- phenixbb - phenix-online.org

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

2 1

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

2 1

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

4 3

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

1 0

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…>

1 0

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

2 1

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

4 3

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?

1 0

.hhr files?
by Patrick Loll 01 Sep '17

01 Sep '17

This feels like a silly question, but I’ve already wasted some time head-banging, so here goes: I would like to generate a .hhr sequence alignment file for use in MR-Rosetta. After running HHPRED, I get a lovely alignment, but I see no place to save it as a .hhr file. Several “how-to” pages talk about a “save” button above the alignment, but the MPI bioinformatics pages seem to have been reformatted in the past few months, and I see no such button. There is a tab labeled “raw output” with a download option, but that appears to give a FASTA format. So…can anyone suggest a way forward? Either by capturing the elusive .hhr file, or by saving the data in some other format that is still useful for MR-Rosetta? Thanks, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pjloll(a)gmail.com pjl28(a)drexel.edu

2 1

Few questions about the model building and refinement of cryo-EM data
by Wang, Bing 28 Aug '17

28 Aug '17

Hi guys, Sorry for the detailed questions from a beginner! I am starting a modeling/refinement work for a set of cryo-EM data. Data basic information: phage data (looks like a ball with P1 space group), map size ~870 MB, resolution ~6 A, two X-ray structures for model building General strategies: I select COOT for the model building; using phenix.real_sapce_refine for the real space refinement with secondary structure restrain and REFMAC for the reciprocal space refinement. Few questions are listed here. 1. The map was too bigger to open it in COOT. The phenix.map_to_structure_factors was used to obtaine ~120 MB sized MTZ file (still a little big for my computer). I manually build up the whole ball-shaped phage with the rigid body fit in COOT (from two X-ray structures to 120 chains). My first question will be: In this case, should I crop the map in Chimera or other software and only focus on a small asymmetric unit to do the model building and the followed refinement. 2. I would like to do a real space refinement after the model building. Input files: A pdb file I just built up from COOT A original MAP file A transfered MTZ file Two restraint files from two X-ray structures by ProSMART (TXT formart) The refinement parameters I would like to select in GUI interface: minimization_global, rigid_body, local_grid_search, adp Use secondary structure restraints Reference model restraints: use starting model as reference, main chain, side chain, fix outliers, secondary structure only Rotamer restraints Ramachandran restraints Show per residue My second set of questions: Should I select the MAP file (~870 MB) or the MTZ file (~120 MB)? Is that necessary to add the two restraint files from ProSMART if I use the starting model as reference? Is the refinement parameters selected properly? 3. I gave a try by phenix.real_space_refine. An first error showed up: Number of atoms with unknown nonbonded energy type symbols: 6840 "ATOM 184 HG1 SER 1 12 .*. H " "ATOM 458 HG1 SER 1 30 .*. H " "ATOM 699 HG1 SER 1 45 .*. H " "ATOM 720 HG1 SER 1 47 .*. H " "ATOM 762 HG1 SER 1 50 .*. H " "ATOM 1241 HG1 SER 1 81 .*. H " "ATOM 1465 HG1 SER 1 95 .*. H " "ATOM 1747 HG1 SER 1 113 .*. H " "ATOM 1758 HG1 SER 1 114 .*. H " "ATOM 2173 HG1 SER 1 141 .*. H " ... (remaining 6830 not shown) I tried phenix.ready_set to fix this problem according to a previous discussion but it gave me another error: ENDMDL record missing at end of input. Thus my third question will be how to fix the first error? Thank you for patience! I would really appreciate your help! Bing

2 1