April 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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Virtual Crash Course - Understanding PDBx/mmCIF | May 3rd | REGISTER NOW!
by Chenghua Shao 02 May '23

02 May '23

*Use PDB data to their full extent: Understanding PDBx/mmCIF * Wednesday, May 3rd 2023 | 1:00 PM EDT Registration: go.rutgers.edu/u3vpwjet <https://go.rutgers.edu/u3vpwjet> * This RCSB Protein Data Bank (PDB) virtual course will be broadcast on Zoom. Please fill out the registration form to receive the Zoom link. Registration will be available online from March 1, 2023 to May 3, 2023. LEARNING OBJECTIVES Understand the basics of PDBx/mmCIF data dictionary and file format that underpin archiving of more than 200,000 experimentally determined three-dimensional biostructures in the PDB. Learn about software tools for generating and working with PDBx/mmCIF files, and programmatic access for harvesting PDB data. Main topics: * PDBx/mmCIF format description and examples * PDBx/mmCIF data model * Software tools for generating, editing, and visualizing PDBx/mmCIF files * PDBx/mmCIF dictionary extensions, including ModelCIF for computed structure models (CSM) from AI/ML * Parsing data from PDBx/mmCIF files for your research *WHO SHOULD ATTEND * Professionals and graduate students interested in learning about strategies to take full advantage of PDB data in the fields of: * Structural biology * Cheminformatics and computational chemistry * Bioinformatics and computational biology *PROGRAM* | Download Printable Program <https://iqb.rutgers.edu/sites/iqb.rutgers.edu/files/crashcourses/mmCIF-cras…> 1:00–1:10 PM Welcome Stephen K. Burley, M.D., D.Phil. Director, RCSB PDB and Founding Director, Institute for Quantitative Biomedicine, Rutgers University 1:10–1:25 PM Introduction and course objectives Gregg Crichlow, Ph.D., RCSB PDB, Rutgers University 1:25–1:45 PM PDBx/mmCIF format - Not your parents’ legacy PDB format Ezra Peisach, Ph.D., RCSB PDB, Rutgers University 1:45–2:05 PM PDBx/mmCIF data files - Lifting the lid off the black box Brian Hudson, Ph.D., RCSB PDB, Rutgers University 2:05–2:50 PM Programmatic data access and analysis using PDBx/mmCIF files Irina Persikova, Ph.D. and Chenghua Shao, Ph.D., RCSB PDB, Rutgers University 2:50–3:00 PM Closing remarks and acknowledgements Stephen K. Burley, M.D., D.Phil. Development and management of the PDBx/mmCIF data dictionary is a collaborative effort involving RCSB PDB, Worldwide Protein Data Bank (wwPDB, wwPDB.org <http://www.wwpdb.org/>) partners, and members of the wwPDB PDBx/mmCIF Working Group (wwpdb.org/task/mmcif <https://www.wwpdb.org/task/mmcif>). CO-ORGANIZERS RCSB PDB Biocurators: Gregg Crichlow, Justin Flatt, Sutapa Ghosh, Brian Hudson, Yuhe Liang, Ezra Peisach, Irina Persikova, Monica Sekharan, Chenghua Shao, Jasmine Young (Rutgers, The State University of New Jersey). *QUESTIONS* Contact Michelle Sanghera msanghera(a)iqb.rutgers.edu *CO-SPONSORS * ** RCSB Protein Data Bank rcsb.org <https://www.rcsb.org/> RCSB PDB is managed by Rutgers, UCSD/SDSC, and UCSF. RCSB PDB is supported by grants from the NSF (DBI-1832184), the US DoE (DE-SC0019749), and the NIH (R01GM133198). RCSB PDB is a founding member of the wwPDB. Institute for Quantitative Biomedicine iqb.rutgers.edu <https://iqb.rutgers.edu/>

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Fwd: Postdoc position in San Antonio, TX
by Yogesh Gupta 14 Apr '23

