January 2023 - phenixbb - phenix-online.org

map deposition strategy after density modification
by Daniel Larsson 20 Sep '23

20 Sep '23

Hi Phenix community, I’ve been using density modification with some success for my data and am considering the most appropriate way to do model building/refinement and then deposition of my results. Here are some questions/observations: 1) Which map should I refine against (most importantly, do the final minimization using phenix.real_space_refine)? The DM map is the most clear one, so I’m favoring to do it against this one (as long as the geometry/validation is also best for this one). 2) Which map should I deposit as my main map? Is it the autosharpened one or the DM one? Since the DM map looks the best, I want the user who only downloads one map to see this one, so again I favoring this map. 3) Which nominal resolution should I quote for my reconstruction? Since the procedure seems to introduce correlation between the two maps (see point 4 below), it does not seem to be possible to obtain a gold-standard FSC value between two truly independent half-maps. As the DM procedure supposedly actually improves the map (by leveraging knowledge about what solvent and macromolecular maps usually looks like and thereby improves the Fourier coefficients), it feels like it would be misrepresenting the data by quoting the FSC_0.143 from the original reconstruction. Should I use the FSC_0.5 estimated value that phenix.resolve_cryo_em outputs? 4) Which FSC curve should I deposit? When I calculate the FSC between the two density modified half-maps, I get a funny (or rather not so funny) looking curve with a bump at around 3Å and it does not go to zero at Nyquist (which does not agree with the map quality). This must again be due to the induced correlation between the maps, presumably during the masking of solvent and macromolecule density. Phenix.resolve_cryo_em calculates a FSC curve to calculate the FSC_0.5 value, which according to the manual page corrects for the correlation induced between the two maps: "Density modification introduces some correlations between half-maps due to solvent flattening. This can have a small effect on the resolution estimates obtained with half-map FSC. The resolution estimates provided by the program are corrected for this effect." But is this curve good enough? I think OneDeposit wants to have the gold-standard FSC curve, right? 5) Which (nowadays mandatory) half-maps should one deposit? Here I would say that the original half-maps before DM makes more sense, since these are less processed. But if one specify these as the half-maps, there will be inconsistencies during validation, since the DM map will look quite different from the average between the two original half-maps. Also the automatic FSC curve will be very different from the deposited one. So in conclusion, despite what I say above, the most conservative thing would be to deposit the conventionally sharpened map as my main map and use the original half-maps for calculating the FSC-curve and use the 0.143 threshold from this curve to estimate the resolution. The DM map can be used during rebuilding/refinement, but I think final minimization should be against the main map during deposition (with restraints if the geometry gets worse). The DM map can be deposited as an auxiliary map. Do the community and the developers agree? 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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Postdoctoral position in YSBL, University of York
by Jon Agirre 31 Jan '23

31 Jan '23

Dear all, Applications are invited for a Postdoctoral Research Associate position, funded by the Royal Society, for up to 30 months to work with Dr Jon Agirre in the Department of Chemistry. The successful applicant will join a vibrant team of researchers at the heart of the world-leading York Structural Biology Laboratory (YSBL). The work of the laboratory over the years has included the delivery of world-leading methods and experimental discoveries, training and nurturing hundreds of outstanding scientists in the process. Role In collaboration with Dr. Elisa Fadda (Maynooth University, Ireland), we have developed proof-of-concept software that models protein glycosylation into AlphaFold models. This task has been automated and integrated into the new Python interface of the carbohydrate-specific Privateer software. In parallel, we have developed infrastructure and analyses that allow us to get a clear picture of glycans and their interactions. We expect that this technology will enable the successful applicant to, based on existing glycobiological knowledge, extend the Privateer software to predict, build and adapt models of glycans onto AlphaFold models. Main duties and responsibilities: - To develop and extend the Privateer software to predict, build and adapt models of glycans onto AlphaFold models. - To further our existing collaborations with CCP4, CCP-EM, PDB-REDO, the Protein Data Bank and the AlphaFold Protein Structure Database. For informal enquiries: please contact Dr Jon Agirre, jon.agirre(a)york.ac.uk To apply: https://jobs.york.ac.uk/vacancy/research-associate-513495.html Department The Department of Chemistry is one of the largest and most successful departments at York and we are renowned internationally for our research. As a department, we strive to provide a working environment that allows all staff and students to contribute fully, to flourish, and to excel. We are proud of our Athena Swan Gold Award. The Department of Chemistry values all employees for the qualities and skills they bring to the workplace and aims to be a diverse and egalitarian community in which all can thrive. Many thanks for making it this far in the advert! With best wishes, Jon -- Dr Jon Agirre [image: A button with "Hear my name" text for name playback in email signature] <https://www.name-coach.com/jon-agirre> Royal Society Olga Kennard Research Fellow CCP4 ED&I champion | instruct-ERIC representative @ 3D-Bioinfo (Elixir) York Structural Biology Laboratory, Department of Chemistry University of York, Heslington, YO10 5DD, York, UK http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ Office: /B/K/065 Phone: +44 (0) 1904 32 8252 Twitter: @glycojones

