[phenixbb] Phenix version 1.15 released

Paul Adams pdadams at lbl.gov
Thu Apr 18 15:58:20 PDT 2019

The Phenix developers are pleased to announce that version 1.15 of Phenix is now available (build 1.15.2-3472). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site:


Highlights for this version:

New and improved tools

- New algorithm for phenix.map_to_model is faster and builds longer chains
- phenix.trace_and_build can build protein into maps at resolutions as low as 4.5 A
- phenix.fix_insertions_deletions can build models in places where the map is poor
- phenix.refine_ca_model for optimizing C-alpha only models
- phenix.comparama for generating Kleywegt-like plots that show how residues moved in the Ramachandran 
  plots before and after refinement
- eLBOW can find unique instances of a ligand from the PDB and optionally create Polder OMIT maps
- Updated structural library for phenix.structure_search
- Updated ligand library for phenix.ligand_identification
- Improved reporting of cis-peptides for residues with altloc atoms
- Output of mmCIF format files by default by major tools: phenix.refine, phenix.real_space_refine, phenix.pdbtools
- Bugfixes in Phaser-2.8.3

Other improvements

- Updated mmCIF support (stuct_conn loop, ligand restraints, sequence)
- phenix.refine, phenix.real_space_refine, and phenix.pdbtools will also output models in mmCIF format by default
- Dependencies are now based on conda packages, which will be more compatible with new operating systems and will 
  improve consistency across all platforms (macOS, linux, Windows)
- Bug fixes

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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