14 Apr '23

*NIH-funded Postdoctoral Associate position in Structural Virology at the University of Texas Health Science Center, San Antonio* The laboratory of Dr. Yogesh Gupta (http://ccri.uthscsa.edu/YGupta.html) is seeking an enthusiastic Postdoctoral Associate to study the structures and specificity of RNA modification enzymes. We will mainly use X-ray crystallography and cryo-EM to study the mechanisms and develop small molecule antiviral candidates. We provide a rich multi-disciplinary environment and access to cutting-edge technologies to our trainees. Further details of our recent work can be found here: Elife. 2022 Jan 21;11:e67150. doi: 10.7554/eLife.67150 <https://elifesciences.org/articles/67150>. Nature Communications. 2021 Jun 2; 12: 3287. PMID: 34078893. doi: 10.1038/s41467-021-23594-y <https://www.nature.com/articles/s41467-021-23594-y> Nature Communications. 2020 Jul 24;11(1):3718. PMID: 32709886. doi: 10.1038/s41467-020-17496-8 <https://www.nature.com/articles/s41467-020-17496-8> Preference will be given to applicants with demonstrated experience in protein purification from insect or mammalian cells, protein/nucleic acid biochemistry, X-ray crystallography, and cryo-EM. Candidates are expected to possess strong organizational and interpersonal skills and the ability to work independently but also effectively and collaboratively as part of a team. An ideal candidate should hold (or soon expect to) a Ph.D. or equivalent degree in biochemistry/biophysics/structural biology. The Greehey Children’s Cancer Research Institute (GCCRI) is a unique, specialized cancer research center of UT Health Science Center San Antonio, focusing on basic and translational research. It occupies a state-of-the-art 100,000 sq. foot research facility on the university’s Greehey Academic and Research Campus. The GCCRI has significant external funding, a large endowment from the state, and links to philanthropic entities. San Antonio is the nation’s seventh-largest city and is located at the edge of the beautiful Texas Hill Country. San Antonio offers a rich, multicultural community, affordable cost of living, excellent weather, and a thriving biomedical industry. There is no state income tax in Texas. Salary is competitive and commensurate with experience. Interested candidates can apply by sending a short description of their research accomplishments and a CV with the contact information of 3 references to Dr. Yogesh Gupta (email: guptay(a)uthscsa.edu). *All Postdoctoral appointments are designated as security-sensitive positions. UT Health San Antonio is an Equal Opportunity/Affirmative Action Employer, including protected veterans and persons with disabilities.* -- Yogesh Gupta, Ph.D. Associate Professor Department of Biochemistry and Structural Biology University of Texas Health Science Center at San Antonio 8403 Floyd Curl Drive, San Antonio, TX, USA 78229 http://ccri.uthscsa.edu/YGupta.html

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Potential website disruptions
by Billy Poon 11 Apr '23

11 Apr '23

Hi everyone, We are doing some maintenance on our websites, https://phenix-online.org and https://cci.lbl.gov, over the next few days. There may be some disruptions. Thanks in advance for your patience. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

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ALS Webinar April 10th
by Paul Adams 05 Apr '23

05 Apr '23

Dear Colleagues, A reminder that we will be hosting a webinar (registration link below) that provides information for the synchrotron structural biology user community about accessing the resources at the Advanced Light Source in Berkeley. This is timely because of the imminent closure of the Advanced Photon Source for a year for their upgrade. Synchrotron capacity for biosciences research will be significantly impacted, and we want to be sure that the community has information about alternative facilities during the APS dark time. http://als-enable.lbl.gov/wordpress/2023/03/14/als-enable-webinar-april-10t… The webinar will cover capabilities at the beamlines in macromolecular crystallography, small angle X-ray scattering, and X-ray footprinting, as well as information on how to apply for beamtime. While the webinar is of most relevance to the US research community, we welcome participation by anyone who is interested. Cheers, Paul -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 268 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Postdoctoral position in structure of sugar and phytohormone transporting membrane proteins at Aarhus University, Denmark.
by Bjørn Panyella Pedersen 03 Apr '23

03 Apr '23

Dear colleagues, Please pass this along anyone who might be interested. Thanks! /Bjørn Postdoctoral position in structure of sugar and phytohormone transporting membrane proteins at Aarhus University, Denmark. online posting: https://www.au.dk/om/stillinger/job/postdoctoral-position-in-structure-of-s… We are looking for a highly skilled and motivated postdoc with an interest in working on sugar and hormone transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins. The position will be open from summer 2023, but starting date is negotiable. Funding is available for at least 2 years of employment, with an extension possible for up to 4 years. The position: The position seeks to strengthen ongoing activities in the our group related to the function and mechanism of sugar-transporting and hormone-transporting membrane proteins in plants (pedersenlab.dk). Examples of our research can be found in: Bavnhøj et al. “Molecular mechanism of sugar transport in plants unveiled by structures of glucose/H+ symporter STP10” Nature Plants 7 (2021) Ung et al. “Structures and mechanism of the plant PIN-FORMED auxin transporter” Nature 609 (2022). The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems and proton driven transport, and the methods uses are primarily structural biology (cryo-EM, crystallography) and biochemistry. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - an exciting interdisciplinary environment with many national, international and industrial collaborators. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. See “life in Denmark” at Aarhus and surroundings for further details on the city and the university (https://international.au.dk/life/locations/aarhusandsurroundings). Deadline: All applications must be made online and received by 15. May. 2023. See deails here: https://www.au.dk/om/stillinger/job/postdoctoral-position-in-structure-of-s…

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