December 2018 - phenixbb - phenix-online.org

mmCIF for deposition
by Patrick Loll 19 Mar '19

19 Mar '19

Hi all, Following the instructions given here: https://www.phenix-online.org/documentation/overviews/xray-structure-deposi… I’m attempting to use mmtbx.prepare_pdb_deposition to insert sequence information into the mmCIF that contains the model coordinates. Unfortunately, the program fails with an error (shown below). The sequence file is FASTA format, and contains an entry for each of the (4) chains in the AU, i.e. >A MSEQNCE… >B MSEQNCE… etc. Any bright ideas? ============this is what happens (vide infra)==================================== [PJL-iMac:blahblah/PJL_final] loll% mmtbx.prepare_pdb_deposition filename.cif seq_name.fasta Starting mmtbx.prepare_pdb_deposition on Mon Oct 1 11:16:23 2018 by loll =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, filename.cif Found sequence, seq_name.fasta Processing PHIL parameters: ------------------------------------------------------------------------------- No PHIL parameters found Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = “filename.cif" } default_model = “filename.cif" sequence_files = "seq_name.fasta" default_sequence = "seq_name.fasta" } Starting job =============================================================================== Validating inputs Using model: filename.cif Using sequence: seq_name.fasta Creating mmCIF block for sequence Traceback (most recent call last): File "/Applications/phenix-1.14-3260/build/../modules/cctbx_project/mmtbx/command_line/prepare_pdb_deposition.py", line 9, in <module> run_program(program_class=prepare_pdb_deposition.Program) File "/Applications/phenix-1.14-3260/modules/cctbx_project/iotbx/cli_parser.py", line 71, in run_program task.run() File "/Applications/phenix-1.14-3260/modules/cctbx_project/mmtbx/programs/prepare_pdb_deposition.py", line 98, in run alignment_params=self.params.mmtbx.validation.sequence.sequence_alignment) File "/Applications/phenix-1.14-3260/modules/cctbx_project/iotbx/pdb/hierarchy.py", line 1190, in as_cif_block_with_sequence assert len(chain.residue_groups) + chain.n_missing_start + chain.n_missing_end == len(sequence) AssertionError (gouts of smoke, terrified squealing) The ‘No PHIL parameters found’ message is concerning, but the program clearly seems to be finding the input file names. Suggestions welcome. 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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unrestrained refinement
by Kaiser, Jens T. 29 Jan '19

29 Jan '19

Hi! I'm trying to do unrestrained refinement of a small molecule in phenix. I have done this many years ago, but it seems whatever I try, phenix.refine now complains about missing nonbonded energy type for all atoms. The pdb file I supply has the following format (just one line) HETATM 33 C81 UNK 1 3.117 14.425 18.765 1.00 1.45 C I tried unchecking all references to geometry restraints in the GUI, setting wc and wu to 0 I also started from a default .eff file and set all references to restraints to either True of False (depending what they said). I also tried the line from the phenix.refine documentation: phenix.refine ../cif_in/mkt_a.ent ../data/181119/proc/137C3/XDS_17000.HKL strategy=individual_sites wc=0 refinement.input.symmetry_safety_check=warning refinement.input.xray_data.r_free_flags.generate=True I'm using phenix v 1.14-3260 from an sbgrid environment. Any pointers welcome. Cheers, Jens

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mmCIF in Phenix 1.14-3260
by Dominik Oberthuer 30 Dec '18

30 Dec '18

Dear all, I recently found that phenix.refine in version 1.14-3260 generates coordinate mmCIFs that the PDB deposition system can't handle. After struggling with this for some time I used an installation of Phenix 1.13-2998 I still have on my MacBook and used the mmCIF/PDB-conversion tool from this version and had no more trouble with uploading the mmCIF to the PDB. Maybe it is worthwhile to check which changes from 1.13 to 1.14 might have caused these issues. Thanks! Dominik -- Dr. Dominik Oberthür CFEL - Center for Free-Electron Laser Science - DESY Coherent Imaging Division Notkestrasse 85 22607 Hamburg Germany phone: +49 (0)40 8998 6394 dominik.oberthuer(a)cfel.de

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smaller the cell parameter of EM map
by dancingdream＠163.com 30 Dec '18

