- phenixbb - phenix-online.org

file location changed
by Cygler, Miroslaw 14 Oct '19

14 Oct '19

Hi, In order to allow synchronization of files on my mac with the cloud server I had to move all files used by Phenix to a new directory, including the main Phenix folder. How do I change the paths to these files in phenix so that they are accessible to the software? Phenix would not start without the main Phenix folder returned back to the old location. How do I rectify this as well? Thanks for your help, Mirek

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advert for PostDoc position @Singapore
by SR Bharath 14 Oct '19

14 Oct '19

Dear Colleagues, We are seeking an enthusiastic and self-motivated postdoctoral research fellow to study proteins involved in maintaining genome stability and the Hippo signaling pathway. We take a combinatorial approach of molecular biology, biochemical and biophysical methods, and structural biology (macromolecular crystallography and electron cryomicroscopy). Significant aspects of our projects have translational potential. The candidate is expected to be involved in the development of small molecules/peptides for cancer therapeutics. Singapore is an excellent environment to do research with many research groups close by in Biopolis [https://www.a-star.edu.sg/imcb]. A*STAR offers highly competitive salaries with benefits including housing allowance and 1-3 months performance bonus. Requirements: · PhD in biochemistry, biophysics, molecular & cell biology or in medicinal chemistry · Practical experiences in structural biology (Electron Cryomicroscopy and/or X-ray crystallography) or in medicinal chemistry · Good publication record · Competent in scientific writing Interested applicants should send a CV and three confidential letters of reference to: Prof. Haiwei Song (Email: *haiwei(a)imcb.a-star.edu.sg <https://webmail2.imcb.a-star.edu.sg/owa/redir.aspx?C=EzRllkOmnk2jjotDLR8t5a…>*), Institute of Molecular and Cell Biology, A*STAR, Singapore. Cheers, Bharath

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Masked FSC estimation failure
by ze li 12 Oct '19

12 Oct '19

Hello: I have three cryo-ET full maps, not in halves, to estimate their resolutions. I intended to estimate the resolution of the maps with the high-resolution models in the PDB databank. Is it the best to get a map to model FSC estimation at 0.5 cut-off? I calculated three maps with cryo-EM module in Phenix, but only one gives the masked and unmasked curves, the other two only have the unmasked results.I tried many times but failed to figure out the questions of these two maps. What is the possible reason for them? Or Is there any other ways to get the unmasked and masked FSC? Thank you for your help. Sincerely, Ze

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Berkeley Server Outage (Starting October evening 8th)
by Paul Adams 12 Oct '19

12 Oct '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. We have been informed that the weather this week meets their criteria for a shutdown in our part of the Bay Area. Therefore several of the Berkeley servers will be shut down today and will return later in the week. 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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University of Maryland/Open-Rank Tenure-Line Faculty Position
by Hasan, Syed Saif 09 Oct '19

09 Oct '19

Dear Colleagues, The Institute for Bioscience & Biotechnology Research (IBBR) and the University of Maryland, College Park Department of Chemistry & Biochemistry invite applications for an open-rank, tenure-line faculty position in structural biology, with an emphasis in the area of biomolecular cryo-electron microscopy, starting August 2020. A detailed ad is attached to this email. Applications, consisting of a cover letter, curriculum vitae, statement of research plans, statement of educational interests, and three references, must be submitted electronically at: https://ejobs.umd.edu/postings/74094 Review of applications will begin November 15, 2019. We will continue to accept applications until the position is filled. Direct inquiries and/or nominations to the chair of the search committee, at: cryoemsearch(a)ibbr.umd.edu Saif S. Saif Hasan, PhD https://www.medschool.umaryland.edu/profiles/Hasan-S-Saif-Hasan-Syed-Saif/ https://www.ibbr.umd.edu/profiles/s-saif-hasan

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positional restraints in real_space_refine?
by Daniel Larsson 08 Oct '19

08 Oct '19

Hi all, I'm working on a cryo-EM reconstruction where I have some flexible low-resolution elements (RNA double helices). They have different orientations relative to my reference model, but I would like to model them in the approximately correct position. I've tried real_space_refine with morphing and simulated annealing, but neither accomplish what I want. Now I'm thinking of cutting out these helices and manually position them approximately where I want them. But I fear that this will case headache at the "joint". Is it possible to use the manual positions as a reference for positional restraints, but use the original model as the reference for the torsion angles. Is this possible with real_space_refine? Or is there a better way of refining this structure? Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Phenix 1.17-3644 installation problems
by Hernando J Sosa 07 Oct '19

07 Oct '19

Dear Phenix developers, Trying to install Phenix in a Linux computer (OpenSuse Leap 15.1)I got the error messages listed below. Any help to fix this problem(s) would be appreciated. Thks. H. Precompiling .py files... Generating SOLVE/RESOLVE license file... Rebuilding HTML documentation... Error rebuilding documentation! Creating rotamer/Ramachandran database files... Traceback (most recent call last): File "./bin/install.py", line 244, in <module> installer(sys.argv[1:]).install() File "/home/hsxx/Downloads/phenix-installer-1.17-3644-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 201, in install self.install_finalize() File "/home/hsxx/Downloads/phenix-installer-1.17-3644-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 542, in install_finalize self.product_specific_finalize_install(log) File "./bin/install.py", line 130, in product_specific_finalize_install call([os.path.join(self.build_dir, 'bin', 'mmtbx.rebuild_rotarama_cache')], log=log) File "/home/hsxx/Downloads/phenix-installer-1.17-3644-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/installer_utils.py", line 53, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/home/hsxx/Programs/Phenix/phenix-1.17-3644/build/bin/mmtbx.rebuild_rotarama_cache' failed with exit code -4

