[phenixbb] Phenix version 1.7.3 released

Paul Adams pdadams at lbl.gov
Mon Dec 12 16:56:47 PST 2011

The Phenix developers are pleased to announce that version 1.7.3 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site:


Some of the new features in this version are:

Graphical interface:
- New GUIs: MR-Rosetta
- viewer for diffraction images (also available as phenix.image_viewer)
- editable heavy-atom sites in HySS and AutoSol

- New commands: phenix.ncs_average, phenix.model_vs_sequence, phenix.image_viewer, 
                phenix.find_alt_orig_sym_mate, phaser.MRage
- support for CNS v1.3 reflection files

- Reduced memory requirement for map related calculations
- Improved handling of parameter files in the GUI
- RNA geometry target now includes pucker & base type-specific Chi 1 parameters
- TLS group definitions from PDB file header will be automatically used if no groups 
  are provided by the user
- Bug fix in clashscore calculation for large structures with duplicate chain IDs plus SEGIDs
- Torsion NCS restraints uses SEGIDs if present in input PDB file

Molecular Replacement:
- phaser (version 2.4):
  - support for pseudo-translational non-crystallographic symmetry (tNCS) in molecular replacement
    - detects presence of tNCS from inspection of native Patterson
    - characterizes tNCS parameters (translation, small rotational difference
      between copies)
    - accounts for effect of tNCS in molecular replacement calculations
    - note: support currently limited to one tNCS operator relating two
      molecules (or sets of molecules)
  - FAST search method turned on by default, replacing FULL search method
  - MR possible with a model containing a single atom 
  - B-factor refinement turned on by default in molecular replacement
  - Bug fix for occasional and irreproducible segmentation faults for 32 bit
    binary running on 64 bit Linux
  - Packing function accepts cases where an ensemble with internal point group
    symmetry is on a special position, and pdb file output deletes atoms
    overlapped due to the symmetry of special position

- phaser.MRage (version 0.1.0) - automated MR:
  - New command-line switches for common actions, e.g. setting the verbosity,
    getting PHIL parameters, etc
  - Define component by sequence, but calculate molecular weight from available models if
    sequence is omitted
  - Calculate number of copies to find from Matthews coefficient
  - Ability to perform homology search (currently only BLAST is supported, either local installation 
    or NCBI service)
  - alignments automatically generated for "template" if target sequence is known
  - various options for queueing systems, e.g. qslot
  - option to automatically write out solutions
  - fully parallel space group exploration

- phenix.find_alt_orig_sym_mate (new command):
  - For different molecular replacement solutions from the same dataset, finds
    the copy of moving_pdb closest to reference_pdb with respect to all
    symmetry operations and alternative origin shifts permitted by the
    spacegroup in moving_pdb

Experimental Phasing and Model Building:
- AutoSol:
  - Fixed problems with clean_up=True deleting overall_best.pdb
  - Allow data file names of any length
  - Use NCS in scoring by default if ncs copies > 2
  - Correct anisotropy and sharpen by default

- AutoBuild: 
  - Automatic anisotropy correction and sharpening for all maps

- phenix.multi_crystal_average: 
  - Automatic anisotropy correction and sharpening
  - Automatic filling of reflections to highest resolution of any dataset
  - Masking heavy-atom sites from averaging
  - Inputs grouped by crystal

- phenix.ready_set/phenix.reduce:
  - Improved handling of alternate conformations
- phenix.cif_as_mtz
  - Support for files containing multiple datasets
  - Extraction of Hendrickson-Lattman coefficients and anomalous arrays
  - New map_to_asu and remove_systematic_absences options
- phenix.maps:
  - Added atom selection parameter for simple omit maps (omit.selection)
- phenix.ligand_identification:
  - Implemented methods to generate custom ligand library based on parent
    protein's SCOP or CATH terms, Pfam accession numbers, GO accession numbers,
    or InterPro ID
  - Improved ligand geometry after real-space refinement

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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