30 Dec '18

Dear all, The cell parameter of the EM map is always too large, which will make the model building program running very slow. But in factor, the structure is a smal part of cell. So can I smaller the cell parameter when I use phenix.map_to_structure_factors to convert the EM map to mtz file. Thank a lot! Wei

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RapiData at SSRL 2019 - application closing data extended
by Smith, Clyde 26 Dec '18

26 Dec '18

Hi everyone, It has come to our attention that due to scheduled computer and power outages at SLAC over the Christmas/New Year period, the connection to the server supporting the RapiData 2019 page is down. Please use the following link to apply for the workshop: https://app.certain.com/profile/2831400 Because of this issue, we will be extending the closing date for applications to January 6 2019. If you have any problems don't hesitate to contact one of us. Cheers, Clyde Smith, Silvia Russi and Jeney Wierman (Organizers) csmith(a)slac.stanford.edu srussi(a)slac.stanford.edu jwierman(a)slac.stanford.edu

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RapiData at SSRL 2019 reminder - just a week left to apply!
by Smith, Clyde 21 Dec '18

21 Dec '18

Hi all, A reminder that there is only a week left to apply for a place at the RapiData 2019 @ SSRL workshop. Applications close at the end of this month, December 31 2018. The workshop will be held from May 5-10 2019 on the SLAC campus in Menlo Park, California. 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. Successful applicants will be notified early in January 2019 and invited to register at that time. A limited amount of travel support funding may be available. We look forward to seeing you all out in sunny California in May 2019! Silvia Russi, Clyde Smith and Jeney Wierman (Organizers) srussi(a)slac.stanford.edu jwierman(a)slac.stanford.edu csmith(a)slac.stanford.edu

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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 21 Dec '18

21 Dec '18

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission for the January 2019 issue is 20 January 2019. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. 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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phenix.refine does not work with afitt
by Guenter Fritz 20 Dec '18

20 Dec '18

Dear phenix developers, I am trying to run phenix.refine with afitt (phenix 1.14 3260, afitt 2.4.1.2). However, I receive the an error: "Sorry: Unknown command line parameter definition: use_afitt = True" This I get on my mac or on my linux box . Is support for afitt discontinued? Any help is appreciated! Thanks and best regards, guenter

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JRH Report on International Data Week 2018
by John R Helliwell 20 Dec '18

20 Dec '18

Dear Colleagues, I mention that my report on International Data Week 2018 can be found here:- http://forums.iucr.org/viewtopic.php?f=39&t=409 and which I imagine will be of general interest. All best wishes, John Emeritus Professor John R Helliwell DSc IUCr Representative to CODATA and Chairman of the IUCr Committee on Data

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Postdoctoral position at the Drug Discovery Institute at Purdue University
by John M Hausman 17 Dec '18

17 Dec '18

Dear All: A position is available for a highly qualified and motivated postdoc with a strong background in Molecular/Cell Biology or Immunology. The successful applicant will be responsible for conducting research aimed at identifying and characterizing new drug targets for treatment of important human diseases. Activities may involve i) expressing and characterizing proteins that are upregulated in various disease states, ii) cloning, mutating, expressing and developing assays for studying functional aspects of the target proteins, iii) immunofluorescent staining of tissue sections from diseased tissues, iv) shRNA knockdown of desired proteins in cultured cells, and v) immunoblotting and other common biochemical assays. Management of day-to-day research goals and priorities, supervision of graduate students assigned to the same project, and mentoring of other research personnel regarding the design and execution of specific research methods/approaches may also be required. The lab is directed by Professor Philip S. Low in the new Drug Discovery Institute on the West Lafayette Campus of Purdue University. Other members of the lab are involved in designing new therapies for cancer, fibrotic diseases, infectious diseases, sickle cell disease, bone fractures and related pathologies, and autoimmune diseases, etc. Participation in some of these existing projects may also be required. Please send CV and list of three names of potential referees to: Philip S. Low Presidential Scholar for Drug Discovery Ralph C. Corley Distinguished Professor Department of Chemistry Purdue University 720 Clinic Dr. West Lafayette, IN 47907 Email: plow(a)purdue.edu<mailto:[email protected]> ________________________________

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