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Protein Crystallography Facility Manager, MRC Laboratory of Molecular Biology, Cambridge, UK
by David Barford 31 Oct '18

31 Oct '18

Protein Crystallography Facility Manager, MRC Laboratory of Molecular Biology, Cambridge, UK The MRC Laboratory of Molecular Biology (LMB) seeks to appoint a Protein Crystallography Facility Manager. The LMB is one of the birthplaces of structural biology and remains at the forefront of methods development as protein crystallography is a critical technique for understanding the mechanisms of macromolecular complexes, one of the major goals of the LMB. The post-holder will provide support to researchers from all Divisions of the LMB in the collection of X-ray diffraction data using both synchrotrons and in-house X-ray facilities, will maintain and develop the in-house facilities, will provide expert advice and support during subsequent structure determinations, and will act as the coordinator for LMB's synchrotron access. It is expected that there will be the opportunity for collaboration on structural projects with research groups at the LMB. The successful applicant will have several years of post-doctoral experience in the field of protein crystallography including data collection at synchrotrons and all aspects of structure determination. Excellent communication and inter-personal skills are required because the post will involve interacting with a diverse range of scientists with different levels of expertise. Closing date for applications: 28th November 2018 For further details and information on how to apply please visit: Jobs.ac: https://www.jobs.ac.uk/job/BNU298/protein-crystallography-facility-manager-… <https://www.jobs.ac.uk/job/BNU298/protein-crystallography-facility-manager-…> Nature: https://www.nature.com/naturecareers/job?id=661643 <https://www.nature.com/naturecareers/job?id=661643> Informal enquires should be addressed to Dr. David Barford. E.mail: dbarford(a)mrc-lmb.cam.ac.uk <mailto:[email protected]>

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Protein Crystallography Facility Manager, MRC Laboratory of Molecular Biology, Cambridge, UK
by David Barford 31 Oct '18

31 Oct '18

Protein Crystallography Facility Manager, MRC Laboratory of Molecular Biology, Cambridge, UK The MRC Laboratory of Molecular Biology (LMB) seeks to appoint a Protein Crystallography Facility Manager. The LMB is one of the birthplaces of structural biology and remains at the forefront of methods development as protein crystallography is a critical technique for understanding the mechanisms of macromolecular complexes, one of the major goals of the LMB. The post-holder will provide support to researchers from all Divisions of the LMB in the collection of X-ray diffraction data using both synchrotrons and in-house X-ray facilities, will maintain and develop the in-house facilities, will provide expert advice and support during subsequent structure determinations, and will act as the coordinator for LMB's synchrotron access. It is expected that there will be the opportunity for collaboration on structural projects with research groups at the LMB. The successful applicant will have several years of post-doctoral experience in the field of protein crystallography including data collection at synchrotrons and all aspects of structure determination. Excellent communication and inter-personal skills are required because the post will involve interacting with a diverse range of scientists with different levels of expertise. Closing date for applications: 28th November 2018 For further details and information on how to apply please visit: Jobs.ac: https://www.jobs.ac.uk/job/BNU298/protein-crystallography-facility-manager-… <https://www.jobs.ac.uk/job/BNU298/protein-crystallography-facility-manager-…> Nature: https://www.nature.com/naturecareers/job?id=661643 <https://www.nature.com/naturecareers/job?id=661643> Informal enquires should be addressed to Dr. David Barford. E.mail: dbarford(a)mrc-lmb.cam.ac.uk <mailto:[email protected]>

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RNA starting with triphosphate
by Phoebe A. Rice 25 Oct '18

25 Oct '18

A question from my collaborators: what is the best way to get phenix to handle a GTP as nt #1 of an RNA chain? That is, what is the best way to specify a covalent bond with the proper geometry between the 3’ O of GTP1 and the 5’ P of nt #2? Thanks in advance, Phoebe ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Phoebe A. Rice Dept. of Biochem & Mol. Biol. and Committee on Microbiology https://voices.uchicago.edu/phoebericelab/