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reference torsion restraints for nucleic acids in real_space_refine
by Daniel Larsson 07 Oct '19

07 Oct '19

Hi all, In phenix.real_space_refine, I'm using a reference model for torsion restraints for a RNA/protein complex. I noticed in the log file under the section "Adding Reference Model Restraints (torsion)" that only the amino acid residues and some modified nucleotides are listed in the "Reference Model Matching Summary" but not the standard nucleotides. Does this mean that they are not restrained? I checked the _initial.geo file and there are no torsion restraints for the standard nucleotides in the "Reference torsion angle restraints" section. Are they not supported by default? My workflow was this: run ready_set on the initial model and then supply real_space_refine with a reference model and the ready_set cif file with the ligands. Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Base-pair restraints and high resolution cryoEM maps
by Stephen Cusack 07 Oct '19

07 Oct '19

Dear All, (1) Is it possible to add RNA base-pair restraints into Phenix Real-space-refinement of a lowish resolution cryoEM structure? If so how? (2) We are also lucky enough to have some impressively high resolution cryoEM maps (2.4 A average) which show among other things hundreds of water molecules. I was wondering whether Phenix Real-space-refinement was really adapted to high resolution, e.g. it uses grouped B-factor refinement and has no water handling options (putting them in manually is a pain and you always miss some). How have other people dealt with these issues ? thanks for any help Stephen Cusack -- ********************************************************************** Dr. Stephen Cusack, FRS Head of EMBL Grenoble Group leader in the structural biology of protein-RNA complexes and viral proteins ********************************************************************** Email: cusack(a)embl.fr, stephen.cusack(a)embl.org Website: http://www.embl.fr Tel: (33) 4 76 20 7238 Secretary (33) 4 76 20 7123 Fax: (33) 4 76 20 7199 Postal address: EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue des Martyrs, 38000 Grenoble, France **********************************************************************

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PhD and postdoc position - Structural Biology Methods development at Wuerzburg University
by Andrea Thorn 06 Oct '19

06 Oct '19

Dear colleagues, for two projects in structural biology methods development, we are looking for a PHD CANDIDATE (m/f/d) and a POSTDOCTORAL RESEARCHER (m/f/d) The Thorn Laboratory the Rudolf Virchow Center at the University of Wuerzburg develops new methods for macromolecular X-ray crystallography and Cryo-EM. In these exciting projects you will improve how well we understand, measure and model macromolecular crystal structures using practical experiments and big data analyses. We are looking for candidates with skills in data analysis and programming. Any previous experiences in crystallography, molecular biology, machine learning, image or statistical analysis are also a bonus. You should be a good communicator. For the PhD project, we offer a 36-month full- or part-time position, embedded in the Würzburg Graduate School for Life Sciences (GSLS); for the postdoctoral position, we offer a 30-month full- or part-time position with a competitive salary as well as career and family support. Women are particularly encouraged to apply. For more details, see: https://www.uni-wuerzburg.de/fileadmin/43020000/2019/Stellenanzeige_PhD_Tho… https://www.uni-wuerzburg.de/fileadmin/43020000/2019/Stellenanzeige_Postdoc… If you have any questions, please email me: andrea.thorn(a)uni-wuerzburg.de. Best wishes, Andrea Thorn. _____ Dr. Andrea Thorn group leader Rudolf Virchow Center for Experimental Biomedicine University of Wuerzburg Josef-Schneider-Str. 2 97080 Wuerzburg Germany andrea.thorn(a)uni-wuerzburg.de https://www.uni-wuerzburg.de/en/rvz/research/associated-research-groups/tho…

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Position Available: Crystallography Facility Manager (Research Assistant Professor) - CUNY Advanced Science Research Center, New York City
by Keedy, Daniel 03 Oct '19

