November 2022 - phenixbb - phenix-online.org

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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IUCr meeting in 2023
by Tom Peat 23 Nov '22

23 Nov '22

Hello All, Some of you may have noticed that the deadline for abstract submission for the IUCr meeting in Melbourne, Australia passed just recently. There are reasons for the early deadline, but please forgive us for that. There is an extension/ second call for abstracts which will be advertised in the near future. In the meantime, the portal is still open and you are welcomed and encouraged to continue to submit and register for this conference (where we hope to see many of you). This link should work to get you there: https://icmsaust.eventsair.com/iucr-2023/portal-2 Best regards, Tom

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Fully-funded PhD and two postdoc positions in structural bioinformatics
by Nicholas Pearce 22 Nov '22

22 Nov '22

Hi all, I am currently recruiting for 1 fully-funded PhD and 2 postdoc positions within my new research group at Linköping University in Sweden. Because this is an international board: the PhD position is a 4-year employed position with salary, healthcare coverage, pension, other employment benefits, etc. The starting salary for PhD researchers is 30 500 SEK/month (in 2022). The postdoc positions are initially for 2 years, and salaries for postdocs are negotiated on an individual basis. PhD Student in Structural Bioinformatics (Macromolecular Flexibility & Dynamics) I am looking for a PhD student to develop machine learning and data-science approaches to characterise heterogeneous/disordered regions of crystallographic structures from multi-dataset experiments (fragment screening/multi-temperature/time-resolved experiments), in order to study flexibility and dynamics of these systems. If you have a background in machine learning approaches, and are interested in applying these approaches to biological data, or a background in (computational) structural biology, and looking to further develop your data-science/programming skills, please get in touch! Read more and apply here: https://liu.se/en/work-at-liu/vacancies?rmpage=job&rmjob=20567&rmlang=UK Postdoctoral Researchers in Structural Bioinformatics (Macromolecular Flexibility & Dynamics) I am also looking for two postdoctoral researchers to 1) develop and deploy methods for quantifying and analysing flexibility in macromolecular structures using machine learning approaches, and 2) develop new modelling and refinement protocols for structures from multi-dataset experiments (fragment screening/multi-temperature/time-resolved experiments) that enable visualisation and quantitative analysis of weak features in multi-dataset macromolecular structural data. Once more, please don’t hesitate to get in touch if you have questions about the positions! Read more and apply here: Position 1: https://liu.se/en/work-at-liu/vacancies?rmpage=job&rmjob=20513&rmlang=UK Position 2: https://liu.se/en/work-at-liu/vacancies?rmpage=job&rmjob=20539&rmlang=UK About the research group In the Data-Driven Determination of Macromolecular Structures (d3ms) group at Linköping University, we develop data-driven methodologies for determining and analysing macromolecular structures, focussing on structural disorder and dynamics in the context of biomedical applications. One of our primary focuses is the development of multi-dataset and integrative approaches which take advantage of ever-increasing data-collection capacities in both crystallographic and cryoEM experiments. This subject area means we use a variety of statistical, data science & machine learning approaches. The group website can be found here: macromolecular.github.io<https://macromolecular.github.io/> We are based in the bioinformatics division within the department of Physics, Chemistry and Biology (IFM) at Linköping University. Our research group is part of the Data-Driven Life Sciences (DDLS) program and the SciLifeLab national network, providing access to national computational resources, expertise and training opportunities. The location of the Swedish national supercomputer centre on the Linköping university campus provides additional access to computational resources. The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) is a 12-year initiative funded with a total of 3,1 billion SEK (~300M€) from the Knut and Alice Wallenberg Foundation. The purpose of the program is to recruit and train the next-generation of data-driven life scientists and to create globally leading computational and data science capabilities in life science in Sweden. The program is coordinated by SciLifeLab, a nationwide research infrastructure and a hub for cross-disciplinary life sciences. The DDLS program promotes collaborative interdisciplinary work and engagement with industry, healthcare and other national and international partners, such as WASP, with the aim of bridging the life science and data science communities. Please feel free to forward this to anyone you think might be interested in the position, Thanks, Nick Nicholas (Nick) Pearce | Assistant Professor in Bioinformatics SciLifeLab Data-Driven Life Sciences (DDLS) Fellow Linköping University, Sweden nicholas.pearce(a)liu.se<mailto:[email protected]> | macromolecular.science<http://www.macromolecular.science/> or macromolecular.github.io<https://macromolecular.github.io/>

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Isolate Protofilament from helical reconstruction
by Christian Tüting 09 Nov '22

09 Nov '22

Dear PHENIX mailing list, I have a question regarding a helical reconstruction, done in cryoSPARC. Usually, I work with "normal" symmetric particles, and there I can simply run phenix.map_box to isolate the asymmetric unit. This is somehow not possible with a helical map. As we also don't have an atomic model yet, we cannot just crop it with map_box. In our helical reconstruction, we have helical twist (in degree) and the helical rise (in Å) and a additional point group symmetry. We would like to isolate a single protofilament for further model building. Is this in principle possible in PHENIX? Additionally, is there a way to rebuild the helical structure, analogous to apply_ncs? Thanks Christian

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Douse adding waters with overlapping residue number
by Adrián González López 02 Nov '22

02 Nov '22

Dear phenix developers, When I run phenix.douse it assigns the waters to the closest chain, but it also attributes them the residue number 0, 1, 2, 3, 4…. which overlaps with the protein residues. Is this a bug? My workaround is to run phenix.sort_hetatms right after and it renumbers them correctly. I am on phenix version 1.20.1-4487-000 Thanks! 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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