- phenixbb - phenix-online.org

(no subject)
by Armando Albert 07 Feb '23

07 Feb '23

Dear all, The registration for the next edition of the Macromolecular Crystallography School in Madrid from the 8th to the 12th of May 2023 is open. The workshop has been organized at Instituto de Química Física Rocasolano CSIC since 2010 and it is meant for 25 graduate students or researchers with previous expertise in crystallography and/or CryoEM who need a deeper insight into the most advanced crystallographic and CryoEM techniques to carry out their research projects. The program traditionally covers aspects such as sample preparation, structure solution, model building, crystallographic refinement, validation, and analysis of the structural results, as well as an overview of the newest structural biology technologies. On top of these subjects, this year's program will include those aspects related to the impact of Artificial Intelligence methods on structure solution and low-resolution refinement. In addition, we will cover dynamic crystallography at XFEL and synchrotron and ligand building for drug discovery. You may find further information on our website (https://www.xtal.iqfr.csic.es/MCCS2023/index.html <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fwww.xtal.iqfr.csic.es%2…>) Hoping to see you In Madrid Juan and Armando Armando Albert and Juan A. Hermoso Departamento de Cristalografía y Biología Estructural Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas Serrano 119, 28006 Madrid Spain

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Solving MR solution without sequence information
by Rosenberg, Eric (NIH/NCI) [F] 06 Feb '23

06 Feb '23

Hi all, I'm in a bit of bind here and am seeking some advice. For context, a former graduate student in our lab set crystal trays of an MBP fusion protein, the fused part after MBP being ~400 amino acids long. This region is also predicted to be mostly unstructured, but has a C-terminal SH3 domain. Our graduate student then graduated and before throwing out some of her trays a year or two later, we found some hits of the MBP fusion protein that actually diffracted to 2.9 Angstrom. I spent some time working on it after we collected the data (June 2021), but because I didn't know what crystallized specifically, it was impossible to phase, and replicating seemed next to impossible, too. The Matthew's coefficient was predicting ~130 amino acids in the ASU, space group C222 or C2221. Since whatever crystallized was clearly a degradation product of the MBP fusion, I tried phasing with SH3 domains and a lot of other things to no avail. As a final last ditch effort I eventually submitted the .mtz file to SBGrid to perform a Wide Search MR job, and low and behold it actually found MR solutions that had TFZ scores ~17 in space group C2221! So here's my current situation-I have been able to phase the data set using the MR search model, but again, I don't know what specifically it is that I've crystallized. I'm currently able to get the Rfree to ~0.4, but can't seem to improve it. I am really at a loss of what to do, since there are obvious backbone issues with the protein (as seen from iterative build composite omit maps), but every time I try to manually correct them it seems to make the Rfree worse. The MR solution does not align very well at all to the MBP fusion, only ~20 identity, and again, I don't know to which ~130 amino acids I crystallized out of the ~400 of the MBP fusion. Is it one continuous stretch, two copies of a shorter stretch, etc.? I tried phasing with a polyalanine model of the MR search model and then tried autobuilding just a polyalanine sequence to get the backbone right, but that doesn't seem to work. Autobuild also fails when trying to various fragments of the MBP fusion sequence. Other than opening coot and manually building the entire polypeptide chain, is there an easier method? I think that once the backbone is totally right the phases will improve so I can start putting in side chains, but I'm not sure. My latest effort is to just use Sculptor prior to Phaser in order to force the sequences to match, but again, I don't know precisely what sequence was crystallized. I have tried both the Phenix and CCP4 software suites, for reference. Any and all help would be much appreciated (and yield an acknowledgement on a paper, if this ever works). Best, Eric Rosenberg CRTA Postdoctoral Fellow Randazzo Lab Laboratory of Cellular and Molecular Biology National Cancer Institute, US

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Re: [phenixbb] Solving MR solution without sequence information
by Dom Bellini 04 Feb '23

04 Feb '23

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Re: [phenixbb] Solving MR solution without sequence information
by Kay Diederichs 04 Feb '23

04 Feb '23

Hi Eric, I'd try the following: 1) use SIMBAD to potentially find other/better models 2) use ISOLDE for model building - maybe ask Tristan Croll for help 3) submit your best model to the DALI server to retrieve closer models HTH, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

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Postdoctoral position in YSBL, University of York
by Jon Agirre 01 Feb '23

01 Feb '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 13 Jan '23

13 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 04 Jan '23

04 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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staraniso/phenix.refine
by Andrea Piserchio 23 Dec '22

23 Dec '22

Dear all, I am trying to validate and then (hopefully) deposit a structure generated using the autoproc/staraniso staraniso_alldata-unique.mtz file as input for phenix.refine. Autoproc also produces a cif file ( Data_1_autoPROC_STARANISO_all.cif) specifically for deposition. Long story short, the PDB validation server complains about the lack of a freeR set for both files. I realized that, at least for the cif file, the r_free_flag is missing (but why does the .mtz for the isotropic dataset work??),so I then tried to use for validation the *.reflections.cif file that can be generated by phenix.refine. This file can actually produce a validation report, but I still have some questions: 1) Is it proper to use the .reflections.cif file for this purpose? During the upload I do see some errors (see pics); also, the final results show various RSRZ outliers in regions of the structure that look reasonably good by looking at the maps on coot, which seems odd ... 2) In case the *.reflections.cif is not adequate/sufficient for deposition (I sent an inquiry to the PDB, but they did not respond yet), can I just add a _refln.status column to the autoproc cif file (within the loop containing the r_free_flag) where I insert “f” for r_free_flag = 0 and “o” everywhere else? Thank you in advance, Andrea

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Labeling centric and acentric reflections
by Andre LB Ambrosio 22 Dec '22

22 Dec '22

Hi, Is there a way to label centric and acentric reflections in the .mtz file and output an additional column, let's say, with values 0 (acentric) and 1 (centric), similar to R_free flags? Many thanks for your attention. -- Andre LB Ambrosio Associate Professor, IFSC/USP - Brazil www.ifsc.usp.br/alba

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