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Berkeley Lab Exascale Computational Crystallographer
by Nicholas Sauter 19 Feb '20

19 Feb '20

Discover your future at Berkeley Lab! Berkeley Lab’s Molecular Biophysics & Integrated Bioimaging Division ( https://biosciences.lbl.gov/divisions/mbib/) has an opening for an Exascale Computational Crystallographer Project Scientist. The Project Scientist, with a strong interest in high-performance computing and an intuitive feel for experimental data, will be affiliated with the Exascale Computing Project, specifically Nick Sauter’s Data Analytics for X-ray Free Electron Lasers (XFELs) group focusing on scientific software for X-ray crystallography. The next decade of structural biology at the Linac Coherent Light Source (LCLS) will include groundbreaking advances in time-domain crystallography, performed at room temperature to preserve biologically relevant dynamic mechanisms. Considering the anticipated scale of these datasets, we have an ambitious collaboration between SLAC, LANL, and LBNL to utilize national supercomputer facilities for near real-time analysis, in close collaboration with scientists at NERSC (also located in Berkeley). The group’s projects will include: • Photosystem II, discovering the sequence of redox events leading to the release of molecular oxygen, using a combination of time-resolved crystallography and X-ray emission spectroscopy. https://doi.org/10.1038/s41586-018-0681-2 • Examining the electronic environment of metalloenzyme catalytic metals, with detection based on anomalous scattering. The Project Scientist will be positioned to launch into high-performance computing careers at a light source or other experimental facilities. https://doi.org/10.1107/S2059798320000418 Please have a look at our job posting at https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=89727 Nicholas K. Sauter, Ph. D. Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720 (510) 486-5713

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Macromolecular Crystallography School, Madrid 2020 (MCS2020)
by Armando Albert 19 Feb '20

19 Feb '20

Dear colleagues, We are pleased to announce the 10th edition of the Macromolecular Crystallography School 2020, to be held at the Institute Química-Física Rocasolano- CSIC (Madrid, Spain). Dates: April 13 - 18, 2020 The workshop has been designed for postgraduate, postdoctoral and research scientists that deal with macromolecular crystallography and cryo EM but need further knowledge on the routine uses, the state of the art and fundamentals that underlie the modern techniques for macromolecular crystallography and cryo EM. The topics will cover crystallographic computing and fundamentals using XDS, CCP4 and Phenix, as well as the state of the art on topics such as the strategies for protein production, data collection, phasing, automated pipelines at synchrotron and refinement with ARCIMBOLDO, SHELX and SIR2014 and modeling with COOT. MCS2020 will provide six days of lectures and workshops. The course is designed for 25 highly motivated attendants. Requests to participate must be sent by a free-formated E-mail, before March 11th, 2020 to the following address: cursos(a)fgua.es <mailto:[email protected]>, indicating the motivation to participate and experience on macromolecular crystallography and including a letter of recommendation from PhD Director (only for PhD students). Invited speakers and tutors: - Maria Solá, Barcelona, Spain - Isabel Usón, Barcelona, Spain - Paul Adams, Berkeley, USA - Pavel Afonine, Berkeley, USA - Kay Diederichs, Konstanz, Germany - Paul Emsley, Cambridge, UK - Rafael Fernández-Leiro, Madrid, Spain - Carmelo Giacovazzo, Bari, Italy - Eugene Krissinel, Oxford, UK - Jose. A. Marquez, Grenoble, France - Claudia Millan, Barcelona, Spain - Begoña Monterroso, Madrid, Spain - Rob Nicholls, Cambridge, UK - Santosh Panjikar, Australia - Carmen San Martín, Madrid, Spain Please find attached the program of the Workshop, the application form and further information at http://www.xtal.iqfr.csic.es/MCS2020/ <http://www.xtal.iqfr.csic.es/MCS2020/> Organizers: Armando Albert (xalbert(a)iqfr.csic.es <mailto:[email protected]> ), Juan A. Hermoso (xjuan(a)iqfr.csic.es <mailto:[email protected]>) and Isabel Usón (iufcri(a)ibmb.csic.es <mailto:[email protected]>)

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EMBO meeting on “Molecular Neurobiology” 8-12 May 2020
by Janssen, B.J.C. (Bert) 17 Feb '20

