- phenixbb - phenix-online.org

"Headless" install
by Jared Sampson 25 Sep '17

25 Sep '17

Hi all - Is it possible to download and install the latest Phenix release to a node on a computing cluster (i.e. without a screen and therefore web browser)? I've tried pasting the latest download links into `curl` and `wget` commands but get zero-size files as a result. Thanks, Jared

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Deadline reminder: XChem fragment screening at Diamond (and iNEXT) - SUNDAY 1st OCTOBER
by Frank von Delft 23 Sep '17

23 Sep '17

Dear Protein Crystallographers and Drug Discoverers A reminder that we are again inviting proposals for performing crystal-based fragment screening at Diamond's XChem facility at beamline I04-1, for the next allocation period (April 2018 to Sept 2018). *The deadline for proposals is NEXT SUNDAY 1st OCTOBER 5PM.* *Details of how to submit at this page <http://www.diamond.ac.uk/Beamlines/Mx/Fragment-Screening/Applying-for-Fragm…>. * Full details of the facility are available here <http://www.diamond.ac.uk/Beamlines/Mx/Fragment-Screening.html>. It supports the full crystal-to-structure experiment, and since opening for users in 2015, it has hosted over 50 users from academia and industry, with over 65 experiments (>50k crystals) consistently yielding credible, high quality fragment hits. With the right crystals, it'll keep you busy for less than a few weeks; and you get lots of support and advice. The calls are heavily oversubscribed, so please pay close attention to the instructions and guidelines. Access for EU users is funded via iNEXT <http://www.inext-eu.org/> (but only if you follow the instructions!); however we welcome all international proposals. -- Prof Frank von Delft Associate Professor Principal Beamline Scientist: I04-1 Diamond Light Source +44 1235 778997 Principal Investigator: Protein Crystallography Structural Genomics Consortium Oxford University +44 1865 617583 Visiting Professor Department of Biochemistry University of Johannesburg South Africa

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refine error message
by Jiemin Zhao 22 Sep '17

22 Sep '17

Hi， I got an error message when I try to refine a molecular replacement result. It says "number of nonbonded interaction distances<0.001:10. Please inspect the out put above(or in the log window) and correct the input model file." Could you help me with this problem? The error happens when I add Mg to pdb file. Thanks! Best regards, Jiemin

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Weird occupancy values in HySS
by Dominic Gilzer 21 Sep '17

21 Sep '17

Dear everybody, I am using Phenix HySS to solve the substructure of an iodine soak. I tried several high resolution cut-offs and a varying amount of heavy atoms to search for, but consistently get occupancies of > 1.0. Has anyone noticed such values for occupancies before, and by chance knows how or why these occur? Best regards, Dominic

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refine error message
by Jiemin Zhao 18 Sep '17

18 Sep '17

Hi, I got an error message when I try to refine a molecular replacement result. It says Fatal problems interpreting model file: Number of atoms with unknown nonbonding energy type symbols: 18 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply-cif-modification and apply-cif-link parameter definitions if necessary. Could you help me with this problem? Thanks! Best regards, Jiemin

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Academic position in cryoEM at The University of York
by Jon Agirre 14 Sep '17

14 Sep '17

The Department of Chemistry at The University of York is seeking to make an appointment of a Lecturer/Senior Lecturer/Reader/Professor in the area of Cryo Electron Microscopy, the position being based in the world-renowned York Structural Biology Laboratory within the Department. The Department has been awarded >£2M by the Wellcome Trust and Wolfson Foundation to invest in state-of-the-art equipment and a bespoke building to house a modern 200 kV cryo-electron microscope, supported by significant investment from the University and a private donor. We are now seeking to appoint a high-calibre researcher in cryo-electron microscopy, with a clear vision to lead their own programme of excellent research within YSBL <https://www.york.ac.uk/chemistry/research/ysbl/>. Your research will complement the X-ray crystallography and NMR techniques currently used in the YSBL, and will bridge the gap between X-ray work and the optical microscopy in the Biology Technology Facility. The role is available at any level and we welcome interest from talented academics with an impressive research profile appropriate to the level of application and a collegiate approach to their work. You will be a dynamic research leader with a consistent track record in the application of cryo-electron microscopy to challenging biochemical/biological problems. We welcome applications from researchers with an interest in diverse areas of structural and cell biology, with particular interest in those working on mammalian systems. The Department of Chemistry is one of the UK's leading Chemistry departments and is renowned internationally for its research, having performed exceptionally strongly in the recent Nature Index 2017 Innovation Table <https://www.york.ac.uk/chemistry/news/deptnews/nature-index-2017-innovation…>. Combined with a commitment to high-quality teaching and outstanding student satisfaction, it is recognised consistently for its family-friendly policies and is proud of its Athena SWAN Gold Award. *Key requirements:* (viewed relative to the level of post applied for – see candidate briefs for more details) - PhD in Chemical, Biochemical or Physical Sciences - Specialist knowledge in cryo electron microscopy - Ability to undertake high-quality research and publish in leading, peer-reviewed journals - Ability to define, lead, manage and attract funds for research, operating across disciplinary boundaries - Experience of and commitment to teaching and learning at undergraduate level. - Demonstrable capacity for creative thinking and planning - Substantial recent publication record in leading peer-reviewed journal - Evidence of national and/or international collaboration *Why York?* We are a dynamic, research-intensive university and have experienced significant growth over the past ten years, securing national and international recognition for our academic excellence. Our attractive, landscaped campus has seen significant development which will continue as the University continues to develop. Chemistry is a multidisciplinary department with an international reputation for excellence in research and teaching. www.york.ac.uk/chemistry *Salary will be commensurate with experience and grade* Lecturer: £38,832 to £47,722 Senior Lecturer: £49,149 to £56,950 Reader: £49,149 - £60,410 Professorial: current minimum £62,585 *To apply* Informal enquiries may be directed to Head of Department Professor Duncan Bruce (chem-hod(a)york.ac.uk; +44 (0)1904 322500) or the Academic Group Leader in YSBL Professor Tony Wilkinson (tony.wilkinson(a)york.ac.uk; +44 (0)1904 328261) Link: https://jobs.york.ac.uk/wd/plsql/wd_portal.show_job?p_web_site_id=3885&p_we… *Closing date:* 9 October 2017 *Interviews will be held in York on:* 29 November 2017 -- Dr Jon Agirre Royal Society University Research Fellow 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 8270 Twitter: @alwaysonthejazz

