinformatics and Protein Engineering (LBPE) at the International Institute of Molecular and Cell Biology (IIMCB), Warsaw, Poland, headed by Prof. Janusz M. Bujnicki, is looking for a Postdoctoral Researcher for experimental structure determination of large RNAs (in particular lncRNAs and viral RNAs) and their complexes with proteins (RNPs). LBPE is an interdisciplinary and international team, focused on developing new approaches to determine RNA and RNP structures with the combined use of experimental methods and computational modeling. This position is ideal for you if you have solid experience (documented in publications) in at least one of the following techniques: 1) X-ray crystallography, 2) SAXS 3) cryo-EM, 4) AFM, and if you wish to learn new techniques of integrative structural biology, including computational modeling methods. You are expected to have a strong publication record, which includes at least one first-author publication in a very good international peer-reviewed journal. You are expected to take a lead and apply for fellowship/grant funding within the first year of your employment, with a project that combines the initial research area (structural analyses of large RNAs) with your own ideas. We are particularly interested in candidates interested in the gradual development towards scientific independence (next stage: junior group leader elsewhere) or growing towards a position of a senior scientist within our organization (long-term cooperation, involvement in multiple projects, supervision of junior scientists). The Postdoctoral Researcher will be selected from candidates in an open competition, according to the procedure complying with the rules of the European Charter for Researchers and the Code of Conduct for the Recruitment of Researchers as a part of HR Excellence in Research strategy https://www.iimcb.gov.pl/en/institute/hr-excellence . Application deadline: September 14th, 2019. For more details, please visit http://genesilico.pl/employment . With regards, Sunandan

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Selenium Nucleic Acids
by SeNA Research Institute 06 Sep '19

06 Sep '19

Dear Chemical and/or Structural Biologists, To serve our community, we have developed the selenium-atom specific derivatization of nucleic acids for crystallographic studies. We have discovered that virtually without any perturbations, the incorporated Se-atoms on nucleic acids can (I) rationally solve the phasing problem and (II) significantly facilitate nucleic acid crystallization (even with higher resolution and much larger crystals) in many cases, including protein-nucleic acid complexes. Currently, we are looking for collaborators and would be happy to offer free samples of Se-DNAs and Se-RNAs for your structure-and-function investigations. If you are interested, please contact us at SeNA(a)senaresearch.org Thanks, Mike SeNA Research Institute Email: SeNA(a)senaresearch.org Web: www.SeNAresearch.org http://www.senaresearch.org/

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Postdoctoral position
by Tobias Beck 05 Sep '19

05 Sep '19

Dear all, The Beck group is moving to Hamburg, where we will have labs well-equipped for chemistry, biochemistry and molecular biology. Moreover, state-of-the-art facilities for structural characterizations such as PETRA III are close by. We are looking for a postdoctoral fellow, funded by the Boehringer Ingelheim Foundation, for a project involving protein redesign, protein production and functionalization, and application in imaging and therapy. You should have a PhD degree in chemistry, biochemistry or biology and some experience with protein production and purification. Skills in structural biology / computational design are a plus. The post is available from January 01 2020. Full details of the post and the applications process are available here: https://www.uni-hamburg.de/uhh/stellenangebote/wissenschaftliches-personal/… The group homepage can be found here: https://www.chemie.uni-hamburg.de/institute/pc/arbeitsgruppen/beck.html https://www.ac.rwth-aachen.de/extern/beck/ The deadline for applications is Oct 06 2019. Please contact me for further information or informal inquiries: tobias.beck(a)chemie.uni-hamburg.de Best, Tobias. -- ___________________________________________ Dr. Tobias Beck - independent group leader - RWTH Aachen University Institute of Inorganic Chemistry Landoltweg 1, office: 304N 52056 Aachen, Germany phone: +49-241-80-90057 fax: +49-241-80-99003 web: http://www.ac.rwth-aachen.de/extern/beck/ ___________________________________________ >From October 01: ____________________________________________________________ Prof. Dr. Tobias Beck University of Hamburg Department of Chemistry Institute of Physical Chemistry Grindelallee 117 D-20146 Hamburg Germany email: tobias.beck(a)chemie.uni-hamburg.de web: www.chemie.uni-hamburg.de/institute/pc/arbeitsgruppen/beck/ ____________________________________________________________

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77th Annual Pittsburgh Diffraction Conference
by Leighton Coates 03 Sep '19

