- phenixbb - phenix-online.org

Running Phaser with a already placed solution from a previous job
by vincent Chaptal 05 Oct '17

05 Oct '17

Dear everyone, this sounds trivial but I somehow can't make it work so I would appreciate any pointer. I have placed a component using phaser and would like to expand my search using this already placed component as partial solution. I open the full-featured interface of phaser in the GUI and select the box "Use partial solution from previous job" and select the job (nothing seems to happen there). I define my ensembles with ensemble_1 as "fixed partial solution" and ensemble_2 the one to search for. I then get the error message that "ense_1 from previous job is not specified on the current ensemble tab". Using the info button I see that "It is best to do this by modifying the configuration of the GUI from the previous Phaser run instead of starting from scratch, because the stored solutions do not contain the definitions of the search ensembles" but I don't understand what is asked for me to do here. When I restore the previous job, I can't see how I can start a new search from there. Any help would be greatly appreciated. Thanks Vincent I'm using phenix 1.12-2829. -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr

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map model correlations in real_space_refine
by Daniel Larsson 04 Oct '17

04 Oct '17

In version 1.12, what does the new map correlation numbers CC_mask, CC_volume and CC_peak in the log mean? How do they relate to the old "Map CC (whole unit cell)" and "Map CC (around atoms)" values (which in my opinion are more intuitive/descriptive and very useful numbers and I don't understand why they are no longer written to the log). Regards, Daniel

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help with phenix.ligand_identification
by Edward A. Berry 28 Sep '17

28 Sep '17

I'm having some problems using ligand_identification. I would like to restrict the search to a specific density peak, even if it is not the highest unmodeled peak or the highest Fo-Fc peak in the map. I tried using options: search_center="67.5 18.3 11.8" or ligand_near_res=S2063, Will the search be restricted to that region, or if a particuar ligand doesn't fit that blob, will it search through the rest of the map? If it is restricted, in what radius? Is this radius affected by the "search_dist" or "local_search" parameters? and local_search = True is default? Is there a threshold level for density level, below which building a ligand in a blob will not be attempted? I've tried with both search_center= and ligand_near_res=, and something gets built far away from that site. But there were errors, so I may have something wrong: phenix.ligand_identification mtz_in=sqr2803or13_031.mtz input_labels="2FOFCWT PH2FOFCWT" \ model=sqr2803or13_031.pdb ligand_near_res=S2063 nproc=2 After preparing the ligand library, then: Running LigandFit process 1... Number of atoms in ligand suc.pdb is 23 Running job sequence 1, ligand 2, in /tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_1... Evaluating all ligands in ligand-lib now...and placing fittedligand ### in resolve_ligand_###.pdb Number of atoms in ligand 2pe.pdb is 28 Running job sequence 0, ligand 1, in /tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_0... Process Process-2: Traceback (most recent call last): File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/sw/lnx/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/ligand_identification.py", line 1382, in RunLigandFit shutil.rmtree(ligandfit_dir) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 247, in rmtree rmtree(fullname, ignore_errors, onerror) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 256, in rmtree onerror(os.rmdir, path, sys.exc_info()) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 254, in rmtree os.rmdir(path) OSError: [Errno 39] Directory not empty: '/tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_1/LigandFit_run_1_/TEMP0' Process Process-1: Traceback (most recent call last): File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/sw/lnx/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/ligand_identification.py", line 1382, in RunLigandFit shutil.rmtree(ligandfit_dir) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 247, in rmtree rmtree(fullname, ignore_errors, onerror) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 256, in rmtree onerror(os.rmdir, path, sys.exc_info()) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 254, in rmtree os.rmdir(path) OSError: [Errno 39] Directory not empty: '/tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_0/LigandFit_run_1_/TEMP0' Evaluating LigandFit results ... The run continues, but it does not test any more ligands after those first two but goes on to evaluate the results. With nproc = 1, only 1 ligand gets tested. In all cases the first ligand in the library (2PE.pdb) is evaluated as the best. It is placed in density, but density that has already been built out with (and looks more like) a string of water molecules. And this is far from the selected residue or coordinates specified. The directory that raised the error when attempting to be deleted does eventually get removed: after the run there is no TEMP_N in the parent directory. Any suggestions would be welcome. Ed P.S. - running with .eff file: ['--show_defaults'] ligand_identification { mtz_in = sqr2803or13_031.mtz mtz_type = *F diffmap model = sqr2803or13_031.pdb ncpu = 1 n_indiv_tries_min = 30 n_indiv_tries_max = 300 n_group_search = 4 search_dist = 10 local_search = True search_center = "67.5 18.3 11.8" # ligand_near_res = S2063 verbose = False debug = False use_ligandfit = True search_mode = *default LigandFit temp_dir = Auto dry_run = False # number_of_ligands = 1 cc_min = 0.75 open_in_coot = False non_bonded = True keep_all_files = False # cif_def_file_list = real_space_target_weight = 10 # job_title = None ligandfit { } } gives: [['2pe.pdb', 'suc.pdb', . . . 'upl.pdb']] /tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2 ******************************************************************************* Sorry, the protein model file None does not seem to exist? ******************************************************************************* Running LigandFit process 0... Process Process-1: Traceback (most recent call last): File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/sw/lnx/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/ligand_identification.py", line 1122, in RunLigandFit shutil.copyfile(mtz_in,data_local) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 82, in copyfile with open(src, 'rb') as fsrc: IOError: [Errno 2] No such file or directory: 'None' Evaluating LigandFit results ... Lig_seq Placed/total cc_all cc cc_adj score Code HBscore Cannot find overall_ligand_scores.log0. This could mean that none of that (sub)set of ligand fitted well. None of the ligand fit the difference desity well enough. Please try the following -- 1) if you input a custom library, try to use the default library (no extra keywords needed), or 2) if you used the default library already, ususlly this means that the density is too small (> 6 atome or more is needed.) Exiting ...... No good ligand found.