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RapiData 2019 applications open!
by Smith, Clyde 24 Oct '18

24 Oct '18

Dear all, Applications are now open for the 2019 edition of RapiData at SSRL. RapiData is a practical course in macromolecular X-ray diffraction data collection, data processing and structure solution. The aim of the RapiData course is to educate and train young scientists in data collection and processing methods at synchrotron beamlines, using state-of-the-art software and instrumentation. The course will be held at the Stanford Synchrotron Radiation Lightsource (SSRL) located on the SLAC National Accelerator Laboratory campus in Menlo Park, CA, from May 5-10 2019. Course organizers for 2019 are Silvia Russi, Clyde Smith and Jeney Wierman. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and lectures on the following topics: Specimen preparation, Data collection strategies, X-ray light sources, X-ray detectors, Data reduction, Structure solution by MAD, SAD and Molecular Replacement, Complementary methods (spectroscopy and small angle scattering) Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2019/ and use the links on the "registration" page to apply for the course. The application deadline is December 31 2018. Successful applicants will be notified early in January 2019 and invited to register and book accommodation at the SLAC Guesthouse at that time. A limited amount of travel support funding may be available. Please direct questions to Silvia Russi (srussi(a)slac.stanford.edu), Jeney Wierman (jwierman(a)slac.stanford.edu) or Clyde Smith (csmith(a)slac.stanford.edu).

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Computational cryo-EM faculty position at the Morgridge Institute for Research and UW-Madison
by Eric Montemayor 19 Oct '18

19 Oct '18

Dear Colleagues, A great faculty-level opportunity between the Morgridge Institute for Research and the University of Wisconsin-Madison. We seek to hire a tenure-track assistant/associate/full professor in the broad area of cryo-EM centered quantitative image processing and analysis. This position is part of a major campus cryo-EM expansion, comprising new faculty hires in experimental and computational cryo-EM, and a facility to house four new cryo-microscopes including Thermo Fisher’s 300 kV Titan Krios, 200 kV Talos Arctica, 120 kV Talos L120C, and Aquilos cryo-FIB-SEM. For more information about this post and the application process, please click the link below. Deadline for applications is December 15, 2018. Morgridge (computational cryo-EM) - https://morgridge.org/job-posting/investigator-cryo-em/ For more information about the other cryo-EM related faculty positions, please click the links below. Each search has its own deadline for receipt of applications. The positions will remain open until filled. Biochemistry - http://jobs.hr.wisc.edu/cw/en-us/job/499479/biochemistry-faculty Virology - http://jobs.hr.wisc.edu/cw/en-us/job/499366/virus-proteinnucleic-acid-ultra… Bacteriology - http://jobs.hr.wisc.edu/cw/en-us/job/499304/assistant-professor For additional information, please contact Liz Wright (erwright2(a)wisc.edu). -- Eric J. Montemayor Associate Scientist Department of Biochemistry University of Wisconsin Madison 433 Babcock Dr. Room 145 Madison, WI 53706

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Submit Phenixbb
by 张晓帅 19 Oct '18

19 Oct '18

i want to post to list.Thank you.

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New Solvent Modeling/Analysis Tool
by Paul Smith 17 Oct '18

