- phenixbb - phenix-online.org

Real-space refinement fails to restrain CYS SG ZN properly
by Aaron Oakley 02 Mar '20

02 Mar '20

I'm trying to refine a structure containing ZN bound to four cysteine residues. I have had trouble with Real-space refinement mangling the residues around this ZN. At first, Real-space refinement tried to turn the cysteine into disulfides. I tried switching this off with… resname CYS and name SG …in the disulphide bond exclusion selection string under the Model interpretation menu (there are no disulfides in the protein). But the cysteine-zinc cluster continued to be mangled. Inspection of the .geo file shows that the SG-ZN distance is being restrained, but the CB–SG–ZN angle is not. I checked the relevant dictionary file... phenix-1.17.1-3660/modules/chem_data/mon_lib/list/mon_lib_list.cif And the correct bond and angle restraints do seem to be present: . . . ZN-CYS 1 ZN 2 SG single 2.340 0.020 . . . ZN-CYS 1 ZN 2 SG 2 CB 109.000 3.000 . . . Suggestions on how to fix this welcome. –å

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Dock in map fails with search map file.
by Aaron Oakley 27 Feb '20

27 Feb '20

Salvete! I am trying to use Dock in map to superimpose one map onto another. The job runs, but fails with PHENIX error: “Job294_sharpened_relion.mrc_as_model_refine_001.pdb" is not a known model type. Inspection of this file suggests that it is indeed a proper PDB file. (The original map I am trying to move is job294_sharpened_relion.mrc). Any solutions? Thanks, –å

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real space correlation coefficient from the command line
by Daniel Larsson 25 Feb '20

25 Feb '20

Hi, When running a real-space refine, there is an option in the results to save a text file with real-space correlation coefficients (correlation_coeficients.txt). Is there a way to calculate these numbers from the command line? It would save me a lot of clicking, sinceI have dozens of maps which I want to run in parallel and analyze using scripts. 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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IUCr2020 Computing School in Nove Hrady - 17th to 22nd August - Registration opened
by Claudia Millán Nebot 24 Feb '20

24 Feb '20

Dear all, We announce the IUCr Computing School in Nove Hrady (Czech Republic) which will take place between 17th and 22nd August 2020 prior to the IUCr Congress in Prague. Registration has already started. Further information about the school can be found on the website: https://www.xray.cz/iucr/workshops/nh/default.htm. Follow also our hashtag on Twitter, #IUCr2020CompSchool. Active developers of crystallographic software, tools and methods are invited to participate at this Computing School. The school is not introductory and it is recommended that participants already have some basic programming skills and crystallographic knowledge. Our aim is to discuss and exchange ideas and to tackle the challenges related to the method development in crystallography. Participants can be early-career scientists (PhD students, Postdocs, etc.) as well as established developers. Our confirmed speakers are: - Simon Billinge (Columbia University, USA) - Luc Bourhis (Bruker, France) - Paul Boyle (Western University, London, Ontario, Canada) - Iracema Caballero (Institut de Biologia Molecular de Barcelona, Spain) - Gemma de la Flor (Karlsruhe Institute of Technology, Germany) - Dorothee Liebschner (Lawrence Berkeley National Laboratory, USA) - Rafiga Masmaliyeva (Institute of Molecular Biology and Biotechnology, Azerbaijan) - Garib Murshudov (Laboratory of Molecular Biology-MRC, UK) - Reinhard Neder (Institute of Condensed Matter Physics, Erlangen, Germany) - Alexandre Ourjoumtsev (Institut de Génétique et de Biologie Moléculaire et Cellulaire, France) - Randy Read (University of Cambridge, UK) - Massimo Sammito (University of Cambridge, UK) - Arkadiy Simonov (Eidgenössische Technische Hochschule Zürich, Switzerland) - Melanie Vollmar (Diamond Light Source Ltd, Harwell Science & Innovation Campus, United Kingdom) - Thomas White (Center for Free-Electron Laser Science, Hamburg, Germany) For any questions regarding the school please contact us. Best wishes, Claudia Millán (cmncri at ibmb.csic.es) Martin Lutz (m.lutz at uu.nl) Jan Rohlicek (rohlicek at fzu.cz) PD. Please find attached a poster about the school that you can forward, together with this email, to people potentially interested in participating in the Computing School. ---------------------------------------------------------------------------------------- Claudia Millán (cmncri(a)ibmb.csic.es) Crystallographic Methods Group http://chango.ibmb.csic.es Institut de Biologia Molecular de Barcelona (IBMB-CSIC) Barcelona, Spain LinkedIn: es.linkedin.com/in/claudiamillan/ <http://es.linkedin.com/pub/claudia-mill%C3%A1n/60/a76/821/> ResearchGate: https://www.researchgate.net/profile/Claudia_Millan?ev=hdr_xprf Twitter: https://twitter.com/cheshireminima

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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 14 Feb '20

14 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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