17 Feb '20

Dear all, We would like to draw your attention to the EMBO workshop on "Molecular Neurobiology", taking place on the beautiful island of Crete on 8-12 May 2020. The meeting brings together world leading scientists, group leaders and young researchers with a keen interest in the latest science occurring at the interfaces of structural biology, biophysics, molecular & cellular imaging and neuroscience. Given its cross-disciplinary nature, the meeting presents a broad overview of molecular neurobiology, ample opportunities for discussions and a sneak peek into the latest developments. See http://meetings.embo.org/event/20-molneuro for more information and application guidelines, registration deadline is 15 Feb. 2020. Organizers: Alain Chédotal, Institut de la Vision, France Bert Janssen, Utrecht University, the Netherlands Chenghua Gu, Harvard University, USA Elena Seiradake, University of Oxford, UK Nektarios Tavernarakis, IMBB FORTH, Greece Best wishes Bert Bert Janssen Bijvoet Center for biomolecular research Utrecht University Padualaan 8, 3584 CH, Utrecht

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PhD position available
by Tobias Beck 17 Feb '20

17 Feb '20

Dear all, There is an opening for a PhD position in my group. The Beck group recently moved to Hamburg, where we have labs well-equipped for chemistry, biochemistry and molecular biology. Moreover, state-of-the-art facilities for structural characterizations such as PETRA III are close by. The project involves protein redesign, protein chemistry and characterization and more. The post is available immediately / upon arrangement. Full details of the post and the applications process are available here: https://www.uni-hamburg.de/uhh/stellenangebote/wissenschaftliches-personal/… The group homepage can be found here: https://www.chemie.uni-hamburg.de/institute/pc/arbeitsgruppen/beck.html Deadline for applications is March 15 2020. Please contact me for further information or informal inquiries: tobias.beck @chemie.uni-hamburg.de Best, Tobias. ____________________________________________________________ Prof. Dr. Tobias Beck University of Hamburg Department of Chemistry Institute of Physical Chemistry Grindelallee 117 D-20146 Hamburg Germany phone: +49 4042838 8210 fax: +49 4042838 3462 web: www.chemie.uni-hamburg.de/institute/pc/arbeitsgruppen/beck/ ____________________________________________________________

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Job Posting: Surrozen Inc., RA / SRA - Biophysics / Biochemistry
by Parthasarathy Sampathkumar 15 Feb '20

15 Feb '20

Dear All, Please allow me to post this link for RA / SRA - Biophysics / Biochemistry Position at Surrozen with focus on Antibody Developability and Structural Biology. https://apply.workable.com/surrozen/j/75748FA62D/ I request interested job seekers to apply directly online using the above link. Thanks, Best Wishes, Partha __________________________ Parthasarathy Sampathkumar PhD Senior Scientist, Surrozen Inc., 171 Oyster Point Blvd., Suite 400 South San Francisco, CA 94080 Email: partha(a)surrozen.com

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Neutrons in the Environment and Life Sciences Workshop - HANDS 2020
by Meilleur, Flora 13 Feb '20

13 Feb '20

First announcement HANDS 2020 HFIR/SNS Advanced Neutron Diffraction and Scattering Workshop Oak Ridge, TN. June 1 - June 5, 2020 Oak Ridge National Laboratory, in conjunction with North Carolina State University, and support from the National Science Foundation and the Shull Wollan Center - a Joint Institute for Neutron Scattering, celebrates a decade of neutron scattering education in structural biology at ORNL with the HFIR/SNS Advanced Neutron Diffraction and Scattering workshop (HANDS 2020). Detailed information can be found on the workshop web page: https://conference.sns.gov/event/217/. Application deadline: April 24, 2020 Fellowships to support travel and accommodation are available (subject to availability of funds) The workshop aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Participants of HANDS 2020 will become familiar with neutron techniques with hands-on experiments in sample preparation, crystallography, small angle scattering, reflectometry and neutron spin echo. The workshop is designed for graduate students, post-doctoral fellows and faculty with limited to no experience with neutron sciences. Flora Meilleur, Ph. D Neutron Scattering Scientist, Neutron Scattering Division Oak Ridge National Laboratory Associate Professor, Molecular and Structural Biochemistry North Carolina State University

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IUCr Committee on Data Workshops at IUCr Congress Prague
by John R Helliwell 13 Feb '20

13 Feb '20

Dear Colleagues, The IUCr Committee on Data has two workshops, one in macromolecular & one in chemical crystallography, to be held at IUCr Congress Prague, each to be held August 22nd 2020. See https://forums.iucr.org/viewtopic.php?f=39&t=429 Best wishes, John Emeritus Professor John R Helliwell DSc Chairman of the IUCr Committee on Data

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Phenix workshop at ACA 2020 (San Diego)
by Pavel Afonine 12 Feb '20

12 Feb '20

Dear Colleagues, please make a note of upcoming Phenix workshop focusing on crystallography and Cryo-EM tools for structure solution, August 2nd 2020 in San Diego, California. This is a day-long satellite workshop prior to ACA meeting. For schedule and registration see ACA 2020 web site: www.acameeting.com <https://www.acameeting.com/workshops> (Program -> Workshops). Looking forward to see you there! Pavel

