[phenixbb] Phenix version 1.8.2 released

Paul Adams pdadams at lbl.gov
Sun Mar 10 14:17:55 PDT 2013

The Phenix developers are pleased to announce that version 1.8.2 of Phenix is now available. Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site:


Highlights from this version:

Ensemble refinement, updated hydrogen parameters in refinement and validation, mmCIF reading and writing, LLG maps output from refinement, ligand pipeline for automated solution of protein/ligand complexes, autobuilding starting from a very accurate but very small part of a model, CC* calculation from unmerged data, maximum entropy maps, and PDB editor.

Graphical interface:
- New GUIs: phenix.merging_statistics, phenix.pdb_editor

- Multiple bug fixes
- phenix.refine, phenix.reduce, and MolProbity updated to use consistent,
  revised, electron-cloud centers for hydrogen positions as default (for X-ray)
  - also see MolProbity website for details: http://molprobity.biochem.duke.edu
- mmCIF format now supported in place of PDB format for input to many programs
- new commands: phenix.ensemble_refinement, phenix.ligand_pipeline, phenix.sort_hetatms,
  phenix.cc_star, phenix.pdb_editor, phenix.maximum_entropy_map

- phenix.refine
  - support for LLG map type - uses Phaser to compute residual anomalous LLG map
    - best when used with group_anomalous strategy, which will flatten the LLG map 
      around existing anomalous scatterers with refined f'/f''.
    - alternatively, anomalous_residual map type (similar but less sensitive)
  - automatic linking in refinement and pdbtools for residues in the same chain
    - enabled with automatic_linking.intra_chain=True; this includes carbohydrate 
      linking to protein and between sugars, and covalently bound ligands.
  - optional output of mmCIF format model and data files

- phenix.ensemble_refinement (new command): 
  - New method for refining ensemble models
  - Combines MD simulation with X-ray restraints that simultaneously account
    for anisotopic and anharmonic atomic distributions.
  - For full description see: Burnley BT, Afonine PV, Adams PD, Gros P. 2012.
    Modelling dynamics in protein crystal structures by ensemble refinement.
    eLife 1:e00311. doi: 10.7554/elife.00311.

Experimental Phasing and Model Building:
- phenix.autobuild:
  - now uses torsion NCS parameterization when NCS is used in refinement
  - building starting from a very accurate but very small part of a model:
    You can now use the keyword rebuild_from_fragments=True to start
    rebuilding from fragments of a model. You might want to use this 
    if you look for ideal helices using Phaser, then rebuild the 
    resulting partial model, as in the Arcimboldo procedure.  The 
    special feature of finding helices is that they can be very accurately
    placed in some cases. This really helps the subsequent rebuilding.
    If you have enough computer time, then run it several or even many 
    times with different values of i_ran_seed.  Each time you'll get a 
    slightly different result.
  - Base-pairing in RNA building -- phenix.autobuild will now try to 
    guess which bases in a model are base-paired, and if there is no
    positive sequence match to the model, the bases that are base-paired
    will be chosen to be complementary. You can set the cutoff for base
    pairing with the keyword dist_cut_base.
  - waters are automatically named with the chain of the closest macromolecule
    if you set sort_hetatms=True. This is for the final model only.
  - you can supply a target position for your model
    with map_to_object=my_target.pdb.  Then at the very end of the run  your
    molecule will be placed as close to this as possible. The center of mass
    of the autobuild model will be superimposed on the center of mass of
    my_target.pdb using space group symmetry, taking any match closer than
    15 A within 3 unit cells of the original position. The new file will be

Molecular Replacement:
- phenix.mr_rosetta
  - You can now give commands for Rosetta in mr_rosetta, including
    a command to specify where disulfide bonds are located
  - The Rosetta models are now identified by an ID number so that they have
    unique names
  - Default number of homology models to download is now 1 (was 5)
  - Default number of NCS copies (if ncs_copies=Auto) is number leading to
    solvent content closest to 50%; if ncs_copies=None then all plausible
    values of ncs_copies are tested.

New commands:
- phenix.ligand_pipeline (new command):
  - combines Xtriage, Phaser, eLBOW, phenix.refine, AutoBuild, and LigandFit
    to automatically solve protein/ligand complexes
  - optional integration with Coot (parameter interactive=True) allows
    semi-interactive operation where more rebuilding is required

- phenix.cc_star (new command):
  - combined assessment of model and data quality, as outlined in Karplus &
    Diederichs (2012) Science 336:1030-3.
  - summary also output by phenix.model_vs_data if additional unmerged_data
    keyword is specified

- phenix.maximum_entropy_map (new command):
  - tool to compute maximum entropy map from map coefficients. The program
    reads input Fourier map coefficients and modifies corresponding synthesis
    using Maximum-Entropy Method (MEM). The MEM modified map is everywhere
    positive, smooth and is of higher resolution. The method uses is a
    modification of Gull & Daniell (1978) algorithm.

- phenix.sort_hetatms (new command):
  - rearranges heteroatoms (ligands, waters, etc.) in a model so they are
    paired with the nearest macromolecule chain, similar to the PDB's
    processing of models

- phenix.pdb_editor (new command):
  - graphical editor for PDB files, based on tree view of model hierarchy
  - perform common operations such as chain renaming, renumbering, manipulation
    of atomic properties, add/remove atoms

- phenix.ready_set:
  - methyl rotations now automatic when adding explicit hydrogens (also in
  - more options adding deuteriums to a model have been introduced

- phenix.xtriage:
  - include merging statistics if unmerged intensities are used as input
- phenix.maps:
  - added wavelength parameter and support for anomalous residual and Phaser
    LLG map coefficients

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
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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