- phenixbb - phenix-online.org

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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