[phenixbb] Phenix version 1.7.1 released
springer at idi.harvard.edu
Fri Apr 29 10:58:07 PDT 2011
Thanks Paul, That is a lot of improvements!
With my best regards,
Timothy A. Springer, Ph.D.
Latham Family Professor of Pathology
Harvard Medical School http://idi.harvard.edu/springer
Immune Disease Institute springer at idi.harvard.edu
Program in Cellular and Molecular Medicine, Dept. Medicine
Div. Hematology Children's Hospital Boston
3 Blackfan Circle, Rm 3103 phone: 617-713-8200
Boston MA 02115 fax: 617-713-8232
On Apr 29, 2011, at 1:40 PM, Paul Adams wrote:
> The Phenix developers are pleased to announce that version 1.7.1 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site:
> Some of the new features in this version are:
> Graphical Interface
> - New interfaces for: phenix.phase_and_build, phenix.mtz2map, phenix.french_wilson
> - Updates to the Structure comparison GUI, which now allows use of non-identical sequences,
> and results viewing in PyMol.
> - A plugin for running multiple sequence alignment
> - Graphical installers for Macintosh (installs in /Applications)
> - Binary installer for 64-bit Mac Intel (OS 10.6 only)
> New Commands
> - phenix.french_wilson (new command):
> - Implements French & Wilson correction of negative and weak intensities (see
> Acta Cryst A34:517 )
> - outputs modified amplitudes in MTZ format
> - used internally by default in Phaser GUI and phenix.refine when intensities
> are provided
> - phenix.reciprocal_space_arrays (new command):
> - this tool takes a PDB model and a data file and outputs an MTZ file
> containing a number of arrays that are typically used in various
> crystallographic calculations, such as R-factors, maps, refinement targets, etc.
> The output arrays include:
> - Fmodel, Fcalc, Fmask, Fbulk, FOM, resolution, Hendrickson-Lattman
> coefficients (input original, computed from model and combined),
> FB_CART (overall anisotropic scale), input Fobs and Rfree-flags and more
> - phaser.brunett (new command):
> - automated molecular replacement using incremental exploration, with support for parallelization
> - quick SSM-superposition-based LLG evaluation for alternative models for the same component
> - "puzzle"-assembly of solutions for a more complete solution
> - novel space group determination algorithm that retains possible space groups until they are
> significantly outperformed by others
> - handles custom models (used without modification), templates (a PDB template and an alignment,
> Sculptor is run to create models from it) and homology searches (PDB and alignment obtained from
> homology search, currently HHPRED and BlastXML; data downloaded from EBI)
> Structure refinement
> - New output MTZ file that contains original data, amplitudes used in refinement, and map
> coefficients (this replaces *_map_coeffs.mtz)
> - French and Wilson procedure automatically applied if intensities are input to refinement
> - Optional automatic rigid-body grouping by polymer chain (rigid_groups_mode=one_group_per_chain)
> - Reference model uses a "top-out" restraint potential with a smooth cutoff
> - Automatic determination of Saenger class for nucleic acid base pairs (if not provided by user)
> - Ability to run phenix.find_tls_groups internally to obtain atom selections
> - option: tls.find_automatically=True
> - Automatic non-bonded distance correction for H-bonded atoms
> Molecular Replacement
> - phenix.mr_rosetta:
> - Bug fixes
> - Added web site with data used in Nature Rosetta+Phenix paper at:
> - Added keyword include_solvation_energy=False to allow use of mr_rosetta for membrane proteins.
> - phenix.automr:
> - bug fix in residue number input, now allows four-digit IDs
> - eLBOW:
> - Geometries can be generated using CSD Mogul substructure searches of
> experimental geometries. Estimated standard deviations of the bonds
> and angles are also included in the restraints file.
> - KiNG (phenix.king):
> - Improved opening multiple electron density maps: tiered windows, with
> automatic deciphering of file name to preset sigma levels and colors.
> - Added -phenix command line option to preset map colors to be more like Coot.
> For a full list of changes see:
> 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:
> There is a Phenix bulletin board:
> Please consult the installer README file or online documentation for
> installation instructions.
> Direct questions and problem reports to the bulletin board or:
> help at phenix-online.org and bugs at 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
> Deputy Division Director, Physical Biosciences Division, 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
> Building 64, Room 248
> Tel: 1-510-486-4225, Fax: 1-510-486-5909
> Lawrence Berkeley Laboratory
> 1 Cyclotron Road
> BLDG 64R0121
> Berkeley, CA 94720, USA.
> Executive Assistant: Kathleen Moody [ KLMoody at lbl.gov ][ 1-510-495-2506 ]
> phenixbb mailing list
> phenixbb at phenix-online.org
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the phenixbb