The Phenix developers are pleased to announce that version 1.7.2 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Some of the new features in this version are: Graphical interface: ==================== - phenix.data_viewer added under Reflection Tools - New GUIs: HySS, phenix.cut_out_density, phenix.reciprocal_space_arrays General: ======== - New commands: phenix.cut_out_density, phenix.data_viewer, phenix.morph_model - Default map output format changed to CCP4 - Native support for CIF-format reflection files (e.g. from PDB) in many commands and GUI Refinement: =========== - New Xray/restraints weight optimization. Keywords optimize_wxc and optimize_wxu replaced with optimize_xyz_weight and optimize_adp_weight, respectively. - Grid searches parallelized: use 'nproc' parameter to set number of CPUs to use - this affects bulk solvent mask optimization, and XYZ and ADP weight optimization (in addition to TLS identification) - can reduce runtime by 75% or more depending on settings (see manual for details) - Modified non-bonded parameters resulting in improved geometry, especially at low resolution - Rigid-body refinement mode defaults to grouping by chain - Printout of validation statistics during coordinate refinement - Bug fix in phase-combined map calculation results in significantly improved maps - Bug fix in X-ray/ADP restraints weight calculation results in smaller B-factors deviations for bonded atoms - Experimental feature (still in testing): - Torsion-space NCS (ncs.type=torsion), automatic parameterization, similar to reference model restraints - Uses top-out potential to allow deviations between NCS related atoms New commands: ============= - phenix.cut_out_density: - carve out a region from map coefficients (MTZ file) - density may be specified as a sphere, a box, or masked around a PDB file - phenix.data_viewer: - visualization of reciprocal-space reflection data - 3D OpenGL view of all data, or 2D view of planes (pseudo-precession photograph) - phenix.morph_model: - Use after molecular replacement to improve model for rebuilding - Morphs model to match a prime-and-switch map Molecular Replacement: ====================== - Phaser (and AutoMR wizard): - significant speedup of fast rotation function Miscellaneous: ============== - phenix.reel: - better integration with main GUI, especially eLBOW - phenix.fobs_minus_fobs_map: - option to disable strict unit cell isomorphism check - phenix.ramalyze: - optional output of PNG images of Ramachandran plots; add --plot to command line arguments - phenix.fetch_pdb: - new flags: --all fetches PDB, CIF, and FASTA files simultaneously --mtz runs phenix.cif_as_mtz on downloaded CIF file 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: [email protected] and [email protected] 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 Deputy Division Director, Physical Biosciences Division, 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 Head, Berkeley Center for Structural Biology Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ [email protected] ][ 1-510-495-2506 ] --