[phenixbb] Phenix version 1.9 released

Paul Adams pdadams at lbl.gov
Mon May 12 16:33:22 PDT 2014

The Phenix developers are pleased to announce that version 1.9 of Phenix is now available. Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site:


Highlights from this version:

Significant changes to the content and presentation of documentation, major improvements to HySS and AutoSol for SAD phasing in cases of weak signal, new Phenix/Rosetta refinement program for difficult low resolution refinements, new real space refinement program for refinement against a density map (e.g. cryo-EM), feature enhanced maps (FEM) enhance weak features and reduce noise and bias, new composite omit map program, unified MolProbity validation program (consistent with the MolProbity web server), proximity restraints for group displacement parameter refinement in phenix refine, and option for automated chemical linking in phenix.refine.

Graphical interface:
- Rearranged main interface to accompany documentation changes
- New Phenix releases may be downloaded directly from the GUI (requires
  previously registered academic email address or permanent user credentials)
- Added command to remove large data files (.geo, .kin, .ccp4, etc.) from a project directory to 
  conserve disk space
- Changes to support Mac OS 10.9 ("Mavericks")

- Re-organized and updated documentation
- Binary installers for Ubuntu (10.04 or later) available
- Python built as shared library in Linux builds (facilitates Rosetta hybrid)
- new commands: phenix.composite_omit_map, phenix.rosetta_refine,
  phenix.molprobity, phenix.sceds, phenix.fem, phenix.real_space_refine,
  and many smaller utilities

- phenix.refine:
  - similarity restraints for group isotropic B-factor refinement
    - set by group_b_iso.use_restraints (default=True)
    - data/restraints targets weight is determined automatically; can be
      adjusted by setting group_b_iso.restraints_weight (larger value makes
      restraints stronger)
  - various rotamer handling bug fixes
  - Automatic linking generation in phenix.refine and other programs that
    require restraints can be requested using the parameters link_all=True
    - handles any appropriate ligand-protein or ligand-nucleic acid covalent
      bonds, including sugars, amino acid modifications, and other prosthetic
    - behavior can be adjusted by setting maximum bond distances parameters
  - added "bfactor" and "occupancy" keywords to atom selection syntax (also
    applies to phenix.pdbtools)
  - Integration with DivCon suite (http://www.quantumbioinc.com) for QM
    refinement of ligands (requires separate license and installation)

- phenix.rosetta_refine (new command):
  - Hybrid Rosetta/Phenix refinement of protein X-ray crystal structures
    for difficult cases at low resolution
  - reference: DiMaio et al. (2013) Nature Methods

- phenix.ensemble_refinement:
  - enabled use of experimental phases (MLHL target)

- phenix.real_space_refine (new command):
  - tool to refine a model against a map (especially EM maps)

- phenix.morph_model:
  - fixed serious bug present in versions 1449-1626 that resulted in incorrect
    offset being applied

Experimental Phasing and Model Building:
- HySS (phenix.hyss):
  - Substructure search much more fully automated:
    - Search first with Patterson seeds and direct method
    - If no clear solution, try more seeds, Phaser completion, and varying
    - Full parallelization makes the search rapid
- AutoSol:
  - Now much more powerful for weak SAD data:
    - Incorporates new automated Hyss search
    - Classic solvent flipping density modification after Resolve density
    - Tests several values of smoothing radius for solvent boundary
      identifcation for weak data
    - Iterates heavy-atom substructure search with Phaser completion including
      density after density modification and using model after model-building
    - Require solutions scored by correlation to be substantially better than
      altermatives before eliminating alternatives
  - Building with helices_strands_only set as default for data at lower than
    3 Angstroms

- AutoSol, AutoBuild, and LigandFit:
  - You can now specify the value of the test set flag for the free data with

Molecular Replacement:
- phenix.sceds (new command, formerly phaser.splitter):
  - implements normal mode-based domain finding method
  - reference: McCoy et al. (2013) Acta Cryst D69

- phenix.find_alt_orig_sym_mate:
  - offset the produced MLAD value with log(0.9) to avoid 
    negative values if identical structures were to be compared.
    Consequently older versions therefore yield MLAD values which are
    0.10536 smaller than the current version.

New commands:
- phenix.rosetta_refine (new command):
  - Hybrid Rosetta/Phenix refinement of protein X-ray crystal structures
    for difficult cases at low resolution
  - reference: DiMaio et al. (2013) Nature Methods

- phenix.molprobity (new command):
  - Unified validation tool for command-line users; similar to existing
    comprehensive validation in the Phenix GUI
  - optional output of script for viewing results in Coot, or kinemage file

- phenix.composite_omit_map (new command):
  - Default method uses very fast iterative de-biasing procedure
  - Can also generate either a simple or composite omit map with refinement
    and optional simulated annealing
  - Will generate multiple map types at once
  - parallelizable on multi-core systems or managed clusters

- phenix.sceds (new command, formerly phaser.splitter):
  - implements normal mode-based domain finding method
  - reference: McCoy et al. (2013) Acta Cryst D69

- phenix.real_space_refine (new command):
  - tool to refine a model against a map (especially EM maps)

- phenix.fem (new command): 
  - Compute "feature-enhanced" map ("FEM") - this protocol modifies a 2mFo-DFc
    sigmaA-weighted map such that the resulting map has strengthened weak
    signal, if present, and a reduced amount of noise and model bias.
    - combines randomization and averaging, treatment of missing reflections,
      residual composite omit map, and histogram equalization
    - resulting maps are more interpretable and have less bias compared to the
      starting 2mFo-DFc map
    - very fast procedure, no refinement required

- phenix.map_to_structure_factors (new command):
  - convert map into structure factors (also intended for EM)

- phenix.angle (new command):
  - compute angle between two axes or two atom selections

- phenix.model_model_distances (new command):
  - Given two PDB files compute distances per atom, residue, chain, model and
    overall. It is assumed (and asserted in the code!) that the amount and
    order of atoms in both files are identical.

- phenix.fab_elbow_angle (new command):
  - Calculating Fragment Antigen-Binding (Fab) elbow angle

- phenix.f000 (new command):
  - Given PDB file estimate F(0,0,0); includes atomic model and bulk-solvent

- phenix.ligand_identification:
  - Now you can use ligand cif files (in addition to .pdb files) to build your
    own custom ligand library.  Just specify "Ligand directory" (GUI) or use
    keyword "ligand_dir" (command line) to tell the program to use .pdb or .cif
    files in your own ligand directory.
  - Bug fix to properly handle mtz labels when using difference maps.

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
Laboratory Research Manager, ENIGMA Science Focus Area

Building 64, Room 248
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 64R0121
Berkeley, CA 94720, USA.

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

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