November 2016 - phenixbb - phenix-online.org

gtk glib error messages and too large fonts when starting phenix 1.11.1-2575
by Martin Moche 18 Nov '16

18 Nov '16

Dear colleagues, Today I install latest stable phenix 1.11.1-2575 without problems - output attached. When starting the phenix GUI, the fonts are too large and I get a lot of Gtk, GLib error messages - see below These error messages can be found online as well https://mail.gnome.org/archives/meld-list/2015-January/msg00007.html and are therefore likely not related to phenix. Perhaps somebody knows how to get rid of them and get smaller fonts into phenix GUI? Best regards, Martin ############### my Glib Gtk error messages ############## [x_marmo@triolith2 ~]$ phenix (main.py:60858): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:60858): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:60858): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:60858): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:60858): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:60858): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:60858): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:60858): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed Already checked for new versions in last 24 hours, skipping Martin Moche, Ph.D. Head of Protein Crystallography Karolinska Institutet MBB/PSF Scheeles väg 2 171 77 Stockholm Sweden phone: +46-8-524 868 43 mobile: +46-73-322 93 27 fax: +46-8-524 868 68 email: Martin.Moche(a)ki.se

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Sorry: Refinement of multiple models not implemented.
by Murpholino Peligro 17 Nov '16

17 Nov '16

I was looking at pdb 2d6b and I try to do a refinement with phenix. (First I generated the cif file with phenix.elbow for 202 ( https://www3.rcsb.org/ligand/202). Then I retry the refinement and I got the error "Sorry: Refinement of multiple models not implemented." How to proceed? Thanks MP

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Why can't I use bootstrap.py in cctbx to compile phenix?
by Taimin Yang 17 Nov '16

17 Nov '16

Dear Professor, My name is Taimin Yang and I am a PhD student in Stockholm University. I try to compile my own phenix using bootstrap.py but here is the error information: root@Linux-main:/usr/local/crystallography_software/phenix# python bootstrap.py --builder=phenix --with-python=/usr/local/anaconda2/bin/python hot update build Performing actions: hot update build Traceback (most recent call last): File "bootstrap.py", line 2034, in <module> run() File "bootstrap.py", line 2029, in run enable_shared=options.enable_shared, File "bootstrap.py", line 926, in __init__ map(self.add_module, self.get_codebases()) File "bootstrap.py", line 1051, in add_module action = MODULES.get_module(module)().get_url(auth=self.get_auth()) File "bootstrap.py", line 553, in get_url raise Exception('No anonymous access method defined for module: %s. Try with --%s'%(self.module, e.args[0])) Exception: No anonymous access method defined for module: chem_data. Try with --cciuser What should I do to compile my own phenix? Thank you very much. Best regards, Taimin

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Failed to refine B factors of some residues and ligands
by Zhou, Tongqing (NIH/VRC) [E] 16 Nov '16

16 Nov '16

Dear All, I am refining a structure with diffraction to 2.2A resolution and 95 % overall completeness. Now the Rs are at 18% and 23%, respectively. But the program failed to refine B factors for several ligands, atoms had high B factors while showing positive Fo-Fc map around them. Occupancy was set to 1 and I also tried to reset B to mean B of the whole PDB. Any of you seeing this phenomenon? Thanks! Shown below is HEPES that has high B factor and positive density around it after refinement: [cid:[email protected]] Best regards, Tongqing Tongqing Zhou, Ph.D. Co-head and Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4609B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 761-7068 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************

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phenix fails to configure on fedora 20
by abhisek Mondal 04 Nov '16