17 Oct '18

Dear fellow PHENIX users, My lab group has developed a new PHENIX-based tool for automated identification and building of solvent molecules in x-ray crystal structures. The software, dubbed PeakProbe, and a basic README are available on GitHub: https://github.com/paulsmith638/PeakProbe Fair warning: the project is still undergoing development and the linked version generates excessive output and not all features are fully tested. The feature extraction stage of the program is slow, figure about 1s per peak analyzed. Currently, PeakProbe can do the following: -- Analyze and remodel existing solvent -- Build water/sulfate and a few ions de novo -- Indicate where other species, such as glycerol or PEG, should be considered -- Identify possible model errors such as missing alternate conformations PeakProbe requires only an input structure PDB (with or without solvent) and a structure factor file in any format supported by PHENIX. The program uses a model derived from analysis of over 2.2 million density points in the PDB in structures with limiting resolutions as low as 5.0A. Features from these points are scaled/transformed to allow comparison of input peaks to well-defined feature distributions at any resolution followed by calculation of the relative likelihood of a given type of solvent existing at a given point. Feel free to try PeakProbe and I welcome all feedback, bug reports, and questions. Thanks again to Nigel, Nat, Tom and all of the PHENIX/CCTBX team for their help and for developing the battery of CCTBX tools upon which PeakProbe is based. --Paul -- The untold want, by life and land ne’er granted, Now, Voyager, sail thou forth, to seek and find. --W. Whitman +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. Paul Smith Assistant Professor Department of Chemistry Fordham University 441 E. Fordham Road Bronx, NY 10458 phone: 718-817-4461 fax: 718-817-4432 email: psmith66(a)fordham.edu office: JMH 638 PGP Public Key at https://pgp.mit.edu/

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superpose CryoEM map onto an Xray map?
by vincent Chaptal 11 Oct '18

11 Oct '18

Dear all, I am trying to superpose a CryoEM map onto a Xray map. I tried the "superpose maps" under the map section of phenix 1.14 but it only takes "reflections" and not the .mrc format of the CryoEM map. should I transform the CryoEM map into structure factors using "Map to structure factors" or is there a better way to do this? Thank you for your feedback. Best Vincent -- Vincent Chaptal, PhD MMSB -UMR5086 Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://mmsb.cnrs.fr/en/

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CCN resend
by Nigel Moriarty 09 Oct '18

09 Oct '18

Folks It seems that 50% of people got an email that was 50% greek. I have tried to remove this by removing formatting. Hope this helps. The second 2018 issue of the CCN is now available at http://phenix-online.org/newsletter/ Articles include · Fitting tips #16 – Vicinal disulfides: Have you seen one of these strange gems? · CaBLAM: A C-Alpha Based Low-resolution Annotation Method for secondary structure and validation · Tools for interpreting cryo-EM maps using models from the PDB · Using the New Program Template 62 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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Computational Crystallography Newsletter
by Nigel Moriarty 09 Oct '18

09 Oct '18

Folks The second 2018 issue of the CCN is now available at http://phenix-online.org/newsletter/ Articles include · Fitting tips #16 – Vicinal disulfides: Have you seen one of these strange gems? · CaBLAM: A C-Alpha Based Low-resolution Annotation Method for secondary structure and validation · Tools for interpreting cryo-EM maps using models from the PDB · Using the New Program Template 62 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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Rosetta installation problems
by Simone Pellegrino 08 Oct '18

08 Oct '18

Dear all, I encounter a problem running the rosetta.run_tests after having compiled rosetta for interfacing with phenix. I have the following error: DEBUG dumping error message ERROR: Rosetta exited with status 139 stderr output: Segmentation fault (core dumped) Traceback (most recent call last): File "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 307, in <module> run(sys.argv[1:], create_dir=True) File "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run debug=params.output.debug) File "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__ self.run_jobs() File "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/modules/phenix/phenix/rosetta/refine.py", line 387, in run_jobs check_result(result) File "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/modules/phenix/phenix/rosetta/refine.py", line 378, in check_result raise RuntimeError("Aborted due to error in job %d." % result.job_id) RuntimeError: Aborted due to error in job 1. Could you please help me in solving this issue? Many thanks in advance Best regards Simone -- Dr. Simone Pellegrino I.G.B.M.C. 1, Rue Laurent Fries 67404 Illkirch Cedex France

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Crystallography/drug development Post-doc opportunity
by Flaherty, Daniel P 02 Oct '18

02 Oct '18

Hello All, My name is Daniel Flaherty and I am an Assistant Professor at Purdue University. I am seeking a post-doc with experience in structural determination of protein targets and ligand-bound protein structures to support our drug development projects. Please find the position announcement at this website: https://www.flahertylab.com/positions Cheers, Dan

