[phenixbb] Phenix version 1.13 released

Paul Adams pdadams at lbl.gov
Tue Jan 9 09:26:40 PST 2018

The Phenix developers are pleased to announce that version 1.13 of Phenix is now available (build 1.13-2998). Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site:


Highlights for this version:

- phenix.map_to_model - better symmetry support and improved runtime efficiency 
- phenix.structure_search - structural library and internal support for mmCIF 
- phenix.ligand_identification - limit ligand size for search 
- Phaser 2.8.1 - various bug fixes 
- Structure Comparison - more/improved validation information (ligands, waters, cis/trans peptides, HIS protonation) 
- GUI - automatic validation after phenix.real_space_refine; visual improvements in validation
- Improved handling of model mmCIF input/output
- New Phenix video tutorials  
- Internal bug fixes and performance improvements


  - Phenix.map_to_model:
    - Allows cases where symmetry that is neither point-group nor
       helical is present
    - Allows splitting runs into many small independent steps
    - Set defaults for quick=True to run somewhat more quickly

  - Validation information added to phenix.real_space_refine results
  - phenix.real_space_refine GUI accepts input for reference models
  - Polygon stand-alone GUI deprecated; rolled into Comprehensive Validation GUI
    - Old Polygon jobs cannot be restored
  - Validation GUI
    - Stoplight colors (green/orange/red) added to validation summary
    - In rotamer outlier table, uncalculated chi angles now display blank instead of None
    - Validation table columns adjusted to reduce whitespace

- Updated dependencies
  - Python 2.7.13 -> 2.7.14
  - Boost 1.56 -> Boost 1.63
  - Numpy 1.8.1 -> 1.8.2

- phenix.structure_search:
  - Updated to November 2017 RCSB non-redundant library
    (representatives of 100% sequence-identity clusters.)
  - Changed to mmcif-based coordinate handling internally.

- phenix.ligand_identification:
  - Added search limit on ligand sizes (Non-H atoms)
  - Run LigandFit algorithm internally as default.

- Phaser-2.8.1
  - bugfixes
    - anisotropy correction of map coefficients after MR
    - detection of duplicate solutions
    - correct cell for PDB after refinement of cell for input data
    - packing places molecules near origin in compact arrangement

- Structure Comparison
  - Updated to include favoured, allowed and outliers for validations tabs
    such as rotamers
  - Add featurs such as ligands information & locations; water locations;
    cis/trans peptides; and histidine protonation
  - General increase of robustness and flexibility
  - Greater flexibility for model/data input including directory tree travesal
    and user defined scripts

- Restraints
  - Added better SF4 restraints
  - Added mechanism to improve SF4 linking

- Various performance enhancements

- Better handling of model mmCIF input/output

- New Phenix video tutorials:
  - Cryo-EM tools in Phenix - overview
  - How to run MolProbity - step by step (web interface and Phenix GUI)
  - MolProbity: All atom contacts tutorial

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
Division Director, Molecular Biophysics & Integrated Bioimaging, 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 33, Room 347
Building 978, Room 4126
Tel: 1-510-486-4225, Fax: 1-510-486-5909

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 33R0345
Berkeley, CA 94720, USA.

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

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