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"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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.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 17 Aug '17

17 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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Appplying symmetry to a Cryo-EM map in phenix map_to _model
by Joshua Jude Lobo 11 Aug '17

11 Aug '17

Hi Phenix Group I am very new to model building and using phenix . I am trying to use phenix.map_to_model to generate a model just using my cryo-EM map( mrc format) and a fasta sequence .My protein has octahedral symmetry . I found the use_space_group_symmetry argument but am not sure what argument to give to impose the symmetry . Any inputs are appreciated Sincerely Joshua Lobo University of Minnesota Twin Cities

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seeking advice on how to configure Phaser-MR (full-featured) to use a previous partial solution
by Emilia C. Arturo (Emily) 08 Aug '17

08 Aug '17

Hello. I have a 3-domain protein (let's say it's organized from N to C as A-B-C) whose structure I am working to determine now. Although several single- (A alone, B alone), double- (A+B and B+C) and 3-domain (A+B+C) structures of this protein (from a different organism whose primary sequence is, overall, ~85% identical to the one on which I'm working) have already been determined and deposited in the PDB, I would ideally like to use a minimal probe (i.e. as few domains as possible) in order avoid model bias that could be imposed on the relative orientation of domains A, B, and C. So far, I have phase solutions (TFZ scores for all in the high-50s and 60s) using B-only, A+B, and B+C pdb files as probes. A-only structures have not given a phase solution (TFZ is ~7 and autobuild gives a solution that looks unbelievable in Coot), perhaps because A is relatively small in size. Here is my problem: I suspect that A and B sit relative to one another in an interesting way in this particular structure, so I'd like to use Phaser to search for a solution given the fixed partial solution from a B-only search, together with an A-only structure as a separate probe. So far no MR solutions have been found when I configure the run with an A-only pdb file and a B-only-derived Phaser result that is input as a fixed partial solution. I'm writing to ask for advice on how to configure the search. I think that the problem is my configuring the search, and not that a solution cannot be found from these coordinates. This is the reason I think that my problem is in configuring the search; please correct me if I'm wrong: Using a Phaser result derived from using an A+B structure as probe, I cut up the resulting pdb file into 2 pdb files - one containing an A' and another containing a B', where A' is the A domain of the Phaser result, and B' is the B-only part. Then I configured a Phaser result with B' as an ensemble that is a fixed partial solution, and A' as a separate ensemble/probe. I searched for 4 of each since 4 chains is the most likely composition in the ASU. I expected to get a result similar to what Phaser calculated when I input the A+B structure as an intact probe. Instead of getting a solution where 4 A+B chains were placed as they were in the first Phaser result, which gave one solution with a TFZ score of 65, I got 13 solutions, the top scoring a TFZ of 7.5, and each solution having a total of 9 chains - 4 As and 5 Bs. Is anyone willing to help me troubleshoot the above before I throw up my hands and settle on either manually building two domains onto the single-domain solution, or one domain onto the 2-domain solution, keeping in mind the potential for model bias? I am keen on using the B-only solution as a fixed partial solution to place domain A because all the B-only structures provide coordinate information for a portion of domain B that is unresolved in any of the multi-domain structures that contain domain B. I am using the Phenix gui, version 1.12rc1-2807. Regards, Emily. -- "Study as if you were going to live forever; live as if you were going to die tomorrow." - Maria Mitchell "I'm not afraid of storms for I'm learning to sail my ship." - Louisa May Alcott

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Very low rmsd bond length
by Mark Saper 07 Aug '17

07 Aug '17

Hi all, A reviewer points out that my refined structures (which have already been deposited in PDB) have very small RMSD values for bond lengths (0.005–0.002) (refinement resolutions are 2.0–2.8 Å), and that my weights should be decreased. The weights were calculated with “Optimize XYZ Weight” option turned ON. This seems to be the case with all of the structures that I have refined during the past 5 years. My impression from previous discussions is that deriving explicit weights from these optimized ones is not straightforward and so I have never tried to relax the weights. Moreover inspecting the optimization results in the log file, suggest that changing the weights to increase the RMSD would increase the Rfree. (I can post this if its helpful). How do I address the reviewer’s concerns? Thanks, Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School Room 3220B, MSRB III saper(a)umich.edu +1 (734) 764-3353

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Comput. Cryst. Newsl. (2017) 2
by Nigel Moriarty 04 Aug '17

04 Aug '17

The latest Computational Crystallography Newsletter is available for download. Below is the clickable table of contents. July 2017 <https://www.phenix-online.org/newsletter/CCN_2017_07.pdf> Short Communications - phenix.mtriage: a tool for analysis and validation of cryo-EM 3D reconstructions <https://www.phenix-online.org/newsletter/CCN_2017_07.pdf#page=6> - More TLS validation with phenix.tls_analysis <https://www.phenix-online.org/newsletter/CCN_2017_07.pdf#page=8> Fitting tips #14 – How Ser & Thr behave oddly on helices <https://www.phenix-online.org/newsletter/CCN_2017_07.pdf#page=2> Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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mrc to mtz conversion to open map in coot
by Joshua Jude Lobo 03 Aug '17

03 Aug '17

Hi phenixbb I am new to phenix and am trying to convert a cryo-em map(mrc format) to mtz format using the phenix.map_to_structure_factors command .This proceess finishes without errors but the resultant mtz file is not viewable in coot . I have tried both the phenix.map_to_model and the phenix.map_to_model_histogram_1.12-2829 How is the best way to troubleshoot this ? Any inputs would be appreciated Sincerely Joshua Lobo University of Minnesota Twin Cities

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