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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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.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

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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

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Opening phenix X-ray/neutron maps in Coot without the Phenix GUI
by Derek Logan 23 Aug '17

23 Aug '17

Hi ccp4bb and phenixbb, Is there a convenient way to open MTZ files in Coot that are the result of joint X-ray/neutron refinement in phenix.refine, but where phenix.refine was run in command-line mode? I would like achieve what is done in the Phenix GUI at the click of a button, i.e. open Coot with the structure and 2Fo-Fc and Fo-Fc maps for both neutron and X-ray. At the moment I have to open each MTZ file four times in the Coot GUI, once for each type of map. Is there a script buried somewhere in the Phenix installation that can be modified? /Derek ________________________________________________________________________ Derek Logan tel: +46 46 222 1443 Associate Professor mob: +46 76 8585 707 Dept. of Biochemistry and Structural Biology www.cmps.lu.se<http://www.cmps.lu.se> Centre for Molecular Protein Science bit.ly/2d0HxmS Lund University, Box 124, 221 00 Lund, Sweden

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Master Your Proteins, NKI Amsterdam, 20-23 November 2017
by Anastassis Perrakis 18 Aug '17

18 Aug '17

Dear all, Applications for the Instruct-ERIC course on Biophysical Characterisation of Macromolecules and Quantification of Biomolecular Interactions are now open. The course aims to provide the theoretical background of popular biophysical methods that are often used in relation to Structural Biology research, and practical experience both in performing experiments and in analysing the resulting data. The rationale behind an extended kit of experiments to characterise macromolecules and their interactions will be explained. You will be shown how to perform and analyse the related experiments in dedicated practical sessions. The course will include theory and practical sessions on thermal shift assays (also label free), Surface Plasmon Resonance, sothermal Titration Calorimetry, Miscroscale Thermophoresis , Fluoresence Methods, Stopped Flow, and the Graphpad/Prism and Kintek analysis software. Details can be found at: https://www.structuralbiology.eu/events/biophysical-characterisation-of-mac… <https://www.structuralbiology.eu/events/biophysical-characterisation-of-mac…> On the behalf of the organisers, Tassos

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Macromolecular Crystallography workshop in South America
by Alejandro Buschiazzo 18 Aug '17

18 Aug '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). http://pasteur.uy/mx2017 Dates: November 13 - 23, 2017 Confirmed speakers and tutors (so far... a few more may join the crew): Alejandro Buschiazzo, Montevideo, Uruguay Paul Emsley, Cambridge, UK Richard Garrat, São Carlos, Brazil 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 (this www site will be updated regularly, so stay tuned!) 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 Looking forward to welcoming you in Montevideo! -- Alejandro Buschiazzo, PhD Associate Professor Laboratory of Molecular & Structural Microbiology Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://pasteur.uy/en/laboratorios-eng/microbiologia-estructural-y-molecular…

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Postdoctoral position at the University of Chicago
by Robert Keenan 15 Aug '17

15 Aug '17

The Keenan lab at the University of Chicago has an opening for a postdoctoral scientist to study the structure and function of protein complexes involved in membrane protein biogenesis and quality control. Applicants should be nearing completion of a PhD in structural biology and have a strong academic record with significant publications. Experience in molecular biology, protein purification and electron microscopy/x-ray crystallography is required. To apply, please send a CV and a short statement describing your motivation for wanting to join the lab. Please be prepared to arrange for three letters of reference to be sent by email. For more information, please visit our webpage: http://keenanlab.bsd.uchicago.edu

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Phenix.real_space_refine
by Reza Khayat 11 Aug '17

11 Aug '17

Hi, I am refining a virus into an image reconstruction and have been having issues using the NCS capability of phenix.real_space_refine_1.12-2829. I think it may be my misunderstanding of the manual. The virus has 60subunits and I am feeding phenix a complete oligomer. I manually modify the first subunit with coot (simple movements and such), define an NCS group file where the first subunit is the reference and the other 59 are selection, and feed these into phenix.real_space_refine. Does phenix recapitulate my modifications of the first subunit into the remaining 59 subunits to create an oligomer that contains all my modifications before starting refinement? Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

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