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Deadline for Diamond XChem proposals next Wednesday
by Frank von Delft 28 Sep '18

28 Sep '18

Dear aspiring drug discoverers A reminder that the deadline for the next round of proposals for XChem fragment screening is *next Wednesday*, as part of Diamond's general Call for Proposals. Full details <https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening/Applying-for-XC…> are on the XChem webpage <https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening.html>. *NEW*: we are now inviting a broader set of projects: * Two-tiered access: if you have an exciting system but don't yet know how to progress it, you can ask for exploratory access ("Tier 1") * BAG access: several labs and collaborations have requested increased flexibility, and they can now apply as Block Allocation Groups. If you wish to submit this route, I suggest you also email me directly. Happy screening! Frank -- Prof Frank von Delft Associate Professor Principal Investigator: Protein Crystallography Structural Genomics Consortium Oxford University +44 1865 617583 (office: W,F) Principal Beamline Scientist: I04-1 Diamond Light Source +44 1235 778997 (office: M,T,T) +44 7471 026103 (mobile)

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Postdoctoral Position available - University of Warsaw, Poland
by Paulina Dominiak 27 Sep '18

27 Sep '18

Dear colleagues, I would like to draw your attention to a post-doctoral position available in my research group. For all the details, please see the complete call text below. If you need any further information, please contact me directly. Best regards, Paulina Dominiak An announcement for Post-doctoral position Position of Post-doctoral Researcher in the OPUS project entitled "More accurate models of the electrostatic potential of biological macromolecules and organic crystals necessary for proper interpretation of data from cryo-electron microscopy and from electron diffraction – feasibility study" financed by NCN is open for application. Project leader: dr hab. Paulina M. Dominiak, prof. UW Available positions: 1 Project description: The Dominiak’s group works on developing new methods of electron density modelling for X-ray and electron crystallography, chemistry and structural biology. The project aims at development of new models of electrostatic potentials for electron crystallography. The models will considerably deviate from the conventional spherical independent atom model currently used. With new models more information should be extracted from electron scattering experiments on biological macromolecules and organic crystals, and improved quality of geometric data and quantitative estimates of molecular electrostatic potentials should become easily available. For further information see http://cnbch.uw.edu.pl and http://www.chem.uw.edu.pl. Position description: You will be mainly responsible for development and verification of new databanks of atomic electron densities on the basis of existing procures published in: Acta Cryst. 2012, A68, 139; JCTC, 2014, 10, 1652; ChemPhysChem, 2016, 17, 2455; Acta Cryst. 2017, B73, 610. We are looking for motivated candidates with: -a PhD degree in chemistry or related fields at the moment of starting the job (PhD defended not later than 7 years ago according to NCN regulations, see www.ncn.gov.pl) -experience in crystallography OR/AND computational chemistry proven by scientific article publications -knowledge of macromolecular crystallography OR/AND proven experience in high-resolution x-ray diffraction charge density measurements -basic programing skills OR/AND practical experience in script usage/writing and proven ability to work with large amount of data -experience with structure refinement against electron diffraction or single particle cryoEM data will be an advantage -well-developed analytical skills -good knowledge of written and spoken English -written and spoken presentation skills -ability to work as part of a team We offer: a temporary employment contract with the University of Warsaw: -full time position -a salary approx. 