[phenixbb] Phenix version 1.7.1 released

Paul Adams pdadams at lbl.gov
Fri Apr 29 10:40:27 PDT 2011

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 [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:
  - 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 ]

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