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Institut Pasteur/CCP4 Joint Macromolecular Crystallography School "From data processing to structure refinement and beyond"
by Alejandro Buschiazzo 06 Dec '14

06 Dec '14

Dear colleagues, We are pleased to announce the Workshop: Macromolecular Crystallography School "From data processing to structure refinement and beyond", to be held at the Institut Pasteur de Montevideo (Uruguay). Dates: April 6 - 16, 2015 Invited speakers: Paul Emsley, Cambridge, UK Richard Garrat, São Carlos, Brazil Ronan Keegan, Oxford, UK Eugene Krissinel, Oxford, UK Victor Lamzin, Hamburg, Germany Andrey Lebedev, Oxford, UK Andrew Leslie, Cambridge, UK Garib Murshudov, Cambridge, UK Rob Nicholls, Cambridge, UK Randy Read, Cambridge, UK William Shepard, Paris, France Pavol Skubak, Leiden, the Netherlands Clemens Vonrhein, Cambridge, UK A preliminary program, as well as the application forms and contact information, can be found in this www site <http://www.pasteur.edu.uy/index.php/es/futuroscursos>. (within the page, look for this workshop’s details) The www site will be updated regularly, so stay tuned. This activity is supported by the Reseau International des Instituts Pasteur (RIIP); the Collaborative Computational Project Nº4 (CCP4, UK) & Science and Technology Facilities Council (UK); the International Union of Crystallography (IUCr); and the Institut Pasteur de Montevideo. Organizers: Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay Ronan Keegan, PhD. CCP4, STFC Rutherford Appleton Laboratory, United Kingdom Applicants: 24 students will be selected among the applications. The Course will provide financial support for the students, covering registration fees, and for the case of those coming from abroad, all local expenses (lodging, per diem and local transportation). The application deadline is February 16, 2015. The results will be announced by March 6. Please address further inquiries to: mx2015(a)pasteur.edu.uy <mailto:[email protected]> Looking forward to welcoming you in Montevideo! -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2 020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

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neutron scattering table for specific metal isotope
by Maxime Cuypers 05 Dec '14

05 Dec '14

Hello, I would like to alter the neutron scattering table for phenix.refine so that it takes into account the correct bcoherent value for the metal isotope present in my structure. the difference is significative between the natural occurence bcoh... i have been looking around in chem_data but could not find the neutron scattering tables. does anyone have any idea where to look please? cheerios -- Dr. Maxime Cuypers

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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

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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 +++++++++++++++++++++++++++++++++++++++++++++++++++

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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 = = = = = =

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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

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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 -----------------------------------------------------------------

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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

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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

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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

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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

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Not a suitable array of R-free flags:
by Yamei Yu 27 Nov '14

27 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

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error messages running phenix.mr_rosetta
by Ursula Schulze-Gahmen 26 Nov '14

26 Nov '14

I am running mr_rosetta on a 64bit Linux computer. The model optimization worked without a problem, but now in the molecular replacement step I am receiving error messages, and I am not sure what the problem is. Could anyone provide a suggestion? Thanks Ursula /usr/share/themes/Slider/gtk-2.0/gtkrc:80: error: unexpected identifier `colorize_scrollbar', expected character `}' Fontconfig warning: no <cachedir> elements found. Check configuration. Fontconfig warning: adding <cachedir>/var/cache/fontconfig</cachedir> Fontconfig warning: adding <cachedir>~/.fontconfig</cachedir> (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): Pango-WARNING **: Failed to load Pango module '/programs/x86_64-linux/phenix/dev-1819/phenix-dev-1819/build/intel-linux-2.6-x86_64/base/lib/pango/1.6.0/modules/pango-basic-fc.so' for id 'BasicScriptEngineFc' (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): Gtk-WARNING **: Could not find the icon 'system-file-manager'. The 'hicolor' theme was not found either, perhaps you need to install it. You can get a copy from: http://icon-theme.freedesktop.org/releases -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

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residue selection for rsrl?
by Kevin Jude 26 Nov '14

