- phenixbb - phenix-online.org

Submissions to the Computational Crystallography Newsletter – 30 NOV 19
by Nigel Moriarty 12 Nov '19

12 Nov '19

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission for the January 2020 issue is 30 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…>. 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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Postdoc Position in Berkeley
by Petrus Zwart 08 Nov '19

08 Nov '19

Dear All, We have two postdoc positions open in LBNL's Center for Advanced Mathematics in Energy Research Applications (CAMERA; https://www.camera.lbl.gov/) to work on a diverse set of problems in managing, cleaning and interpreting biophysical data ranging from microscopy to crystallography. https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=88805 https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=88480 Feel free to contact me for more information. Regards Peter Zwart -- ------------------------------------------------------------------------ P.H. Zwart Staff Scientist Molecular Biophysics and Integrated Bioimaging & Center for Advanced Mathematics for Energy Research Applications Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 PHENIX: http://www.phenix-online.org CAMERA: http://camera.lbl.gov/ -------------------------------------------------------------------------

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RapiData at SSRL 2020 reminder - just over a week left to apply!
by Smith, Clyde 04 Nov '19

04 Nov '19

Hi all, A reminder that there is only a week left to apply for a place at the RapiData 2020 @ SSRL workshop. Applications close the middle of this month, November 15 2019. The workshop will be held from March 30 - April 4 2020 on the SLAC campus in Menlo Park, California. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and lectures on the following topics: Specimen preparation, data collection strategies, X-ray light sources, X-ray detectors, data reduction, structure solution by MAD, SAD and molecular replacement, complementary methods (spectroscopy, small angle scattering and cryoEM). Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2020/ and use the links on the "registration" page to apply for the course. Successful applicants will be notified early in December 2019 and invited to register at that time. A limited amount of travel support funding may be available. We look forward to seeing you all out in sunny California in March 2020! Silvia Russi, Clyde Smith and Jeney Wierman (Organizers) srussi(a)slac.stanford.edu jwierman(a)slac.stanford.edu csmith(a)slac.stanford.edu

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Phenix version 1.17 released
by Paul Adams 04 Nov '19

04 Nov '19

The Phenix developers are pleased to announce that version 1.17 of Phenix is now available (build 1.17.1-3660). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Please note that there is a new publication that describes recent Phenix developments for structure determination with X-rays, neutrons and electrons: https://doi.org/10.1107/S2059798319011471 Highlights for the 1.17 version of Phenix: 1.17.1 Changes - Fix bug on Windows where xtriage results would fail to display - Other bug fixes 1.17 Changes - Improved handling of SHELX data in phenix.reflection_file_converter - eLBOW can output files for Amber and supports the Orca QM package - dials.image_viewer is used for viewing diffraction images - Updated map smoothing - Fix inconsistency in clashscore values in phenix.validation_cryoem when hydrogens are in the model For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this new publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Berkeley Lab (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, Berkeley Lab (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source, Berkeley Lab (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source, Berkeley Lab (https://als.lbl.gov) 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: Nikki Humphreys [ nhumphreys(a)lbl.gov ][ 1-510-486-4610 ] --

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Postdoc position available in LBNL
by Peter Zwart 31 Oct '19

31 Oct '19

Dear All, We have a postdoc position available at LBNL to work on the development of computational approaches for twinned crystallographic data. This is an exciting opportunity to address a relatively common phenomenon in crystallographic data analysis for which there are currently limited twinning-aware approaches. The aim is to develop tools that impact substructure solution, molecular replacement, density modification and structure refinement. Click the link below for more info or contact me directly. https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=88480 Regards Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Research Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org SASTBX: http://sastbx.als.lbl.gov -----------------------------------------------------------------

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Understanding Biology through Structure 16-20 March 2020
by Tom Terwilliger 30 Oct '19

30 Oct '19

Hi Colleagues, particularly students and postdocs, I would like to encourage you to sign up for "Understanding Biology through Structure 2020" (https://cvent.me/4kq9P, March 16-20, 2020 in Santa Fe,NM). Student and postdoc fellowships covering registration and hotel are available (awarded competitively after registration on a rolling basis). The conference is a forum where students and postdocs can meet established researchers and discuss the latest methods and results. For a one-line review and info on the last one see https://bit.ly/2Gfkm4t and https://bit.ly/2Gg39rm. Confirmed speakers are Ilme Schlichting, Yvonne Jones, Hao Wu, Peijun Zhang, Christopher Russo, Claudio Ciferri, David Stuart, Blake Wiedenheft, Ci Ji Lim, Robert Stroud, Wayne Hendrickson, Bonnie Murphy, Anne Houdusse-Juille, Sonja Lonrenz, Chris Hill, Chun-wa Chung, Jian Payandeh, Amit Sharma, Marissa Matsumoto, Suzanne Scarlata, Osamu Nureki, Natalia Jura, Erica Ollmann Saphire, Eva Nogales, Andrej Sali, Anke Bill, Joanna Sulkowska, David Eisenberg, Marie Pancera, Karla Satchell, Jacques Philippe Colletier, Tom Terwilliger, Christopher Neale, and Tom Blundell. All the talks will be followed by 10-15 minutes of discussion with participation by students and postdocs especially encouraged. After the main conference there will be an optional Phenix workshop with lectures and hands-on sessions on using Phenix for crystallography and cryo-EM. Registration is first-come first served, with a limit of 120. All the best, 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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GUI reorders file data type in EM validation task
by Ashley Pike 30 Oct '19

30 Oct '19

Hi, I am having problems convincing the GUI which EM map is which for halfmap validation. Version is 1.17-3644 Here is input: [cid:[email protected]] and what is written to Summary tab: [cid:[email protected]] Any tricks to getting this to work? Editing the .eff file written by the gui is an option but running phenix.validation_cryoem on the command line doesn't seem to produce much viewable output. Cheers, Ashley -- Dr. Ashley Pike Membrane Protein Crystallography | Structural Genomics Consortium | University of Oxford Phone: +44 (0)1865 617576 | FAX: +44 (0)1865 617575 | ashley.pike(a)sgc.ox.ac.uk<mailto:[email protected]> | www.thesgc.org<http://www.thesgc.org/> Address: Structural Genomics Consortium, Old Road Campus Research Building, Headington, Oxford OX3 7DQ, UK

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Potential Berkeley Server Outage (October 25)
by Billy Poon 29 Oct '19

29 Oct '19

Hi everyone, 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 weekend meets their criteria for a shutdown in our part of the Bay Area. Therefore several of the Berkeley servers will probably be shut down today and will return next 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. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Berkeley Server Outage (Starting October 26th)
by Paul Adams 25 Oct '19

25 Oct '19

Dear Colleagues, yet again, 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 weekend meets their criteria for a shutdown in our part of the Bay Area. Therefore several of the Berkeley servers will be shut down this weekend and will return later the following 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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real space refine and nonbonded_weight
by Cheung, Alan 25 Oct '19

25 Oct '19

Dear Developers A structure we refined back in 2017, using phenix.real_space_refine on a cryoEM map @ 3.7A (version 1.11.1–2575) produces a clashscore of ~8 but the exact same refinement run with the latest phenix (version 1.17.1) generates a clashscore of ~22. Our refinements with the latest version on other EM structures tend to generate pretty high clashscores too. I think i've tracked this down to the nonbonded_weight parameter, which defaults to 1000 in the older version, and to 100 in the latest version. At which version did the default change, and is there a reason for it? I couldn't find it in the changelog. Alan

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