- phenixbb - phenix-online.org

adding hydrogens to custom peptide bonds
by Dale Kreitler 04 Dec '14

04 Dec '14

Hi All, I am trying to add riding hydrogens to a model that includes beta-3-homoglutamine (B3Q). The monomer is not in the ccp4 library but it is a PDB chemical component. So far I have used elbow to build and optimize my own version of the ligand using the atom naming convention for a beta-amino acid in the PDB (where CB is in the backbone adjacent to the amino group, so the backbone goes like C-CA-CB-N). I am using a TRANS cif link from the monomer library for the N(alpha-amino acid) to C(beta-amino acid), and I have defined my own cif link for the N(beta-amino acid) to C(alpha-amino acid). However when I run phenix.reduce I can't get hydrogens to appear on the peptide bonds between the beta-amino acid and adjacent alpha-amino acids (hydrogens appear every where else on the ligand and in the model). I realize the effect of two hydrogens on the model is inconsequential but I would like to figure out how I can get phenix.reduce to recognize the bonds to my "ligand" as standard peptide bonds and add hydrogens accordingly. Thanks, Dale -- Dale Kreitler Gellman Lab UW Madison, Department of Chemistry

2 1

restraints between molecules in adjacent asymmetric units.
by jens j birktoft 04 Dec '14

04 Dec '14

Hi Everybody. Are there ways to restrain non-covalent interactions between molecules in adjacent asymmetric units? I know the custom bond procedure works well for covalent bonds. However I also would like to add restraints for (1) bond angles, (2) torsion angles (less important) and (3) nucleotide base-pairing. I know that all of these can be generated via the custom bond syntax, but that is a rather tedious and time-consuming process. Perhaps there is a simpler way I know this issue has been raised before but am unaware of any new developments. Cheers Jens -- +++++++++++++++++++++++++++++++++++++++++++++++++++ Jens J. Birktoft Director of Crystallography Structural DNA Nanotechnology Chemistry Department, New York University e-mail: jens.knold(a)gmail.com; Phone: 212-749-5057 very slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 +++++++++++++++++++++++++++++++++++++++++++++++++++

3 2

Intl Conf on Structural Genomics 2015: "Deep Sequencing Meets Structural Biology"
by Terwilliger, Thomas Charles 04 Dec '14

04 Dec '14

Dear Colleagues, We hope that you will be able to attend the International Conference on Structural Genomics 2015 "Deep Sequencing Meets Structural Biology", which will be held on the campus of the Weizmann Institute of Science in Rehovot, Israel June 7-11, 2015. This conference is intended to foster international collaboration and to provide an overview for the most recent developments in Structural Biology and Structural Genomics and future impacts on biology, medicine and disease. The scientific topics to be covered in ICSG 2015 include: · Deep sequencing for modeling and refinement of macromolecular structures · Membrane protein structure and function using complementary methods · Technological advances in XFEL, Cryo-EM, NMR, SAXS, MS, MX and macromolecular complexes · Combining low and high resolution data and modeling for structural biology · Synergistic use of 3D structures and deep sequencing to realize personalized medicine · Protein design and deep sequencing · Cancer, antibiotic resistance and drug discovery In order to widen the opportunities for younger researchers, we have organized satellite workshops before ICSG 2015 (during the day on June 7, 2015). These include: · Cryo-EM developments for structural biology [Sponsored by FEI] · PHENIX: Automated determination of molecular structures · HKL3000: From X-ray diffraction images to structure determination in minutes · Approaches to the translation of deep sequencing data into three-dimensions · Protein expression and characterization workshop · Proteopedia: A Scientific Wiki Bridging the Rift Between 3D Structure & Function You can see all the details of the conference at http://www.weizmann.ac.il/conferences/ICSG2015 . Five oral presentations will be chosen from the posters, and six poster prizes will be awarded, so be sure to submit your abstracts by April 15, 2015! Invited Speakers will include: Keynote Speakers: Shamil Sunyaev - Harvard Medical School Janet Thornton – EMBL/EBI - The FEBS National Lecturer Speakers: Arie Admon – Technion, Haifa Lucia Banci - CERM, University of Florence Pamela J. Bjorkman – CalTech, Pasadena Samir K. Brahmachari - CSIR-Institute of Genomics & Integrative Biology, Delhi Susan Buchanan - NIDDK, NIH, Bethesda Mark Gerstein - Yale University, New Haven Wayne Hendrickson - Columbia University Medical Center, New York Yvonne Jones - University of Oxford Luhua Lai - Peking University, Beijing Michael Levitt – Stanford University Michal Linial – The Hebrew University of Jerusalem Abraham Minsky - Weizmann Institute of Science, Rehovot John Moult - IBBR, University of Maryland, Rockville Nathan Nelson - Tel Aviv University Stefan Raunser - MPI of Molecular Physiology, Dortmund Monica Roth - Rutgers University, Piscataway Dinakar M. Salunke – Regional Centre for Biotechnology, Gurgaon Eran Segal - Weizmann Institute of Science Philip Selenko - Leibniz Institute of Molecular Pharmacology (FMP Berlin) Sachdev Sidhu - University of Toronto Rotem Sorek - Weizmann Institute of Science Jan Steyaert - VIB, Flanders, Brussels Dan Tawfik - Weizmann Institute of Science Gunnar von Heijne - Stockholm University Soichi Wakatsuki - Stanford University Shigeyuki Yokoyama - Genomic Sciences Center, RIKEN Yokohama Institute Ada Yonath - Weizmann Institute of Science Mingjie Zhang – Hong Kong University of Science & Technology We are looking forward to welcoming you to the Weizmann Institute in the June of 2015! Sincerely yours, ICSG 2015 Local Organizing Committee Joel L. Sussman, Gideon Schreiber, Tamar Unger and Israel Silman, Weizmann Institute ICSG 2015 International Organizing Committee Cheryl Arrowsmith, (Structural Genomics Consortium, Toronto) Lucia Banci, (University of Florence, Florence) Jacqui Beckmann, (Swiss Institute of Bioinformatics, Lausanne) Mark Gerstein, (Yale University, New Haven) Yvonne Jones, (University of Oxford, Oxford) Luhua Lai, (Peking University, Beijing) Katsumi Maenaka, (Hokkaido University, Sapporo) Gaetano Montelione, (Rutgers University, Piscataway) John Moult, (Institute for Bioscience and Biotechnology Research, Rockville) John Norvell, Maryland (Founding Director of the NIGMS Protein Structure Initiative) Dinakar Salunke, (Regional Centre for Biotechnology, Gurgaon) Gideon Schreiber, (Weizmann Institute, Rehovot, Israel) Joel L. Sussman, (Weizmann Institute, Rehovot, Israel) Janet Thornton, (European Bioinformatics Institute, Hinxton) Gunnar von Heijne, (Stockholm Bioinformatics Center, Stockholm) Ron Unger, (Bar-Ilan University, Ramat Gan) Shoshana Wodak (University of Toronto, Toronto) International Structural Genomics Organization Executive Committee Lucia Banci Aled Edwards Jennifer Martin Joel Sussman Tom Terwilliger Shigeyuki Yokoyama = = = = = =