26 Nov '14

I am refining a structure at 2.9 Å resolution and have two side chains that keep moving out of density during reciprocal space refinement; both side chains should fit the resulting Fo-Fc density in favored rotamers. Turning on real-space refinement fixes this problem but leads to higher Rfree and poorer geometry overall. Can I select a subset of residues for real space refinement while still performing reciprocal space refinement on the whole asymmetric unit? Thanks for any help Kevin

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phenix rosetta refine
by Andreas Förster 26 Nov '14

26 Nov '14

Dear all, I'm trying to get phenix.rosetta_refine to run. I think it's all set up properly, with Rosetta 3.5 and Phenix 1810 on RHEL 6.3 64bit. However phenix.rosetta_refine model.pdb data.mtz nproc=48 protocol=full > log& fails with the following error in log: End of input processing Sorry: The RosettaScripts executable could not be located. Please add the appropriate directory to your PATH environment variable, or set the variable ROSETTA_BIN to point to it. To me it seems things are defined correctly: andreas@csbstereo in phenix: echo $ROSETTA_BIN /csb/soft/Linux64/share/rosetta3.5/rosetta_source/bin andreas@csbstereo in phenix: ls $ROSETTA_BIN | grep scripts rosetta_scripts.linuxgccrelease@ rosetta_scripts.default.linuxgccrelease@ andreas@csbstereo in phenix: ll $ROSETTA_BIN/rosetta_scripts.linuxgccrelease lrwxrwxrwx 1 csbadmin csb 93 Oct 9 2013 /csb/soft/Linux64/share/rosetta3.5/rosetta_source/bin/rosetta_scripts.linuxgccrelease -> ../build/src/release/linux/2.6/64/x86/gcc/4.4/default/rosetta_scripts.default.linuxgccrelease Any idea of what's wrong would be greatly appreciated. Andreas -- Andreas Förster X-ray Crystallography Facility Manager Centre for Structural Biology Imperial College London

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Alternative conformation of ligand with near zero occupancy
by Singh, Bishal 26 Nov '14

26 Nov '14

Hello everybody, I thank you for clarifying my previous doubts. Your suggestions matter a lot to me. Here I have another doubt. I have structure of a protein in complex with triglycan (fucose-galactose-galactose). The terminal galactose of this triglycan possesses two conformations with occupancies 0.4 and 0.6. In order to satisfy the geometric parameters of this triglycan, I derived the alternative conformation of fucose and the central galactose as well. Then I performed occupancy refinement. The occupancy of alternative central galactose is 0.06 and that of alternative fucose is 0.00. Now the question is, should I delete this fucose of zero occupancy or keep it to maintain the geometric parameters of triglycan? I am looking forward for your opinion. If you like I can provide a snapshot of ligand with electron density. With regards, Bishal Singh PhD student DKFZ, University of Heidelberg, Germany

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input for specifying labin in phenix.find_ncs
by Arka Chakraborty 26 Nov '14

26 Nov '14

Dear Phenix BBers, I have a seemingly trivial problem in specifying column labels in phenix.find_ncs. Following the manual, on entering labels as : phenix.find_ncs xx.pdb yy.mtz params.ncs.labin = "labin FP=F PHIB=PHI FOM=FOM" , phenix returns the error : 'Sorry, cannot interpret the keyword: params.ncs.labin=labin FP=F PHIB=PHI FOM=FOM'. Any clues on what mistake I might be making will be greatly appreciated. Thanks a lot, Regards, Arko -- *Arka Chakraborty* *ibmb (Institut de Biologia Molecular de Barcelona)* *BARCELONA, SPAIN*

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Different space group of coordinate and structure factors
by Singh, Bishal 25 Nov '14

25 Nov '14

Hello everybody, For a data-set, the space group after data-processing was P4222. When I performed molecular replacement through PHASER in phenix keeping the search option 'All possible in same point group", the space group changed to P41212. Now the question is that shall I process the data again in this new space group or should I move on for refinement? Please suggest me your opinion. With regards, Bishal Singh PhD Student DKFZ, University of Heidelberg, Germany