5000 PLN per month (net salary, after taxes and other deductions) -for one year with a possible extension upto three years -appointment starting in November 2018 (the competition may be repeated until a suitable candidate who fulfils all requirements is found) Required documents (in English): -Curriculum Vitae (including list of scientific articles, conference presentations, awards, international internships, scholarships, workshops, participation in research projects), -a motivation letter (What are your scientific interests? What are your key strengths and achievements? Why do you want to work in the project?), -information on the processing of personal data (see the text below), -two recommendation letters (at least one from direct supervisor) sent by the referees directly to prof. Dominiak (pdomin(a)chem.uw.edu.pl). Please submit the documents no later than 26 October 2018 to: pdomin(a)chem.uw.edu.pl (PDF is the preferred format). E-mail entitled: “Post-Doc position” Selected candidates may be invited by e-mail, no later than 30 October 2018, to participate in interview. The interview will take place on 5 or 6 November 2018 in person or via Skype or phone. The results of the competition will be delivered to selected candidates by e-mail till 15 November 2018. In the case of not signing the contract by the candidate, due to the resignation, we reserve the right to choose the next candidate from the ranking list. INFORMATION ON THE PROCESSING OF PERSONAL DATA INFORMATION CLAUSE Pursuant to Article 13 of Regulation (EU) 2016/679 of the European Parliament and of the Council of 27 April 2016 on the protection of natural persons with regard to the processing of personal data and on the free movement of such data, and repealing Directive 95/46/EC (General Data Protection Regulation), University of Warsaw hereby informs: 1. The Controller of your personal data is the University of Warsaw with its registered office at Krakowskie Przedmieście 26/28, 00-927 Warszawa; 2. The Controller has designated the Data Protection Officer who supervises the processing of personal data, and who can be contacted via the following e-mail address: iod(a)adm.uw.edu.pl; 3. Your personal data will be processed for the purpose of carrying out a recruitment process and selecting an employee and concluding a contract for employment at the University of Warsaw; 4. The provided data will be processed pursuant to Article 221 § 1 of the Act of 26 June 1974 Labor Code (uniformed text: Dz.U. of 2018, item 917) and your consent for processing of personal data; 5. Provision of data in the scope stipulated in the Labor Code is mandatory, and the remaining data are processed according to your consent for processing of personal data; 6. The data will not be shared with any external entities; 7. The data will be stored until you withdraw your consent for processing of personal data; 8. You have the right to access your personal data, to rectify, erase them, restrict their processing, object to processing, and to withdraw the consent at any time; 9. You have the right to lodge a complaint to the President of the Office for the Protection of Personal Data. CONSENT CLAUSE I hereby consent to have my personal data processed by the University of Warsaw with its registered office at ul. Krakowskie Przedmieście 26/28, 00-927 Warszawa for the purpose of carrying out a recruitment process and selecting an employee and concluding a contract for employment at the University of Warsaw. I have been informed of my rights and duties. I understand that provision of my personal data is voluntary. ……………………………………………. ………………………………………………… (place and date) (signature of the person applying for employment) -- dr hab. Paulina M. Dominiak, prof. UW Group Leader Electron Density Modelling Group Laboratory for Structural and Biochemical Research (LBSBio) Biological and Chemical Research Centre Department of Chemistry University of Warsaw ul. Zwirki i Wigury 101 02-089 Warszawa, Poland Room: 3.125 E-mail: pdomin(a)chem.uw.edu.pl Phone: (48) 22 55 26 714

