[phenixbb] Phenix version 1.8.4 released

Paul Adams pdadams at lbl.gov
Wed Oct 9 09:35:20 PDT 2013

The Phenix developers are pleased to announce that version 1.8.4 of Phenix is now available. Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site:


Highlights from this version:

Automated MR/ligand fitting/refinement pipeline (phenix.ligand_pipeline), improved determination of bulk solvent masks, improved real space refinement, GUI for ERRASER, improvements to AutoSol and AutoBuild, improvements to Phaser, improvements to Guided Ligand Replacement, 64-bit Windows 7 installer.

Graphical interface:
- New GUIs: ERRASER, phenix.dynamics
- Pause/resume function for most programs on Mac/Linux
- Utilities for conversion to/from mmCIF

- Multiple bug fixes
- 64-bit Windows 7 installer
- Improved bulk solvent mask calculations (phenix.refine, phenix.maps, etc.):
    - analyzes mFo-DFc map to identify spurious negative density blobs in bulk
      solvent regions and applies correction, can decrease R-factors by 0.5-2.0%

- phenix.refine:
  - bug fixes in occupancy refinement, hydrogen addition
  - new local and global real-space refinement (RSR) methods:
    - Global RSR (refine all atoms, as before) runs only if:
        d_min > 1.5, r_work > 0.25, and not neutron data
      or "individual_sites_real_space" is the only selected strategy
    - Local RSR: residue-by-residue, replaces old fix_rotamers option
      - fits both main chain and sidechain
      - only applies to residues with rotamer outlier, poor CC, or clashes
      - new residue fit serves as torsion restrains for subsequent macro-cycle
      - normally not performed when explicit hydrogens present
  - added omit_selection keyword: sets atom occupancies for a selection to zero
    prior to refinement
  - optional harmonic restraints on starting positions - used to maintain structure
    close to starting model during simulated annealing omit map calculation
  - alpha feature: placement of elemental ions (place_ions=True)
    - looks for Mg, Cl, Ca, and Zn by default; specify elements=Cl,Ni,... to
      give explicit list (recommended)
    - works best with anomalous data

Experimental Phasing and Model Building:
- AutoSol:
  - overall_best_refine_data.mtz now contains uncorrected F+,sigF+,F-,sigF-
    data and uncorrected FP,SIGFP.  Previously only the FP,SIGFP was
    uncorrected, and F+,sigF+,F -,sigF- had been corrected for anisotropy and
    sharpened.  Note that output map files from phenix.autosol and
    phenix.autobuild are still sharpened and corrected for anisotropy.
  - For MIR, if quick=True then as soon as a good solution is found with HySS
    all other derivatives are solved by difference Fouriers.  This can speed
    up MIR structure solution. You can disable this feature with

- AutoSol and AutoBuild:
  - It is now possible to specify a different number of copies of different
    chains in the sequence file.  If the sequence file has n copies of chain A
    and m of chain B, it is now assumed that the stoichiometry is
    ncs_copies * (nA, mB).  Previously it had been assumed always that the
    stoichiometry was ncs_copies *(A, B).
  - For structure determination with extremely little phase information there is
    a new keyword extreme_dm=True (default is False). This allows density
    modification to use parameters optimized for very poor phasing if the FOM
    of phasing is less than fom_for_extreme_dm.

- AutoBuild
  - phenix.autobuild now requires that if a hires (or refinement) file is
    supplied, it must have a complete set of free R flags (test set) if the
    datafile also has a test set.  In this case the test set from the
    datafile is ignored and the one from the hires/refinement file is used.
    - You can use the Phenix GUI to extend the test set from your datafile to
      match the data in your hires/refinement file if necessary.

Molecular Replacement:
- Phaser:
  - various speed enhancements
  - new normal modes analysis features for domain finding (phaser.splitter)
  - bug fixes

- MR-Rosetta:
  - You can now tell mr_rosetta to ignore long-running sub-processes and just
    go on with the finished jobs.

New commands:
- phenix.dynamics (new command):
  - simple Cartesian dynamics, replaces equivalent function in PDBTools

- phenix.parallel_autobuild (new command):
  - a tool for running phenix.autobuild many times in parallel, picking
    the best results, and iterating with the new maps as a starting point.
  - can make effective use of as many as 40 processors.

- phenix.ligand_pipeline:
  - numerous bug fixes
  - more flexible handling of input sequence files
  - optional Sculptor step prior to MR to fix residue identities
  - sidechain pruning enabled by default
  - interactive mode now includes ligand selection

- phenix.guided_ligand_replacement:
  - Guided Ligand Replacement (GLR) can now search for a protein-ligand complex
    suitable for the guided fitting using web services on the PDB website or in
    a local directory.
  - GLR ligand input has been reworked to allow the use of the three-letter
    code relying on eLBOW to generate the restraints.

  - simplification and improvement of molecule building
  - support for cis/trans E/Z enantiomers
  - view .geo files 

- PDBTools:
  - simple dynamics option moved to new command, phenix.dynamics
  - remove_alt_confs and truncate_to_poly_ala options made compatible with
    other model modifications

- HySS:
  - converted to use standard Phenix parameter syntax
  - Many new optional features:
    - Parallel pre-scoring of 2-site solutions
    - Parallel completion and scoring
    - Comparison with a fixed solution
    - Resolution cutoff for Phaser rescoring
    - Top-scoring solution written even if no matches found
    - All solutions written
    - Skip direct methods completion
    - LLG completion sigma cutoff
    - Scoring of input sites
    - Randomization of input sites

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
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Berkeley, CA 94720, USA.

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

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