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Postbaccalaureate and postdoc position in membrane protein structure and function lab at the NIH
by Anirban Banerjee 09 Feb '20

09 Feb '20

Dear colleague, I have openings for the two following positions in my lab. I am also attaching a word document if you wouldn’t mind kindly posting it at an appropriate place in your Department *Postbac position* Postbac position in my lab for two years starting from the coming summer. The NIH Postbac IRTA program provides recent college graduates who are planning to apply to graduate or professional (medical/dental/pharmacy) school an opportunity to dofull-time research at the NIH. For this position I am looking for someone who has experience with protein purification, has good organizational skills and work ethics, and the right mindset to pay attention to nitty-gritty details that are essential for working with membrane proteins. The candidate should apply to the NIH Postbac Program (https://www.training.nih.gov/programs/postbac_irta) and get in touch with me as well. Postbac candidates have to be US citizens or permanent residents. *Postdoctoral position* There is an open postdoctoral position for a membrane protein structure-function project in my lab at the NIH. We are currently focusing on integral membrane enzymes (*Science. *2018, doi: 10.1126/science.aao6326) and transporters of transition metal ions (*J Biol Chem.* 2018, doi: 10.1074/jbc.M117.817478). Here is the formal announcement - *EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT, BETHESDA, MD AND SURROUNDING AREA* *Position Description: * The research group of Dr. Anirban Banerjee at the National Institutes of Health (NIH) is seeking candidates for postdoctoral fellows . The broad interests of the lab are in membrane protein structure and function. We combine structural techniques such as macromolecular crystallography and cryoEM together with biophysical and biochemical methods such as reconstitution based assays, high resolution microscopy and small molecule screening to investigate the structural bases of the mechanisms of a number of membrane proteins. The lab has state-of-the-art equipment and facilities. We have dedicated periodic access to the 22-ID beamline at the APS, for crystallographers at the NIH, as well as access to 23-ID and 24-ID beam lines at the APS. NICHD is now part of a consortium that has access to a Titan Krios on a regular basis. Our laboratory is part of the Cell Biology and Neurobiology Branch in the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD). *Qualifications:* The candidates should hold a Ph. D. degree (by the time of joining the lab), be author of at least one first author publication and have a strong background in biochemistry or structural biology. Experience with basic molecular biology, protein expression, purification and biochemical characterization are required. Prior experience in membrane protein biochemistry or mammalian expression system for protein purification will be added advantages. It is absolutely essential the candidate is motivated and prepared to put in the best efforts for fruition of the project goals. We are a small, friendly lab and ability to work as part of a cohesive group is important. Thanks very much in advance for any help and apologies for the bother. Warm regards, Anirban Anirban Banerjee Head, Unit on Structural and Chemical Biology of Membrane Proteins Neurosciences and Cellular and Structural Biology Division Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) National Institutes of Health (NIH) Building 35, Room 2F-127 35A Convent Drive MSC 3758 Bethesda, MD 20892-3758 Tel: 301-496-4855 Fax: 301-402-9319 anirban.banerjee(a)nih.gov https://science.nichd.nih.gov/confluence/display/banerjee/Home >

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Validation_cryoEM Calculation the FSC model-map
by Marta Martinez 05 Feb '20

05 Feb '20

Dear all, we are wondering how the mask and unmasked values of the FSC model-map have been computed and how the mask is defined when the phenix tool phenix.validation_cryoem ("Comprenhensive Validation (cryo-EM)") is used. The motivation of this question comes from the results that we get when we have big maps (e.g. some viruses) and the atomic structure is determined only for the asymmetric subunit. We usually compute the validation considering both the whole map, and a fraction of the map that only contains the atomic structure of the asymmetric subunit (the atomic model is the same in both cases, the asymmetric subunit). We would expect the same results, as it happens for the validation statistics, but the FSC model-map values are different, especially when we talk about masked values. Recently we have checked that we have the same kind of results when we use small maps, so it doesn't seem to be due to the size of the map. Can you kindly explain the reason of these results and what we should expect in general. Is there any restriction when a fraction of the whole volume is selected? Thank you very much in advance. Regards, MARTA -- Marta Martinez Gonzalez Biocomputing Unit (Lab B13) National Center for Biotechnology-CSIC Darwin, 3. Campus de la Universidad Autonoma de Madrid 28049 Madrid. Spain Tel:+34 915854510 Fax:+34 913720112 E-mail: mmmtnez(a)cnb.csic.es

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