03 Sep '19

Dear Colleagues You are invited to the 77th Annual Pittsburgh Diffraction Conference which will be hosted onsite at Oak Ridge National Laboratory in Oak Ridge, Tennessee, USA Start Date: 24th Oct 2019 End Date: 26th Oct 2019 URL: https://conference.sns.gov/event/78/ The conference will take place over three days, and feature sessions focused on all areas of diffraction, from powders to protein crystals. Topics will include Biological Diffraction, Total Scattering, Magnetic scattering, and small molecule Diffraction. The Chung Soo Yoo Award, established by the Pittsburgh Diffraction Society to honor Dr. Yoo’s memory, and a $400 cash prize will be given to the graduate student having the best poster presentation at the conference. Registration for the conference is only $100 and will close on September 20th, and we are still accepting abstracts for posters until that date. Confirmed Speakers are Jahuan Azadmanesh, (University of Nebraska) Emil S. Bozin (Brookhaven National Laboratory) Theodore Betley, (Harvard University) Chris Davies, (Medical University of South Carolina) Bob Von Dreele, (Argonne National Lab) Fred Dyda, (National Institutes of Health, NIDDK) Martin Egli, (Vanderbilt University) Jaime Fernandez-Baca, (Oak Ridge National Laboratory) Dustin Gilbert, (University of Tennessee) Margarida Henriques, (CAS Institute of Physics) Ken Herwig, (Oak Ridge National Laboratory) Patrick Holland, (Yale University) Robert Koch (Brookhaven National Laboratory) Joeseph Kolis, (Clemson University) Cora Lind Kovacs, (University of Toledo) Patricia Langan, (Lentigen Technologies) Jeremy Lohman, (Purdue University) Rebecca McAuliffe (Oak Ridge National Laboratory) Leonard Mueller, (University of California, Riverside) Tim Mueser, (University of Toledo) Robert Philips, (University of Georgia) Raktim Roy, (The Scripps Research Institute) Ella Mara Schmidt, (Friedrich-Alexander Universität Erlangen-Nürnberg) David J. Schuller, (Cornell University) Michael Shatruk, (Florida State University) Timothy Stachowski, (Hauptman Woodward Institute) Corey Thompson, (Purdue University) B.C. Wang, (University of Georgia) Weiwei Xie, (Louisiana State University) Haidong Zhou, (University of Tennessee) Best Wishes Leighton Coates

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Post-doctoral position in membrane protein structural biology
by Hasan, Syed Saif 30 Aug '19

30 Aug '19

A post-doctoral research position is high-resolution structural biology of membrane protein complexes is available in my laboratory at the Institute for Bioscience and Biotechnology Research (IBBR; https://www.ibbr.umd.edu/profiles/s-saif-hasan) in Rockville MD. The post-doctoral researcher will have a choice of multiple structure-focused projects in cancer biology and viral pathogenesis using single particle cryoEM and crystallography. The researcher will have independence to guide the direction of their research and to pursue novel ideas should (s)he find an interesting scientific question related to the general research focus of my laboratory. IBBR is run jointly by the University of Maryland and the National Institute of Standards and Technology (NIST). We are home to a large community of structural biologists and have extensive interactions with national laboratories and private companies located in the DC-Maryland area. Our new cryoEM facility houses a 200 keV Thermo Fisher Talos Arctica microscope equipped with a Falcon 3 direct electron detector. Our facilities will soon be expanded to include a new 200 keV Thermo Fisher Glacios microscope, a Gatan K3 direct electron detector and a Volta phase plate. My lab works in close collaboration with research groups in IBBR that specialize in mass-spectrometry, computational biology, NMR spectroscopy, and small angle X-ray scattering. Applicants should have experience in insect or mammalian cell culture for protein production. Experience in handling membrane proteins will be helpful. Prior training in single particle cryoEM and/or crystallography is desirable but not essential. If you are a membrane protein biochemist, especially with experience in G-proteins, and you want to explore questions in structural biology, this is the position for you. Applicants who have received their PhD or MD/PhD degree should email me (sshasan(a)som.umaryland.edu) a single PDF file containing a short cover letter (no more than one page), a detailed curriculum vitae, contact information for three references, and upto 3 reprints of representative first authorship publication(s). The University of Maryland, Baltimore is an Equal Opportunity, Affirmative Action employer. Minorities, women, individuals with disabilities and protected veterans are encouraged to apply. Saif S. Saif Hasan, PhD Fellow, Institute for Bioscience and Biotechnology Research (IBBR), 9600 Gudelsky Drive, Rockville, MD 20850 Assistant Professor, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD 21201 AND Center for Biomolecular Therapeutics (CBT), 9600 Gudelsky Drive, Rockville, MD 20850 Phone: 240-314-6396 Fax: 240-314-6225 https://www.ibbr.umd.edu/profiles/s-saif-hasan

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Re: [phenixbb] [bruker-axs] cbf to sfrm
by Tim Gruene 29 Aug '19