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polder map with twinning
by James Fraser 27 Sep '18

27 Sep '18

Hi all, I'm trying to make a polder map for a dataset that is refined with a twin law. As such, the R-factors reported during the polder procedure are much higher than those I get out of refinement. Is there a way to pass the twin law as in the composite omit procedure ( https://www.phenix-online.org/documentation/reference/composite_omit_map.ht… )? Thanks! J -- -- James Fraser - http://www.fraserlab.com - @fraser_lab jaimefraser(a)gmail.com // jfraser(a)fraserlab.com (please do NOT use james.fraser(a)ucsf.edu)

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Phenix version 1.14 released
by Paul Adams 25 Sep '18

25 Sep '18

The Phenix developers are pleased to announce that version 1.14 of Phenix is now available (build 1.14-3260). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Highlights for this version: - Reorganization, updates and addition of cryo-EM tools: - phenix.mtriage - assess map and model quality - phenix.auto_sharpen - map sharpening - phenix.map_symmetry - identify symmetry in maps - phenix.map_box - cut out unique parts of maps - phenix.combine_focused_maps - combine different maps - phenix.dock_in_map - automatically place an atomic model into a map - phenix.map_to_model - automatically build atomic model from a map - phenix.sequence_from_map - identify sequence from a map - phenix.real_space_refine - improved refinement of models - phenix.validation_cryoem - separate tool for comprehensive validation of models and maps - phenix.cablam_idealization - Tool to automatically fix Cablam outliers - eLBOW - better support for metals and metal clusters - added plugin for QM package Orca - Phaser-2.8.2 - bugfixes - Phassade substructure search when starting from seed substructure - fix crash in MR_ATOM - problems with cumulative intensity distribution for extremely weak data - improve computation and presentation of data information content - Performance improvements - NCS search - Generation of secondary structure restraints - Clashscore calculation - AmberPrep is more robust - Restraints for ARG improved - New Phenix video tutorials - GUI - New section in main window for cryo-EM tools - Separate validation GUI for cryo-EM structures - Added phenix.map_symmetry - Added phenix.dock_in_map - Added phenix.map_to_structure_factors - Added phenix.combine_focused_maps - Added phenix.sequence_from_map - phenix.ligand_identification: - Added an option to generate ligand library based on sequence and structural homologs of the input pdb model. For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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TER card only at the end of polymer chains of pdb file
by Maxime Cuypers 25 Sep '18

25 Sep '18

Hello, The pdb deposition server only allows deposition of pdb files that have a TER card at the end of polymer chains. But phenix add a ter card at the end of each chain, regardless of the content or whether or not the TER card was present before refinement or not. Would it be possible to have this automagically handled by phenix.refine so the user does not encur the frustrating systematic error during deposition and need to edit the pdb file every time a 'final refinement' is tested for validation ? does that make sense? cheerios to all, Maxime

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Fw: AsCA 2018 / CRYSTAL 32: Early bird Closing
by Christopher Squire 25 Sep '18

25 Sep '18

?? [https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-pub…] Dear Colleagues, Early bird closing 2 October 2018 A friendly reminder that early bird rates to attend the AsCA 2018/CRYSTAL 32 conference will finish on 2 October 2018. Register today using (http://asca2018.org/registration/) to secure the discounted rate. The conference will run from 2-5 December 2018. Keep up-to-date with our conference programme<http://asca2018.org/programme/>, outstanding lineup of workshops<http://asca2018.org/workshops/>, and speakers<http://asca2018.org/speakers/>. Don't forget to get in early and book your accommodation<http://asca2018.org/accommodation/> too! We look forward to meeting you in Auckland. Kind regards, Dr. Christopher Squire (University of Auckland), Professor Ted Baker (University of Auckland), Professor Kurt Krause (University of Otago) and the AsCA 2018/CRYSTAL 32 Committee http://asca2018.org/ [https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-pub…]

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Rfree set with twin refinement
by Matthew Bick 23 Sep '18

23 Sep '18

Hello PhenixBB I am dealing with a structure that is twinned and would like to ensure that the Rfree set I'm using is unbiased. This is what I have done so far. - Generated an initial model after Phaser MR using Autobuild. The input "Experimental Data" for autobuild was an XDS_ASCII.hkl file from data processed with XDS (along with the phaser output mtz as the "initial map"). Autobuild generates the file "exptl_fobs_phases_freeR_flags.mtz" containing the Rfree set, which I have used for all subsequent rounds of Phenix.refine. - I have built the model to completion with Coot and Phenix.refine, without applying the twin law. Only at the final round of refinement did I apply twin refinement, and it is obvious that the data is twinned (Xtriage also suggests twinning). My question - when the Rfree is established during Autobuild, does Phenix take into account all of the possible twin laws, so that the free and working sets are not related in any way by the possible twin laws? I believe Phenix does do this, but I would like to make sure. Space group is P 1 21 1 and the twin law is pseudo-merohedral h,-k,-h-l, in case those are relevant. Thank you. Matthew Bick

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Recruiting fragment/XChem crystallographers
by Frank von Delft 22 Sep '18

