- phenixbb - phenix-online.org

New Solvent Modeling/Analysis Tool
by Paul Smith 16 Oct '18

16 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 26 Sep '18

26 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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