29 Aug '19

Dear Holger, thanks a lot for the prompt reaction! This will be very useful, in particular in case of proper twins. I look forward to the update, Tim On Thursday, August 29, 2019 11:32:00 AM CEST bruker-axs(a)lists.wisc.edu wrote: > Dear Tim, > > > > Thanks for having brought the bug to our attention. It got fixed in the > PROTEUM3/APEX3 2019.1 version which will be available for download next > week. > > > > Cheers, > Holger > > > Dr. Holger Ott > Global Application Coordinator SC-XRD & Senior Application Scientist > Chemical Crystallography > > Bruker AXS GmbH > Oestliche Rheinbrueckenstr. 49 > 76187 Karlsruhe, Germany > > Phone: +49 721 50997-5628 > Fax: +49 721 50997-45628 > > Holger.Ott@bruker<mailto:Holger.Ott@bruker>.com > www.bruker.com<http://www.bruker.com/> > > ________________________________ > > > > Sitz der Gesellschaft/Registered Office: Karlsruhe, HRB 107524 Amtsgericht > Mannheim, Umsatzsteuer-Ident.Nr. DE812037551, Geschäftsführer/Managing > Directors: - Dr. Frank Burgäzy, Dr. Klaus Gohlke > > Diese E-Mail einschließlich etwaiger Anlagen kann vertrauliche Informationen > enthalten. Sie ist daher vom Adressaten vertraulich zu behandeln und darf > nicht veröffentlicht werden. This email, including possible attachments, > may contain confidential information. It should therefore be treated as > confidential by the addressee and may not be published. > > > > > > -----Ursprüngliche Nachricht----- > Von: bruker-axs(a)lists.wisc.edu [mailto:[email protected]] > Gesendet: Sonntag, 28. Juli 2019 18:25 > An: bruker-axs(a)lists.wisc.edu; ccp4bb(a)jiscmail.ac.uk; > phenixbb(a)phenix-online.org Betreff: [bruker-axs] cbf to sfrm > > > > Dear all, > > > > recently the conversion from CBF to SFRM frame format with APEX was > discussed on the Bruker mailing list ("Synchrotron data with Bruker > Software"), including a potential bug that parameters in the frames other > than the first frame are not set correctly. The workaround to re-convert > from SFRM to SFRM a second time did not help in my case. > > > > I therefore updated my program sfrmtools, available at https:// > homepage.univie.ac.at/tim.gruene/research/programs/conv/sfrmtools/ > > > > With the option '-u',you can provide the first frame of the run, and via > '-p' > > a parameter file that contains the critical parameters (see documentation at > above URL) to update the header for all frames in this run. In case you > have twinned data and want to benefit from SAINT, this should be possible > with this feature. > > > > Both 64bit Linux binary and the source code are available. The program has > no dependencies and should compile under any platform. > > > > I did not debug this new feature very thoroughly, but it worked for me so > far. > > Any bug reports are welcome to this address > tim.gruene(a)univie.ac.at<mailto:[email protected]> > > > > I hope this is helpful for one or two users. > > > > I acknowledge the thorough documentation of XDS, of SAINT, and of the SFRM > header format. > > > > Kind regards, > > Tim > > > > cc Bruker mailing list, CCP4BB, phenixBB > > -- > > -- > > Tim Gruene > > Head of the Centre for X-ray Structure Analysis Faculty of Chemistry > University of Vienna > > > > Phone: +43-1-4277-70202 > > > > GPG Key ID = A46BEE1A -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A

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Job posting - CryoEM Research Group Leader in Australia
by Peter Czabotar 29 Aug '19

29 Aug '19

Dear colleagues, I’d like to bring to your attention a job opening for a Research Group Leader specialising in CryoEM at the The Walter and Eliza Hall Institute of Medical Research in Melbourne Australia. For details see - https://www.wehi.edu.au/cryoem-laboratory-head This is a 7-year appointment in the first instance with opportunities for further renewal. WEHI is a highly collaborative world-class institution that has been in operation for more than 100 years and was recently ranked in Nature’s Top 20 non-profit/non-governmental biomedical research institutes globally. The link above contains all necessary information for enquiries and applications. Many thanks and kind regards, Regards Peter Czabotar Associate Professor Peter Czabotar Joint Division Head of Structural Biology The Walter and Eliza Hall Institute of Medical Research 1G Royal Parade Parkville VIC 3052 Australia Phone: +61 (0)3 9345 2311 | Email: czabotar(a)wehi.edu.au _______________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. The Walter and Eliza Hall Institute acknowledges the Wurundjeri people of the Kulin Nation as the traditional owners of the land where our campuses are located and the continuing connection to country and community. _______________________________________________

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rosetta installation problem
by Almudena Ponce Salvatierra 28 Aug '19

28 Aug '19

Dear all, yesterday I spent quite some time trying to install Rosetta, so that I can use all it's modules within Phenix. However, when I am running the tests, rosetta stops and I get the following message (see below). Any help would be much appreciated. Thank you Almudena ======================= ROSETTA/PHENIX X-ray refinement ======================= Traceback (most recent call last): File "/Applications/phenix-1.14-3260/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 307, in <module> run(sys.argv[1:], create_dir=True) File "/Applications/phenix-1.14-3260/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 159, in run default_directory_number=params.output.directory_number) File "/Applications/phenix-1.14-3260/modules/cctbx_project/libtbx/utils.py", line 1925, in create_run_directory os.makedirs(dir_name) File "/Applications/phenix-1.14-3260/base/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/../../../../../../../Python.framework/Versions/2.7/lib/python2.7/os.py", line 157, in makedirs mkdir(name, mode) OSError: [Errno 13] Permission denied: 'rosetta_1' Almudenas-MacBook-Pro:bin almudenaponce$

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