[phenixbb] Phenix version 1.8 released

Paul Adams pdadams at lbl.gov
Fri Jun 22 12:56:54 PDT 2012

The Phenix developers are pleased to announce that version 1.8 of Phenix is now available. Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site:


Some of the new features in this version are:

Graphical interface:
- New GUIs: phenix.multi_crystal_average, phenix.morph_model, phenix.table_one, phenix.find_peaks_holes
- Improved layout for AutoBuild and reflection file editor GUIs
- Editor for custom bond/angle/plane restraints in phenix.refine
- Project groups: manage defaults for similar projects

- New very fast bulk-solvent and overall anisotropic scaling procedure
- Experimental Windows installer (32-bit only)
- Improved support for anomalous difference arrays (F SIGF DANO SIGDANO ISYM)
- New commands: phenix.den_refine, phenix.find_peaks_holes
- Overall Molprobity score now calculated in phenix.model_vs_data and the
  validation/refinement GUIs

- Change in default NCS restraints behavior:
    - use torsion-angle parameterization
    - restraints on NCS-related B-factors turned off
- Automatic matching of chains to reference model; allows multiple chains
    to be restrained to a single reference chain
- Support for multiple reference model files
- New method for filling of missing Fobs using simple density modification

Molecular Replacement:
- phaser (version 2.5):
  - TNCS support enabled by default for both MR and SAD

Experimental Phasing and Model Building:
- AutoSol:
  - TNCS support for SAD phasing

- phenix.pdbtools:
  - ability to set atomic charge field (used for X-ray scattering factors and
    VDW radii in nonbonded restraints)
- phenix.find_peaks_holes (new command):
  - standalone map peak search program: highlight difference map features
  - includes analysis of anomalous maps, flag suspicious "water" molecules
- phenix.maps:
  - simplified execution on command line: "phenix.maps model.pdb data.mtz"
    - generates default map coefficients (2mFo-DFc, mFo-DFc, anomalous if
      available) and 2mFo-DFc CCP4-format map.
- phenix.fetch_pdb:
  - added --maps option: generates 2mFo-DFc and mFo-DFc map coefficients
- phenix.get_cc_mtz_pdb:
  - added atom_selection keyword: compute CC for a subset of atoms
- phenix.real_space_correlation:
  - simplified execution on command line:
      "phenix.real_space_correlation model.pdb data.mtz"
    - calculates CC of model to 2mFo-DFc map
  - added atom_selection keyword: compute CC for a single selection (instead of
    per-atom or per-residue statistics)

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
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 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: Louise Benvenue [ LBenvenue at lbl.gov ][ 1-510-495-2506 ]

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