- phenixbb - phenix-online.org

Potential Berkeley Server Outage (September 23/24)
by Paul Adams 22 Sep '19

22 Sep '19

Dear Colleagues, as a result of the increased frequency of wildfires in California the power company is taking steps to reduce risk under certain weather conditions. This entails shutting down electricity to regions that are experiencing dry windy conditions. They are predicting that Monday or Tuesday this coming week (September 23/24) might meet their criteria for a shutdown in the Bay Area. Hopefully this is just a worst case prediction and nothing will happen. However, there is a possibility that the Berkeley servers will be down for some time during that period (duration unknown). This will affect: - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Berkeley Lab (http://biosciences.lbl.gov/divisions/mbib) Division Deputy for Biosciences, Advanced Light Source, Berkeley Lab (https://als.lbl.gov) Principal Investigator, ALS-ENABLE, Advanced Light Source, Berkeley Lab (http://als-enable.lbl.gov) Group Leader, Computational Crystallography Initiative, Berkeley Lab (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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XChem fragment screening - call for proposals - 2nd October 5pm
by Frank Von Delft 20 Sep '19

20 Sep '19

Dear all, This is a reminder that Diamond Light Source is accepting proposals for its XChem fragment screening facility, for the allocation period April to September 2020. The deadline is Wednesday 2nd October at 5pm (2 weeks from now). Details on how to apply are here - we're oversubscribed, so please follow the instructions! https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening/Applying-for-XC… XChem is a platform for high-throughput crystal-based fragment screening, operational since 2015. We provide fragment libraries (or you can bring your own) and the pipeline entails: rapid crystal soaking with an Echo acoustic liquid handler; high-throughput harvesting of hundreds of pre-soaked crystals using a Shifter; fully unattended data collection using dedicated beamtime on I04-1 beamline; and automated data integration along with tools for ligand detection (PanDDA) and streamlined model building (XChemExplorer). Since April 2019, we offer both standard and Block Allocation Group (BAG) access. Standard access accommodates both Tier 1 and Tier 2 proposals, for exploratory and ready-to-go projects respectively. Since this summer, the FragLites library from Newcastle university (J. Med. Chem.20196273741-3752) is also available for users. More information is on the XChem website: https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening<https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening/Methods-for-Fra…> https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening/Methods-for-Fra…<https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening/Fragment-Librar…> https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening/Fragment-Librar… For more questions, please ask Alice (copied) or myself. We are looking forward to collaborating with you! The XChem team.

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Reminder: MicroED Workshop 2019
by Johan Hattne 19 Sep '19

19 Sep '19

Just a reminder: the application deadline for the 2019 MicroED workshop is October 1, 2019. From the initial announcement: The Gonen Laboratory will hold the 5th MicroED Workshop in 2019. The workshop will be held at the MicroED Imaging Center at the UCLA David Geffen School of Medicine during December 9-12, 2019 and is open to both academia and industry. Space is limited and historically, the workshop is typically oversubscribed. Topics covered: * MicroED conception, practice, and future opportunities * Electron optics for MicroED * Microscope alignment and calibration for MicroED * Sample preparation: protein and organic/inorganic materials, small molecules * Data collection for both protein and small molecules * Data analysis software, structure solution, and refinement * Choice of electron microscope hardware and cameras * MicroED publication standards: what statistics to include and when is your structure publication-ready? Further application information is available from https://cryoem.ucla.edu/pages/Workshop // Best wishes; Johan, on behalf of the organizers Research Specialist @ Gonen Lab ____________________________________________________ UCLA * 615 Charles E. Young Drive South BSRB #347 * Los Angeles, CA 90095

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Re: [phenixbb] CCP4 Study Weekend 2020: registration now open!
by r.joosten＠nki.nl 11 Sep '19

11 Sep '19

Of course we want everyone to register immediately, but if you insist on seeing the programme first, please go to http://www.cvent.com/events/ccp4-study-weekend-2020/event-summary-001c74f5e… Cheers, Robbie, Jon, and Alan On 11 Sep 2019 13:37, "Robbie P. Joosten" <r.joosten(a)nki.nl> wrote: Dear colleagues, We are pleased to announce that the next CCP4 Study Weekend in its 2020 edition will be devoted to the single most synergic task in structural biology: model building. Aside from covering the latest advances in both automated and manual procedures, the meeting will offer sessions on related topics such as refinement, validation and representation, with a focus on helping you produce the best possible model from your experimental data. All sessions will have an integrative character, presenting methods and approaches that may be indistinctly used with X-ray crystallography, and electron cryo-microscopy or diffraction. This meeting will have a couple of innovations too - more announcements will follow in due course. The most important ones will be posted here (as always), but for more fluid news, speaker profiles and direct communication with the organisers, please use hashtag #CCP4SW on Twitter or give us a follow (vide infra). As in recent editions, the event will be held at the East Midlands Conference Centre in Nottingham, from the 7th to the 9th of January 2020. We are very much looking forward to welcoming you in Nottingham. And yes, there will be a Cèilidh (https://en.wikipedia.org/wiki/Cèilidh). Registration and programme details: https://tinyurl.com/ccp4sw2020 Best wishes, Robbie Joosten (@Robbie_Joosten), Alan Roseman (@AlanRoseman3), Jon Agirre (@glycojones), and the rest of CCP4 (@ccp4_mx) _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org

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CCP4 Study Weekend 2020: registration now open!
by Robbie P. Joosten 11 Sep '19

11 Sep '19

Dear colleagues, We are pleased to announce that the next CCP4 Study Weekend in its 2020 edition will be devoted to the single most synergic task in structural biology: model building. Aside from covering the latest advances in both automated and manual procedures, the meeting will offer sessions on related topics such as refinement, validation and representation, with a focus on helping you produce the best possible model from your experimental data. All sessions will have an integrative character, presenting methods and approaches that may be indistinctly used with X-ray crystallography, and electron cryo-microscopy or diffraction. This meeting will have a couple of innovations too - more announcements will follow in due course. The most important ones will be posted here (as always), but for more fluid news, speaker profiles and direct communication with the organisers, please use hashtag #CCP4SW on Twitter or give us a follow (vide infra). As in recent editions, the event will be held at the East Midlands Conference Centre in Nottingham, from the 7th to the 9th of January 2020. We are very much looking forward to welcoming you in Nottingham. And yes, there will be a Cèilidh (https://en.wikipedia.org/wiki/Cèilidh). Registration and programme details: https://tinyurl.com/ccp4sw2020 Best wishes, Robbie Joosten (@Robbie_Joosten), Alan Roseman (@AlanRoseman3), Jon Agirre (@glycojones), and the rest of CCP4 (@ccp4_mx)

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Phenix user workshop just after Understanding Biology through Structure 2020
by Tom Terwilliger 10 Sep '19

10 Sep '19

Hi Structural biologists, particularly students and postdocs! A Phenix crystallography/cryo-EM workshop will be held after the last day of Understanding Biology through Structure 2020 (https://cvent.me/4kq9P, the meeting is March 16-19, 2020 in Santa Fe,NM; the workshop is March 20 and the workshop program is also at https://cvent.me/4kq9P). You can learn how to use the latest X-ray and cryo-EM tools in Phenix this way. Also student/postdoc fellowships are available for Understanding Biology through Structure 2020 (https://cvent.me/4kq9P, March 16-20, 2020 in Santa Fe,NM). The fellowships cover registration and hotel (you still have to get there) and are being awarded after registration on a competitive rolling basis based on a publication you upload. You can register now at https://cvent.me/4kq9P ! Best regards, Tom T -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

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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 09 Sep '19

09 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 07 Sep '19

07 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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