22 Sep '18

Hi all - We have vacancies at SGC (in my and Prof. Paul Brennan's groups) for crystallographers interested in driving a series of new genetically validated targets (inflammation and Alzheimers) from gene to XChem fragment screening and beyond to potency, and helping figure out how to do all of this a lot better than we currently can. Link is here <https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.disp…>, and deadline is in two weeks (October 5th). Frank -- Prof Frank von Delft Associate Professor Principal Investigator: Protein Crystallography Structural Genomics Consortium Oxford University +44 1865 617583 (office: W,F) Principal Beamline Scientist: I04-1 Diamond Light Source +44 1235 778997 (office: M,T,T) +44 7471 026103 (mobile)

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Secondary structure restraints video tutorial
by Dorothee Liebschner 14 Sep '18

14 Sep '18

Dear Phenix users, This is an update for the Phenix video tutorials. We have a new tutorial explaining the use of secondary_structure_restraints <https://www.phenix-online.org/documentation/reference/secondary_structure.h…>, a type of restraints especially useful at low resolution (lower than 3Å, cryo-EM map or X-ray data). References: Programming new geometry restraints: parallelity of atomic groups. Sobolev OV et al. J. Appl. Cryst. 48, 1130-1141 (2015). https://doi.org/10.1107/S1600576715010432 Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. Headd JJ et al. Acta Cryst. D68, 381-390 (2012). https://doi.org/10.1107/S0907444911047834 Feedback about the videos is very welcome. Write an email to tutorials @phenix-online.org or use the comment section on YouTube. If you want to see a tutorial about a certain (Phenix-related) topic, let us know. Best wishes, The Phenix team ------------------------------- Overview of tutorials: https://www.phenix-online.org/documentation/reference/tutorial_channel.html You can also browse the videos on the Phenix Tutorial YouTube channel: https://www.youtube.com/c/phenixtutorials (To see subtitles, hit the cc (closed captions) button in the right bottom of the video screen. Subscribe to see the tutorial videos in your YouTube subscription feed. To get notifications about new videos, tap the bell button, which is next to the "subscribe" button.)

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submission of neutron structure containing "H" atoms on the pdb database problematic
by Maxime Cuypers 11 Sep '18

11 Sep '18

Dear all, i was wondering if others have encountered the same problems with the PDB database curation rules or if this is a first. I am trying to submit a neutron structure with 'free' H atoms (protons) clearly identified. (not D atoms here), this is a situation similar to how D atoms can be reported in a pdb neutron structure close to a carboxylic residue or other situation like in the D‐xylose isomerase (XI). I have first tried to submit the neutron structure with the H atoms part of the complex molecules nearby but i faced refusal and was asked to make it as simple 'H' atoms. once i had done the 'free' H atoms version of the pdb, the structure was again refused by curators because there is no library available to the pdb curators to accept such H atoms. I was explained that it had been decided to ban the 'H' atom only coordinate from depositions some years ago. What would you recommand me to do to get the structure deposited and curated keeping the valid coordinates of the H atoms in the pdb file? PS: this is not fantasy. Dr. Maxime Cuypers

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single atom mmcif bug
by Edwin Pozharski 06 Sep '18

