[phenixbb] Phenix version 1.7.1 released

Timothy Springer 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,
Tim

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:
> 
> 	http://phenix-online.org/download/
> 
> 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
> 
> Installers
> ----------
> - 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 [1978])
>  - 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:
>    http://www.phenix-online.org/phenix_data/terwilliger/rosetta_2011/
>  - 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
> 
> Ligands
> -------
> - 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.
> 
> Visualization
> -------------
> - 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:
> 
> 	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 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
> http://cci.lbl.gov/paul
> 
> Lawrence Berkeley Laboratory
> 1 Cyclotron Road
> BLDG 64R0121
> Berkeley, CA 94720, USA.
> 
> Executive Assistant: Kathleen Moody [ KLMoody at lbl.gov ][ 1-510-495-2506 ]
> --
> 
> 
> 
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> 

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