[phenixbb] Phenix version 1.14 released

Paul Adams pdadams at lbl.gov
Tue Sep 25 14:26:43 PDT 2018

The Phenix developers are pleased to announce that version 1.14 of Phenix is now available (build 1.14-3260). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site:


Highlights for this version:

- Reorganization, updates and addition of cryo-EM tools:
  - phenix.mtriage - assess map and model quality 
  - phenix.auto_sharpen - map sharpening 
  - phenix.map_symmetry - identify symmetry in maps 
  - phenix.map_box - cut out unique parts of maps 
  - phenix.combine_focused_maps - combine different maps 
  - phenix.dock_in_map - automatically place an atomic model into a map 
  - phenix.map_to_model - automatically build atomic model from a map 
  - phenix.sequence_from_map - identify sequence from a map 
  - phenix.real_space_refine - improved refinement of models 
  - phenix.validation_cryoem - separate tool for comprehensive validation of models and maps

- phenix.cablam_idealization - Tool to automatically fix Cablam outliers

  - better support for metals and metal clusters
  - added plugin for QM package Orca

- Phaser-2.8.2
  - bugfixes
    - Phassade substructure search when starting from seed substructure
    - fix crash in MR_ATOM
    - problems with cumulative intensity distribution for extremely weak data
  - improve computation and presentation of data information content

- Performance improvements
  - NCS search
  - Generation of secondary structure restraints
  - Clashscore calculation
  - AmberPrep is more robust
  - Restraints for ARG improved

- New Phenix video tutorials

  - New section in main window for cryo-EM tools
  - Separate validation GUI for cryo-EM structures
  - Added phenix.map_symmetry
  - Added phenix.dock_in_map
  - Added phenix.map_to_structure_factors
  - Added phenix.combine_focused_maps
  - Added phenix.sequence_from_map

- phenix.ligand_identification:
  - Added an option to generate ligand library based on sequence and structural
    homologs of the input pdb model.

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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