04 Nov '16

Hi, I'm using Fedora 20 on a 4 core laptop. When I tried to install phenix it gave following error. Same version installed fine in my workstation but keep failing here. Please help me out here. Thanks. *[root@viralhost phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6]# ./install * * ==========================================================================* * Phenix Installation* * version: 1.10.1-2155* * machine type: intel-linux-2.6* * OS version: 3.19.8-100.fc20.i686* * destination: /usr/local/phenix-1.10.1-2155* * # of processors: 4* * =========================================================================* *Configuring Phenix components...* *Traceback (most recent call last):* * File "./bin/install.py", line 262, in <module>* * installer(sys.argv[1:]).install()* * File "/home/abhisek/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 185, in install* * self.install_from_binary()* * File "/home/abhisek/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 295, in install_from_binary* * self.reconfigure(log=log)* * File "/home/abhisek/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 460, in reconfigure* * call(args=args, log=log, verbose=self.options.verbose)* * File "/home/abhisek/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/installer_utils.py", line 81, in call* * raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc))* *RuntimeError: Call to '/usr/local/phenix-1.10.1-2155/base/bin/python /usr/local/phenix-1.10.1-2155/modules/cctbx_project/libtbx/configure.py --current_working_directory /usr/local/phenix-1.10.1-2155/build --command_version_suffix 1.10.1-2155 phenix phaser solve_resolve labelit' failed with exit code 126* -- Abhisek Mondal *Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA*

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Phenix version 1.11.1 released
by Paul Adams 02 Nov '16

02 Nov '16

The Phenix developers are pleased to announce that version 1.11.1 of Phenix is now available (build 1.11.1-2575). Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ Highlights for this version: New tools for omit maps without bulk solvent in omitted region, automated sharpening of cryo-EM and crystallographic maps, and segmentation of maps. Improved NCS search. New automated model-building tools for low-resolution maps - especially cryo-EM, tools for matching chains (both residues and direction), multiple improvements to phenix.real_space_refine and addition of new GUI. Improved model geometry restraints, many improvements to Phaser, improved validation incorporating new MolProbity features, simplified Rosetta installation, improved support for Amber, updated dependencies, Unicode support in GUI, new unified interface for atom selections. - General - Improved geometry restraints: - Conformation-Dependent Library for omega added (omega_cdl=True) - Installation - Rosetta installation centralised for phenix.rosetta_refine, phenix.mr_rosetta and ERRASER - Improved NCS search procedure with simplified parameters. Provides status of user-supplied NCS groups during validation (refused/modified/ok) - Updated dependencies - biopython 1.64 -> 1.66 - sphinx 1.2.2 -> 1.4.4 - ipython 2.1.0 -> 3.2.1 - pip 6.0.7 -> 8.0.2 - Neutron scattering tables: support ions - Amber refinement - Alpha release dev-2203 - GUI - New interfaces - phenix.map_comparison - phenix.polder - phenix.structure_search - phenix.real_space_refine - New selection editor - Unified interface for selecting atoms - Secondary structure annotations - NCS groups - TLS groups - Refinement strategy options - Unicode support - Non-ASCII characters are supported for most fields (e.g. file paths and job titles) - Using non-ASCII characters in projects/jobs will prevent earlier versions that do not have Unicode support from opening the project list correctly - Migrated validation after phenix.refine to use regular MolProbity for consistency (older versions of Phenix will not open new jobs) - phenix.real_space_correlation can now accept map files - phenix.molprobity can now accept map files - Updated dependencies for Linux - libpng 1.2.52 -> 1.5.26 - freetype 2.4.2 -> 2.6.3 - gettext 0.18.2 -> 0.19.7 - glib 2.12.11 -> 2.46.2 - expat 1.95.8 -> 2.1.0 - fontconfig 2.3.95 -> 2.11.1 - render 0.8 -> 0.11.1 - xrender 0.8.3 -> 0.9.7 - xft 2.1.2 -> 2.3.2 - pixman 0.19.2 -> 0.34.0 - cairo 1.8.10 -> 1.14.4 - pango 1.16.1 -> 1.38.1 - atk 1.9.1 -> 2.18.0 - libtiff 3.6.1 -> 4.0.6 - gtk+ 2.10.11 -> 2.24.29 - matplotlib 1.3.1 -> 1.5.1 - Maps - phenix.polder calculates omit maps which exclude the bulk solvent around the omitted region. This way, weak densities possibly obscured by bulk solvent may become visible. - phenix.model_map: Given PDB file calculate model map and output as CCP4 formatted binary map file. - phenix.mask: Given PDB file calculate bulk-solvent mask and output as CCP4 formatted binary map file. - phenix.auto_sharpen: Optimizes resolution dependence of a map to improve clarity - phenix.segment_and_split_map: Carries out segmentation of a map - Model-building - phenix.map_to_model builds models in low-resolution maps - builds any combination of RNA/DNA/protein - if NCS present, builds the asymmetric unit of NCS and expands to the entire map - phenix.segment_and_split_map breaks up a map into the asymmetric unit of NCS and further subdivides that into contiguous regions of density - phenix.chain_comparison compares CA or P atoms of two models and identifies how many residues match and how many are in the same direction - phenix.real_space_refine: - Support output of refined model in mmCIF format - ADP refinement runs by default at the last macro-cycle. Several CPUs can be used to speed up refinement: use nproc=NUMBER_OF_CPUs parameter for this. - phenix.model_idealization: tool to idealize model geometry while staying as close as possible to the starting model. Currently proteins only. Idealize covalent geometry and secondary structure, as well as eliminate rotamer and Ramachandran plot outliers, C-beta deviations. - phenix.geometry_minimization - ability to use reference torsion restraints - ability to use NCS constraints - phenix.phaser - SOLUTION HISTORY tracks solution through positions in RF/TF/PAK/RNP peak lists - selection by CHAIN and MODEL for PDB coordinate entry - automatic search number for single search ensemble - packing 'trace' molecule can be entered independently of coordinates and map - read TNCS/anisotropy binary files to avoid refinement, when running through scripts - write tNCS and anisotropy parameters to binary files (non-python interface) - default reading of I (or failing that, F) from mtz file (LABIN optional) - trace for ensembles from maps = hexgrid of 1000+/-100 points - trace for ensembles from coordinates above 1000 Calpha = hexgrid of 1000+/-100 points - trace for ensembles from coordinates twixt 1000 atoms and 1000 Calpha = Calpha atoms - trace for ensembles from coordinates under 1000 atoms = all atoms - packing by pairwise percent only, other packing modes obsoleted - packing test during FTF run by default with 50% pairwise packing cutoff - automatic tNCS NMOL determination in presence of commensurate modulation - added MODE GIMBLE, which splits ensembles by chain for rigid body refinement - support for unicode - solution coordinates placed nearest to input coordinates if possible - phenix.reduce - Updated reduce_wwPDB_het_dict as of Aug 12, 2016 - New script for updating het dict - Reduce no longer rotates methionine methyls by default. -DOROTMET flag reinstates old behavior - phenix.ramalyze - Improved handling of residue connectivity - Summary statistics provided for altloc A specifically where multiple altlocs present 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 80, Room 247 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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phenix gui starting up for one, not for other users
by wtempel 01 Nov '16

