[phenixbb] Phenix version 1.7.2 released

Paul Adams pdadams at lbl.gov
Fri Sep 30 15:00:11 PDT 2011

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:


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

- 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

- 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

- 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:


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
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

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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