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Macromolecular Crystallography workshop in South America
by Felipe 12 Sep '17

12 Sep '17

Dear colleagues, We are pleased to announce our sixth edition of the Workshop: Macromolecular Crystallography School "From data processing to structure refinement and beyond", to be held at the Institut Pasteur de Montevideo (Uruguay). This Workshop will cover all aspects of the macromolecular structure determination process using X ray crystallography: starting from data processing, through phasing and refinement to structure completion and analysis. Integrative methods are also being included. In particular, this year an introduction to cryo-electron microscopy has been added to the program. http://pasteur.uy/mx2017 <http://pasteur.uy/mx2017> Dates: November 13 - 23, 2017 Confirmed speakers and tutors: Alejandro Buschiazzo, Montevideo, Uruguay Grzegorz Chojnowski, Hamburg, Germany Paul Emsley, Cambridge, UK Richard Garrat, São Carlos, Brazil James Holton, San Francisco/Berkeley/Palo Alto, USA Ronan Keegan, Oxford, UK Eugene Krissinel, Oxford, UK Andrey Lebedev, Oxford, UK Andrew Leslie, Cambridge, UK Garib Murshudov, Cambridge, UK Colin Palmer, Oxford, UK James Parkhurst, Oxford, UK Randy Read, Cambridge, UK Clemens Vonrhein, Cambridge, UK Please find the program of the Workshop, the application form and further contact information, at http://pasteur.uy/mx2017 <http://pasteur.uy/mx2017> This Workshop is supported by the Collaborative Computational Project Nº4 (CCP4, UK) & Science and Technology Facilities Council (UK); the Centro de Biologia Estructural del Mercosur (CeBEM); the International Union of Crystallography (IUCr); and the Institut Pasteur de Montevideo. Organizers: Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay Ronan Keegan, PhD. CCP4, STFC Rutherford Appleton Laboratory, United Kingdom Richard Garratt, PhD. Instituto de Fisica de Sao Carlos, USP, Brazil Applicants: 24 students will be selected, aiming at advanced PhD, postdocs and young researchers. The Course will provide financial support covering registration fees, and for the case of those students coming from abroad, all local expenses (lodging, per diem and local transportation). Look in the www site for details on application procedures. The application deadline is September 17, 2017. Please address further inquiries to: mx2017(a)pasteur.edu.uy <mailto:[email protected]> Looking forward to welcoming you in Montevideo! Felipe Trajtenberg, PhD Laboratory of Molecular & Structural Microbiology Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 143 Fax: +598 25224185 http://pasteur.uy/en/laboratorios-eng/microbiologia-estructural-y-molecular… <http://pasteur.uy/en/laboratorios-eng/microbiologia-estructural-y-molecular…>

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Gold atoms in cryo-EM
by a.malay＠riken.jp 12 Sep '17

12 Sep '17

Dear all, I hope that this question is neither too off-topic or naive. I am trying to refine a large protein structure against a cryo-EM map using Phenix real-space refinement. The protein complex is unusual in that the oligomeric state is held together via coordinated gold atoms. However, there seems to be a problem with refinement, in that the the gold atoms show extremely high B-factors (>200) after refinement, whereas the B-factors of the protein residues, including those surrounding the gold atoms, adopt more reasonable values. My question is: could the unusually high B-factors of the gold atoms be somehow due to differences in the relative scattering of Au atoms when obtained from X-ray vs. electron beam irradiation? And if so, is there any way to correct for this? Thank you in advance for your kind help. Best, Ali

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SLURM Batch submission
by Heidi Schubert 11 Sep '17

11 Sep '17

Hi Has anyone successful submitted phenix jobs to a SLURM batch queue? I guess, in theory, I did successfully submit a job but it took a while to start and after completion the log files did not successfully link back to the interface losing the graphic feedback. I can’t tell how the job was submitted. Our submission command is sbatch, which is what I put in the Phenix Preference > Processes queue command. But locally we have a header on our sbatch submission which spells out our wall time, account and MPI expectations/requests. Is there an environment file that Phenix reads to provide this information or does it submit generically? I wondered if this was responsible for the long delay of the start of our job (sure – could have been a busy queue). Anyone know how to get the GUI to read the output files when it loses connection to the run? Heidi

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Resolution of datasets for using PHENIX automated ligand identification
by Xiao Lei 01 Sep '17

01 Sep '17

Hi All, I am asking is there any resolution requirement for using the PHENIX automated ligand identification tool. Can I use the tool with 3A resolution protein datasets?

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