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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 22 Sep '19

22 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 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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