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explicit solvent in low resolution refinement
by Guenter Fritz 25 Nov '14

25 Nov '14

Dear all, we have determined the structure of a protein complex at 3.5 A resolution as well as the structures of three subunits of this complex independently at resolutions better than 2 A. I had used the models of the subunits as reference models in refinement, perfect. Now I was wondering whether one could use explicit solvent positions (e.g. inner shell water molecules) from the high resolution structures in the low resolution refinement. This should be superior to a simple bulk solvent model. I placed the inner shell water molecules from the high res structures into the low res model and added harmonic restraints to the water positions in low res refinement. I see a decrease of about 0.5% in Rwork and Rfree versus the model without water molecules. However, adding harmonic restraints excludes the option to use the reference models in refinement. Is it possible to use protein and water atoms from the reference models to generate restraints for the low resolution refinement? Thank you, Guenter

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ready set and H/D addition on waters
by Maxime Cuypers 25 Nov '14

25 Nov '14

hello, after not using phenix for a while, i just realised the new versions do not include the option in ready_set gui to add H or D atoms to waters in the pdb models (and only to the waters without altering the rest of the model would be nice). of course it can be done on the command line but why has it been removed? it is a very neutron crystallographer friendly option don t you think? cheerios, -- Dr. Maxime Cuypers

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Rwork > Rfree
by Singh, Bishal 21 Nov '14

21 Nov '14

Hello everybody, While depositing a structure in PDB, I observed that Rwork was more than Rfree in the highest resolution shell and in a few more shells as well. I shall be delighted if somebody can suggest me the reasons and also what should I do now. With regards, Bishal PhD student, DKFZ, University of Heidelberg, Germany

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MRage against local "select" PDB database on commandline
by Kaushik Hatti 21 Nov '14

21 Nov '14

Hi, I am new to Phenix. Sorry if my question is naive. For a given mtz file, I want to pick templates from a local PDB database (its actually iTasser template library) and perform Molecular Replacement using MRage. I have already installed Blast, downloaded iTasser PDB library (http://zhanglab.ccmb.med.umich.edu/library/PDB.tar.bz2) and extracted sequences from both the downloaded PDB template library set and target protein for which mtz is available. How should I go about building pipeline to perform MR using templates from locally downloaded select PDB database? Are there any more parameters available for parameter name: services under scop: search other than "local" and "ncbi"? Thanks in advance, Kaushik -- People living deeply have no fear of death - Anais Nin Caution: I am still the dumbest person I have ever known :-)

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Submissions for Comput. Cryst. Newsletter
by Nigel Moriarty 20 Nov '14

20 Nov '14

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the January 2015 issue is 17 December 2014 (with some leeway if you are still working on the text, especially as it can be polished over the break). 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 64R0246B, Physical Biosciences Division 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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Re: [phenixbb] Rwork > Rfree
by Ed Pozharski 20 Nov '14

20 Nov '14

Generate a different test set and repeat refinement. Do it twenty times. If R turns out to be systematically higher than Rfree even in few resolution shells, you have an interesting case worth looking at. If not, it's just noise. Sent on a Sprint Samsung Galaxy S® III <div>-------- Original message --------</div><div>From: "Singh, Bishal" <b.singh(a)dkfz-heidelberg.de> </div><div>Date:11/20/2014 9:52 AM (GMT-05:00) </div><div>To: phenixbb(a)phenix-online.org </div><div>Subject: [phenixbb] Rwork > Rfree </div><div> </div>Hello everybody, While depositing a structure in PDB, I observed that Rwork was more than Rfree in the highest resolution shell and in a few more shells as well. I shall be delighted if somebody can suggest me the reasons and also what should I do now. With regards, Bishal PhD student, DKFZ, University of Heidelberg, Germany _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

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GeoStd: was definition of glycosylation in phenix.refine
by Schubert, Carsten [JRDUS] 18 Nov '14