03 Oct '19

To the phenixbb community, The Structural Biology Initiative ( https://asrc.gc.cuny.edu/structbio ) of the CUNY Advanced Science Research Center has an available position for an X-ray Crystallography Facility Manager (Research Assistant Professor) starting immediately. The CUNY Advanced Science Research Center is a new cutting-edge research institution located in New York City, bringing together five Initiatives whose research areas span many length scales: Structural Biology, Nanoscience, Photonics, Neuroscience, and Environmental Science. The Structural Biology Initiative (SBI) features seven tenure-track and research faculty members, pursuing research problems across biological and chemical topics using techniques as diverse as X-ray diffraction, cryo-EM, NMR, solution biophysics, and advanced microscopy. The SBI also hosts state-of-the-art core facilities in three different areas: nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), and X-ray crystallography. The Structural Biology Initiative seeks a Facility Manager/Research Assistant Professor for the X-ray Macromolecular Crystallography Facility, which is already equipped with a Rigaku Alchemist DT liquid handler, two ARI Gryphon crystallization robots, and two Rigaku Minstrel DT crystal imagers at room temperature and 4°C. The selected candidate will be responsible not only for directing day-to-day operations of the facility in concert with users from the ASRC and externally, but also for developing an independent research program that leverages emerging technologies in X-ray crystallography. The ASRC is located in upper Manhattan, immediately adjacent to the New York Structural Biology Center (NYSBC), a consortium of CUNY and eight other New York academic institutions with world-class cryo-EM, NMR, and X-ray facilities on-site and at Brookhaven National Laboratory. BNL, located just 70 miles from the ASRC, includes a newly constructed synchrotron, National Synchrotron Light Source II, which opened in 2015. NSLS-II is now the brightest synchrotron light source in the United State, offering X-rays that are 10,000x brighter than the original NSLS. The ASRC Structural Biology Initiative has access to several cutting-edge microfocus beamlines equipped for automated crystal handling and data collection at NSLS-II, including the NYX beamline via CUNY’s membership in NYSBC and the AMX and FMX beamlines via proposals. Please find more detailed information about the position and officially apply via the following URL: https://cuny.jobs/new-york-ny/macromolecular-crystallization-facility-manag… Review of applications will begin on October 16. Best regards, Daniel Keedy — Daniel A. Keedy, Ph.D. Assistant Professor Structural Biology Initiative, CUNY Advanced Science Research Center Department of Chemistry and Biochemistry, City College of New York Biochemistry and Chemistry Ph.D. Programs, CUNY Graduate Center www.keedylab.org<http://www.keedylab.org> | dkeedy(a)gc.cuny.edu<mailto:[email protected]> (NOT @asrc) | 212-413-3246

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Re: [phenixbb] Figure of merit from refinement
by Alexandre OURJOUMTSEV 03 Oct '19

03 Oct '19

Dear Andre, (I repeat here the same message that I've just sent through the ccp4bb; sorry for answering late) I would strongly advice you to look at the article by Lunin and Skovoroda (Acta Cryst, A, 1995) that addresses exactly your question: https://scripts.iucr.org/cgi-bin/paper?vs0124 The authors remind a very important point that after model refinement ML phase errors are strongly underestimated if using all reflections, as that was done in the original works (see references in the article). While the same ML estimates work perfectly for unrefined models, that's not the case for refined ones, as was observed yet in the beginning of 80ths. These authors show then that using the test-set of reflections (the same as for R-free) is crucial to get the correct phase error estimates and respective FOMs for all cases, as this is implemented now in modern refinement programs, e.g. phenix.refine. See also the article by Pannu & Read (Acta Cryst, A, 1996) https://onlinelibrary.wiley.com/doi/pdf/10.1107/S0108767396004370 A more recent important article on this topic is that by Praznikar and Turk (Acta Cryst, D, 2009) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257616/ who discuss what can be done if a statistically significant test set of reflections is not available. I hope this helps you. I am ready to answer you further eventual questions (probably, in a private correspondence). With best wishes, Sacha Urzhumtsev ________________________________ -------- Forwarded Message -------- Subject: [phenixbb] Figure of merit from refinement Date: Tue, 1 Oct 2019 08:15:14 -0300 From: Andre LB Ambrosio <andre(a)ifsc.usp.br><mailto:[email protected]> To: phenixbb(a)phenix-online.org<mailto:[email protected]> Dear all, How is the FOM calculated for a given reflection specifically in the context of model refinement? How useful is it in assessing the phase quality, when not for initial experimental phases? Many thank in advance, -- Andre LB Ambrosio

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Figure of merit from refinement
by Andre LB Ambrosio 01 Oct '19

01 Oct '19

Dear all, How is the FOM calculated for a given reflection specifically in the context of model refinement? How useful is it in assessing the phase quality, when not for initial experimental phases? Many thank in advance, -- Andre LB Ambrosio

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General interest
by John R Helliwell 30 Sep '19

30 Sep '19

Dear Colleagues, I draw your attention to my posting at the IUCr Committee on Data Public Forum ( https://forums.iucr.org/viewtopic.php?f=39&t=423 ) about the recent USA National Academies Report on Reproducibility and Replicability in Science. Best wishes, John Emeritus Professor John R Helliwell DSc Chairman of the IUCr Committee on Data

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Final reminder: MicroED Workshop 2019
by Johan Hattne 30 Sep '19

30 Sep '19

Final 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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What OS do you use?
by Murpholino Peligro 21 Sep '19

21 Sep '19

I want to know what operating system you use. For that I made a poll, it is anonymous, quite simple and plus you get to see the results. (link https://forms.gle/7VT4pgbHQQmeAvpp8) I hope you contribute. Thanks

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Potential Berkeley Server Outage (September 23/24)
by Paul Adams 21 Sep '19

21 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 19 Sep '19

19 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 18 Sep '19

18 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 09 Sep '19

09 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 08 Sep '19

08 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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