1 0

Phenix.ensemble_refinment questions
by Joseph Brock 04 Dec '14

04 Dec '14

Dear Phenix community, I was hoping that some of you may be able to clarify some questions about Phenix.ensemble_refinement: 1. In the associated publication (Burnley et al. eLife 2012;), the ensemble refinement is validated by comparing the correlation of the ensemble generated map, with the map generated from the experimental phases for PDB entry 1YTT ("The overall correlation coefficient between the electron-density map from the ensemble model (obtained without experimental phases) and the experimentally phased electron-density map was 0.903, compared with 0.873 and 0.895 for the published and re-refined single structures. These seemingly small improvements in over- all quality indicators allow for significant local improvements."). I am confused how one computes an experimentally phased from structure factors deposited in the PDB that contain only anomalous intensities/amplitudes and not Hendrickson-Lattman coefficients. Is there a program within the phenix package that can do this? In addition, the phenix.ensemble_refinement keywords include: * experimental_phases * file_name = None * labels = None * Is it possible to include experimental phases during the rolling average refinement process and could this be beneficial (if the phases were of a sufficient quality)? 2. Is the correct procedure in parameter optimisation to optimise pTLS, then temperature offest and then tx? Or is it possible that the best ensemble may be generated from any (non-directional) combination of the above parameters? 3. What is the function of the "nproc" keyword? If this is the number of CPU cores that can be used in parallel, what is the most efficient way of using phenix.ensemble_refinement on a cluster? 4. Can anybody suggest a good way to compare the ensembles generated by phenix.ensemble_refinement with the trajectories of traditional MD simulations (for e.g. produced by NAMD? ;) Finally, I noticed that I cannot run phenix.ensemble_refinement using a "my_parameters.eff" file, it is necessary to type on the command line. Alternatively, the queueing system for the supercomputer I use is managed by SLURM, however, I cannot submit batch jobs via the appropriate command sbatch with anything other than default parameters (keywords in a parameters.eff or that are typed explicitly following the mycoords.pdb mydata.mtz myrestraints.cif files are not incorporated into the resulting parameters of the .log file). Could these issues be due to my local environment setup? I am running Phenix 1.9-1692 Platform: intel-linux-2.6-x86_64 redhat-e6.5. Sorry for the long email and many thanks in advance for you help! Best regards, Joseph. Joseph Brock | PhD Division of Physiological Chemistry II Department of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 SE-171 77 Stockholm, Sweden

6 9

Fwd: PostDoc position at the ALS
by Peter Zwart 03 Dec '14

03 Dec '14

Dear Colleagues, The Advanced Light Source in Berkeley is now looking to recruit two Postdocs to develop scattering in the tender X-ray regime. In particular using the Phosphors and Sulfur k-edge to enhance scattering. Details may be found here: *http://jobs.lbl.gov <http://jobs.lbl.gov/> * Postdoctoral Researcher - TReXS (Materials/ Physical Science)-80316 *and* Postdoctoral Researcher - TReXS (Biophysical Sciences)-80317 Alexander Hexemer and Peter Zwart Lawrence Berkeley National Lab -- ----------------------------------------------------------------- P.H. Zwart Staff Scientist Berkeley Center for Structural Biology, Science lead Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 SASTBX: http://sastbx.als.lbl.gov BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org -----------------------------------------------------------------