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Feb 9 Free Webinar: New Dimensions - How Computation Is Accelerating Structure Based Drug Design
by Mitchell D. Miller 31 Jan '23

31 Jan '23

Dear all, On Thursday, February 9, 2023 from 12:00 p.m. to 1:00 p.m. ET (17:00-18:00 UTC) Karen Akinsanya, President of Research & Development - Therapeutics, Schrödinger, Inc will present a zoom webinar titled New Dimensions - How Computation Is Accelerating Structure Based Drug Design This zoom webinar is free, but registration is required. Please see the registration link on the National Academies of Sciences, Engineering, and Medicine event page along with Karen Akinsanya's abstract and bio. https://www.nationalacademies.org/event/02-09-2023/new-dimensions-how-compu… A flyer for the webinar is also available https://www.nationalacademies.org/documents/embed/link/LF2255DA3DD1C41C0A42… This is the second presentation in the series -- Advancing Drug Discovery: A Webinar Series of the National Academies of Sciences, Engineering, and Medicine The series is being hosted jointly by the U.S. National Committee for Crystallography (USNC/Cr), the U.S. National Committee for the International Union of Pure and Applied Chemistry (USNC/IUPAC) and the U.S. National Committee for CODATA. More information about the series is on the NASEM website and it will be updated as additional webinars in the series are confirmed. The website also has links to recordings of "past events". https://www.nationalacademies.org/our-work/advancing-drug-discovery-a-webin… Please forward this to any you think would be interested. Sincerely, Mitch P.S. for those who missed the January 10, 2023 webinar presented by Ken Duncan, Deputy Director, The Bill & Melinda Gates Foundation on Pandemic Preparedness: Accelerating the Discovery of New Therapeutics The recording is available on the National Academies of Sciences, Engineering, and Medicine event page along with Ken Duncan's abstract and bio. https://www.nationalacademies.org/event/01-10-2023/pandemic-preparedness-ac…

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RapiData at SSRL 2022 - application deadline extended by two weeks!
by Smith, Clyde 12 Jan '23

12 Jan '23

We have extended the deadline for applications for a place at the RapiData 2022 @ SSRL workshop to next Friday, February 4th 2022! There are still a few spots left, so get your application in! The workshop will be held virtually from May 4 - 14 2022. The course will comprise 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). There will also be several days of software tutorials (HKL3000,XDS, CCP4/DIALS, Phenix, AutoSharp/AutoProc, Shelx, Coot) and you will all get to connect remotely to the SSRL beamlines to collect both monochromatic and MAD/SAD data. There is also an opportunity to ship your own samples to SSRL prior to the workshop, and collect your own data. Please visit https://www-ssrl.slac.stanford.edu/rapidata/rapidata-2022/index.html and use the links on the "registration" page to apply for the course. Successful applicants will be notified later in February 2022 and invited to register at that time (there will be no fee for registration). Regards, Clyde Smith (csmith(a)slac.stanford.edu) and Silvia Russi (srussi(a)slac.stanford.edu) Workshop Organizers

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Jan 10 Free Webinar: Pandemic Preparedness: Accelerating the Discovery of New Therapeutics
by Mitchell D. Miller 03 Jan '23

03 Jan '23

Dear all, On Tuesday, January 10, 2023 from 12:00 p.m. to 1:00 p.m. ET (17:00-18:00 UTC) Ken Duncan, Deputy Director, The Bill & Melinda Gates Foundation will present a zoom webinar titled Pandemic Preparedness: Accelerating the Discovery of New Therapeutics This zoom webinar is free, but registration is required. Please see the registration link on the National Academies of Sciences, Engineering, and Medicine event page along with Ken Duncan's abstract and bio. https://www.nationalacademies.org/event/01-10-2023/pandemic-preparedness-ac… A flyer for the webinar is also available https://www.nationalacademies.org/documents/embed/link/LF2255DA3DD1C41C0A42… This is the first presentation in a new series -- Advancing Drug Discovery: A Webinar Series of the National Academies of Sciences, Engineering, and Medicine The series is being hosted jointly by the U.S. National Committee for Crystallography (USNC/Cr), the U.S. National Committee for the International Union of Pure and Applied Chemistry (USNC/IUPAC) and the U.S. National Committee for CODATA. More information about the series is on the NASEM website and it will be updated as additional webinars in the series are confirmed. https://www.nationalacademies.org/our-work/advancing-drug-discovery-a-webin… Please forward this to any you think would be interested. Sincerely, Mitch

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