06 Sep '18

There appears to be a bug in phenix.cif_as_pdb. I am looking at a bunch of files that contain very few atoms. When it's more than one, mmcif contains multiple HETATM records in a loop. However, single atom entries seem to encode atomic coordinates in a different way, like so # _atom_site.group_PDB HETATM _atom_site.id 4905 _atom_site.type_symbol CA _atom_site.label_atom_id CA _atom_site.label_alt_id . _atom_site.label_comp_id CA _atom_site.label_asym_id L _atom_site.label_entity_id 5 _atom_site.label_seq_id . _atom_site.pdbx_PDB_ins_code . _atom_site.Cartn_x 0.394 _atom_site.Cartn_y -6.965 _atom_site.Cartn_z 18.775 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 2 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_asym_id A _atom_site.auth_seq_id 701 _atom_site.pdbx_PDB_model_num 1 This does not include _loop statement and instead lists parameters directly. If I try to convert this to pdb, cif_as_pdb fails like so (and I suspect that pretty much any cif-file read would fail) Python argument types in double.__init__(double, str) did not match C++ signature: __init__(boost::python::api::object, boost::python::numeric::array) __init__(boost::python::api::object, boost::python::tuple) __init__(boost::python::api::object, boost::python::list) __init__(boost::python::api::object, std::vector<double, std::allocator<double> >) __init__(boost::python::api::object, scitbx::af::const_ref<std::string, scitbx::af::trivial_accessor>) __init__(_object*, scitbx::af::shared_plain<double>) __init__(_object*, unsigned long) __init__(_object*, unsigned long, double) __init__(_object*, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> >) __init__(_object*, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> >, double) __init__(_object*) This has nothing to do with how many atoms are there, obviously - in fact, removing all HETATM records but one from a cif file that has _loop statement does not produce this bug. The obvious guess is that the bug is somewhere in mmdb (I am assuming here that phenix relies on it for cif read/write). This is not a big deal, of course - in most scenarios, a structure contains more than one atom. It does not interfere with me either - I am discarding single atom cases in this analysis anyway (so it is actually serves as an unintentional filter). Still, it looks like a bug. I am not an expert in mmcif format, but iiuc, there is no strict requirement for atom_site category to have a _loop. If there is (I can't find any such syntax requirement), then the source of the data files (PDBe coordinate server) would be at fault for not structuring the data properly. Cheers, Ed.

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Charged Ammonium ligand exploding
by pramod kumar 04 Sep '18

04 Sep '18

Dear All, I have a protein-ligand complex cryo-EM data. The ligand is a primary amine, which at the neutral pH used during data collection, should be NH3+ (alkyl-amonium). However, during realspace refine and despite having provided the CIF file (elbow generated alkyl-ammonium form), the molecule keeps "exploding". Instead, the 'NH2 form' (alkyl-amine) remains stable during refinement and most of the pdb entries having alkylammonium molecules have modeled them as the amine form even when they are expected to be positively charged. Thus, it seems to me that other groups may have gone through the same difficulties when trying to refine ammonium groups. We have already tried: * Ligand build in Lidia and tried prodrg with error (*Unrecognised REFMAC atom type 'HCH3' in input*) * Refmac Acedrg (run201 Error in wrapper refmac) Please help me fix this. I could refine using the amine form, but I know that the amine form is not right. Thank you very much, in advance. -- Promod Jaykar, Ph.D.

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autosol: FATAL RUNTIME ERROR :Wavelength outside range of Sasaki tables.
by Georg Mlynek 27 Aug '18

27 Aug '18

Dear Phaser Developers, we have collected data at diamond at 3A wavelength for Ca-MAD. Running autosol supplying the peak and remote dataset I get a solution. However the resolution is too low for autobuild to be successful. Therefore I continued with MR-SAD supplying the peak data=overall_best_refine_data.mtz This is my input mtz However get this error message: Error message from Phaser: FATAL RUNTIME ERROR :Wavelength outside range of Sasaki tables. Use SCATTERING to specify f' and f" for atom(s) "S" Phaser phasing did not work Scattering factors for Ca will be f'= -6.74 f''= 6.55 Using partial model pdb file as substructure: /home/g/r/aactn1_merge/phaser_31/aactn1_merge_phaser.1.pdb with RMS= 0.7 Data output to : AutoSol_run_32_/TEMP0/phaser_mtz FATAL RUNTIME ERROR :Wavelength outside range of Sasaki tables. Use SCATTERING to specify f' and f" for atom(s) "S" Phaser phasing did not work Analysis failed on solution evaluation *If I specify S as atom it continues without any problem however I get this warning, which I don't understand scientifically.* The same error I get (of course) when I would like to run PHASER-EP I guess the errors are just resulting from the programs not adjusted to the longwavelength beamline. Many thanks, best regards Georg.

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