[phenixbb] Phenix version 1.11.1 released

Paul Adams pdadams at lbl.gov
Wed Nov 2 09:04:55 PDT 2016

The Phenix developers are pleased to announce that version 1.11.1 of Phenix is now available (build 1.11.1-2575). Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site:


Highlights for this version:

New tools for omit maps without bulk solvent in omitted region, automated sharpening of cryo-EM and crystallographic maps, and segmentation of maps. Improved NCS search. New automated model-building tools for low-resolution maps - especially cryo-EM, tools for matching chains (both residues and direction), multiple improvements to phenix.real_space_refine and addition of new GUI. Improved model geometry restraints, many improvements to Phaser, improved validation incorporating new MolProbity features, simplified Rosetta installation, improved support for Amber, updated dependencies, Unicode support in GUI, new unified interface for atom selections.

- General
  - Improved geometry restraints:
    - Conformation-Dependent Library for omega added (omega_cdl=True)
  - Installation
    - Rosetta installation centralised for phenix.rosetta_refine,
      phenix.mr_rosetta and ERRASER
  - Improved NCS search procedure with simplified parameters. Provides
    status of user-supplied NCS groups during validation (refused/modified/ok)
  - Updated dependencies
    - biopython 1.64 -> 1.66
    - sphinx 1.2.2 -> 1.4.4
    - ipython 2.1.0 -> 3.2.1
    - pip 6.0.7 -> 8.0.2
  - Neutron scattering tables: support ions

- Amber refinement
  - Alpha release dev-2203

  - New interfaces
    - phenix.map_comparison
    - phenix.polder
    - phenix.structure_search
    - phenix.real_space_refine
  - New selection editor
    - Unified interface for selecting atoms
      - Secondary structure annotations
      - NCS groups
      - TLS groups
      - Refinement strategy options
  - Unicode support
    - Non-ASCII characters are supported for most fields (e.g. file paths and
      job titles)
    - Using non-ASCII characters in projects/jobs will prevent earlier versions
      that do not have Unicode support from opening the project list correctly
  - Migrated validation after phenix.refine to use regular MolProbity for
    consistency (older versions of Phenix will not open new jobs)
  - phenix.real_space_correlation can now accept map files
  - phenix.molprobity can now accept map files
  - Updated dependencies for Linux
    - libpng 1.2.52 -> 1.5.26
    - freetype 2.4.2 -> 2.6.3
    - gettext 0.18.2 -> 0.19.7
    - glib 2.12.11 -> 2.46.2
    - expat 1.95.8 -> 2.1.0
    - fontconfig 2.3.95 -> 2.11.1
    - render 0.8 -> 0.11.1
    - xrender 0.8.3 -> 0.9.7
    - xft 2.1.2 -> 2.3.2
    - pixman 0.19.2 -> 0.34.0
    - cairo 1.8.10 -> 1.14.4
    - pango 1.16.1 -> 1.38.1
    - atk 1.9.1 -> 2.18.0
    - libtiff 3.6.1 -> 4.0.6
    - gtk+ 2.10.11 -> 2.24.29
    - matplotlib 1.3.1 -> 1.5.1

- Maps
  - phenix.polder calculates omit maps which exclude the bulk solvent around
    the omitted region. This way, weak densities possibly obscured by bulk
    solvent may become visible.
  - phenix.model_map: Given PDB file calculate model map and output as CCP4
    formatted binary map file.
  - phenix.mask: Given PDB file calculate bulk-solvent mask and output as CCP4
    formatted binary map file.
  - phenix.auto_sharpen: Optimizes resolution dependence of a map to improve
  - phenix.segment_and_split_map: Carries out segmentation of a map

- Model-building
  - phenix.map_to_model builds models in low-resolution maps
    - builds any combination of RNA/DNA/protein
    - if NCS present, builds the asymmetric unit of NCS and expands
        to the entire map
  - phenix.segment_and_split_map breaks up a map into the asymmetric
     unit of NCS and further subdivides that into contiguous regions
     of density
  - phenix.chain_comparison compares CA or P atoms of two models and
     identifies how many residues match and how many are in the same direction

- phenix.real_space_refine:
  - Support output of refined model in mmCIF format
  - ADP refinement runs by default at the last macro-cycle. Several CPUs can be
    used to speed up refinement: use nproc=NUMBER_OF_CPUs parameter for this.

- phenix.model_idealization: tool to idealize model geometry while staying as
  close as possible to the starting model. Currently proteins only. Idealize
  covalent geometry and secondary structure, as well as eliminate rotamer and
  Ramachandran plot outliers, C-beta deviations.

- phenix.geometry_minimization
  - ability to use reference torsion restraints
  - ability to use NCS constraints

- phenix.phaser
   - SOLUTION HISTORY tracks solution through positions in RF/TF/PAK/RNP peak lists
   - selection by CHAIN and MODEL for PDB coordinate entry
   - automatic search number for single search ensemble
   - packing 'trace' molecule can be entered independently of coordinates and map
   - read TNCS/anisotropy binary files to avoid refinement, when running through scripts
   - write tNCS and anisotropy parameters to binary files (non-python interface)
   - default reading of I (or failing that, F) from mtz file (LABIN optional)
   - trace for ensembles from maps = hexgrid of 1000+/-100 points
   - trace for ensembles from coordinates above 1000 Calpha = hexgrid of 1000+/-100 points
   - trace for ensembles from coordinates twixt 1000 atoms and 1000 Calpha = Calpha atoms
   - trace for ensembles from coordinates under 1000 atoms = all atoms
   - packing by pairwise percent only, other packing modes obsoleted
   - packing test during FTF run by default with 50% pairwise packing cutoff
   - automatic tNCS NMOL determination in presence of commensurate modulation
   - added MODE GIMBLE, which splits ensembles by chain for rigid body refinement
   - support for unicode
   - solution coordinates placed nearest to input coordinates if possible

- phenix.reduce
  - Updated reduce_wwPDB_het_dict as of Aug 12, 2016
  - New script for updating het dict
  - Reduce no longer rotates methionine methyls by default. -DOROTMET flag reinstates old behavior

- phenix.ramalyze
  - Improved handling of residue connectivity
  - Summary statistics provided for altloc A specifically where multiple altlocs present

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 80, Room 247
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 ]

More information about the phenixbb mailing list