[phenixbb] Phenix version 1.8.1 released

Paul Adams pdadams at lbl.gov
Mon Oct 1 13:50:45 PDT 2012

The Phenix developers are pleased to announce that version 1.8.1 of Phenix is now available. Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site:


Some of the new features in this version are:

Graphical interface:
- New GUIs: phenix.find_alt_orig_sym_mate

- Multiple bug fixes
- New commands: phenix.erraser, phenix.merging_statistics
- Added geometry restraints for over 400 non-standard amino acid entries

- Overall B-cart now applied to individual atomic B-factors (restores pre-1.8 behavior)
- Improvements to torsion NCS rotamer correction
- Real-space refinement (including rotamer fitting) for twinned data

New command:
- phenix.erraser:
  - New method from Fang-Chieh Chou and Rhiju Das (Stanford) combining
    Rosetta nucleic acid rebuilding with phenix.refine (requires separate
    installation of Rosetta 3.4 or more recent)

Molecular Replacement:
- Phaser updated to version 2.5.2:
  - Scattering from HETATM records that represent modified amino acids
    (e.g. MSE/SeMet) included so that maps no longer show holes for these
    HETATM records in the model; occupancies will not be reset.
  - Packing test was incorrectly applied to reoriented molecules where
    there was PTNCS

Experimental Phasing and Model Building:
- AutoSol:
   - Scale of derivative in SIR (for RIP phasing) can be set with keyword
- AutoBuild:
  - Unassigned chains are now given the segid of "UNK" and are normally given
    chain ID="U"

- eLBOW:
  - New option, --multiple-planes, to generate planes around double bonds
  - Saturated rings now have dihedral restraints to maintain chair conformation
  - View relationships between ligands using PubChem fingerprint and tanimoto

- phenix.real_space_correlation:
  - Simplified command-line behavior
- phenix.merging_statistics (new command):
  - Calculate statistics for unmerged data in a variety of formats,
    including <I/sigmaI>, R-merge, R-meas, R-pim, CC1/2
  - References:
    Diederichs K & Karplus PA (1997) Nature Structural Biology 4:269-275
    Weiss MS (2001) J Appl Cryst 34:130-135.
- phenix.kinemage:
  - Improvements to handling of alternate conformations.
- phenix.combine_models:
  - Combine two models, taking the best parts of each to create a new model

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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