18 Nov '14

Hi Nigel, could you please comment on any plans to harmonize the use of these restraints for other refinement programs as well. Phenix originally appears to have implemented the restraint dictionaries from CCP4. Right now there seems to be some kind of parallel development going on with the dictionaries being in sync to some degree. Is there a plan to move to a unified restraints distribution at some point? Thanks Carsten From: phenixbb-bounces(a)phenix-online.org [mailto:[email protected]] On Behalf Of Nigel Moriarty Sent: Tuesday, November 18, 2014 12:38 PM Cc: PHENIX user mailing list Subject: Re: [phenixbb] definition of glycosylation in phenix.refine @Laurent Engin advice is sound but you are having trouble free feel to send me the inputs directly. NB. Any files sent to me will be held in strictest confidence. @Engin I think you will find what you are looking for in the GeoStd. As restraints are improved, they are moved from $PHENIX/chem_data/mon_lib to $PHENIX/chem_data/geostd (which is hosted on SourceForge for anybody's use). The directory structure is the same as the Monomer Library with a geostd_list.cif file corresponding to mon_lib_list.cif which specifies the links. Cheers Nigel --- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov<mailto:[email protected]> Fax : 510-486-5909 Web : CCI.LBL.gov<http://CCI.LBL.gov> On Tue, Nov 18, 2014 at 8:25 AM, Engin Özkan <eozkan(a)uchicago.edu<mailto:[email protected]>> wrote: Hi Laurent, If I am reading the error message right, you did not delete the hydrogens that get removed upon bond formation. That's what it is complaining about. I always thought Phenix probably removed these atoms (the hydroxyl and the hydrogen) automatically when you defined the link, but never tested if it really does it. I also usually remove all hydrogens right away when sugar residues are inserted. Finally, I will recommend that you use automatic linking in the phenix.refine GUI. It works great (I am on the latest nightly, dev-1839; you may need to upgrade). No need to define pesky links anymore. Thank you developers! At the risk of hijacking the thread, I could not find in my installation the cif files for N-linked sugars. Have they been moved elsewhere? Hope this helps, Engin On 11/18/14 10:02 AM, Laurent Maveyraud wrote: Hi, I am currently refining a structure of a glycosylated protein, but I fail to define the appropriate links... The glycosylatin is Asn638-NAG1061-(beta1-4)-NAG1062-(beta1-4)-BMA1063-(ALPHA1-3)-MAN1064 This is what I add in the eff file : apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain D and resname NAG and resid 1061 residue_selection_2 = chain A and resname ASN and resid 638 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain D and resname NAG and resid 1062 residue_selection_2 = chain D and resname NAG and resid 1061 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain D and resname BMA and resid 1063 residue_selection_2 = chain D and resname NAG and resid 1062 } apply_cif_link { data_link = ALPHA1-3 residue_selection_1 = chain D and resname MAN and resid 1064 residue_selection_2 = chain D and resname BMA and resid 1063 } this is correctly read in refine: apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain D and resname NAG and resid 1061 residue_selection_2: chain A and resname ASN and resid 638 apply_cif_link: data_link: BETA1-4 mod_id_1: DEL-HO4 mod_id_2: DEL-O1 residue_selection_1: chain D and resname NAG and resid 1062 residue_selection_2: chain D and resname NAG and resid 1061 apply_cif_link: data_link: BETA1-4 mod_id_1: DEL-HO4 mod_id_2: DEL-O1 residue_selection_1: chain D and resname BMA and resid 1063 residue_selection_2: chain D and resname NAG and resid 1062 apply_cif_link: data_link: ALPHA1-3 mod_id_1: DEL-HO3 mod_id_2: DEL-O1 residue_selection_1: chain D and resname MAN and resid 1064 residue_selection_2: chain D and resname BMA and resid 1063 but generates an error : Number of atoms with unknown nonbonded energy type symbols: 5 "HETATM10951 HO4 NAG D1052 .*. H " "HETATM10973 HO4 BMA D1053 .*. H " "HETATM11028 HO4 NAG D1062 .*. H " "HETATM11050 HO4 BMA D1063 .*. H " "HETATM11070 HO3 MAN D1064 .*. H " and the job stops. Any ideas on what if wrong ? thanks for your help Laurent _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb

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