01 Nov '16

Hello, we run phenix on a ubuntu 14.04 (x86_64) box. Phenix is installed in user x’s home directory. After running . ~x/prog/phenix-1.11.1-2575/phenix_env.sh; phenix, and some *setlocale* warnings, the phenix GUI will show up on the screen for user x. User y, after . ~x/prog/phenix-1.11.1-2575/phenix_env.sh; phenix, will get *setlocale* warnings, a white credit screen (briefly), but the GUI will not show up, but *phenix* does not exit. User does get the expected error messages after typing phenix.molprobity_1.11.1-2575 without specifying input coordinates, as does user y get the (older) GUI upon . ~x/prog/phenix-1.10.1-2155/phenix_env.sh; phenix. Do you have any suggestions as to how I can enable user y to use the 1.11.1 GUI? Thank you. Wolfram Tempel

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postdoc jobs at Oxford
by Cell Guidance 01 Nov '16

01 Nov '16

Hello, May I please draw your attention to two excellent postdoc opportunities at the University of Oxford. Further information is available via the links below. Application deadlines are 30 November and 1 December 2016. Postdoc in Structural Biology: https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_details_form.j… Postdoc in Cell Biology: https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_details_form.j… Many thanks, Elena Dr. Elena Seiradake Dept. of Biochemistry, University of Oxford South Parks Road, Oxford, OX1 3QU, U.K.

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