1 0

pdb file error
by maher alayyoubi 03 Dec '14

03 Dec '14

Hi Everyone, I am having a problem of phenix.refine not accepting a pdb file that I just finished editing in coot. It is a protein RNA compplex where the protein part was built in buccaneer and the RNA strand built in nautilus. I assembled the final model by text editing the pdb file and adding the RNA part. Whenever I feed this pdb file into phenix, it comes back with two errors: " number of atoms with unknown unbonded energy type symbols:6" . "The coot command could not be located" Does anyone know how to fix this problem? I tried converting the file into mmcif and feeding it to phenix but the same error comes back again. Thank you very much, Maher

2 1

norleucine (NLE) restraints
by Daniel Keedy 01 Dec '14

01 Dec '14

Hi everybody, First-time poster! I'm trying to re-refine 2f4k.pdb, but phenix.refine chokes on the non-standard norleucine (NLE) amino acid. I've tried phenix.elbow and phenix.ready_set using different version of PHENIX, with the NLE cards as either HETATM or ATOM, all to no avail. SHELX was used to refine the structure originally, but I'd like to use PHENIX to re-refine it. Any ideas on how to define these restraints? Daniel Keedy James Fraser Lab UCSF

3 3

来自"张士军" <[email protected]>的邮件
by 张士军 01 Dec '14

01 Dec '14

hello everyone how could use phenix phasing to phase a se substructure by search any possible spacegroup

1 0

Generate table 1-error message
by Lau Sze Yi (SIgN) 30 Nov '14

30 Nov '14

Hi, I got an error message when I tried to run the generate table 1 utility: Crystal symmetry mismatch between different files. My input files for pdb, mtz and cif were generated from my ccp4 refmac run. The unmerged data is the mtz output of ccp4 aimless. Did I upload the wrong file? Regards, Sze Yi Research Fellow Singapore Immunology Network (SigN) 8A Biomedical Grove, #03-06 Immunos, Singapore 138648 DID: +65 6407 0640 Fax: +65 6407 0640

2 1

Not a suitable array of R-free flags:
by Yamei Yu 26 Nov '14

26 Nov '14

Dear all, I use phenix.refine to refine a structure. Firstly, I used --dryrun to generate an .eff file. The command is "phenix.refine --dry_run 7_44.mtz 7_44.pdb refinement.input.xray_data.r_free_flags.generate=True refinement.input.xray_data.r_free_flags.max_free=1000” Then I use run the program by typing “phenix.refine 7_44_refine_001.eff” It runs correct! After that I use coot to modulate some parts of the structure, then I want to refine the structure again. I type “ phenix.refine 7_44_refine_002.def” This time I got the following error message: Not a suitable array of R-free flags: refinement.input.xray_data.r_free_flags.label=R-free-flags Sorry_Not_a_suitable_array: Not a suitable array of R-free flags: refinement.input.xray_data.r_free_flags.label=R-free-flags To override the suitability test define: refinement.input.xray_data.r_free_flags.disable_suitability_test=True I checked the generated file by phenix “7_44_refine_data.mtz” I does contain a column labeled as R-free-flags. I paste part if it below. * Space group = 'P1' (number 1) OVERALL FILE STATISTICS for resolution range 0.000 - 0.277 ======================= Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 ASC -32 31 0 100.00 -2.2 11.9 49.44 1.90 H H 2 NONE -46 45 0 100.00 -2.5 17.8 49.44 1.90 H K 3 NONE 0 49 0 100.00 18.8 18.8 49.44 1.90 H L 4 NONE 0.9 271.3 0 100.00 26.52 26.52 49.44 1.90 F F-obs 5 NONE 0.2 5.1 0 100.00 1.25 1.25 49.44 1.90 Q SIGF-obs 6 NONE 0.0 1.0 0 100.00 0.01 0.01 49.44 1.90 I R-free-flags No. of reflections used in FILE STATISTICS 143215 Then I regenerate a new mtz file with FreeRflag by XDSCONT, then I revise the .def file accordingly and rerun the program. I got same error message:Not a suitable array of R-free flags: refinement.input.xray_data.r_free_flags.label=FreeRflag Sorry_Not_a_suitable_array: Not a suitable array of R-free flags: refinement.input.xray_data.r_free_flags.label=FreeRflag To override the suitability test define: refinement.input.xray_data.r_free_flags.disable_suitability_test=True I checked my new mtz file, it dose contain a column labeled as FreeRflag Why there is an error message? How to solve it? Thank you so much!! Best wishes! yamei ************************************************ Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyuxtal(a)gmail.com ymyuxtal(a)163.com yamei_yu(a)scu.edu.cn

3 2