[phenixbb] Phenix version 1.6.4 released

Paul Adams PDAdams at lbl.gov
Sat Jul 31 09:43:33 PDT 2010

The Phenix developers are pleased to announce that version 1.6.4 of  
Phenix is now available. Binary installers for Linux, and Mac OSX  
platforms are available at the download site:


Just some of the new features in this version (1.6.4) are:

- GUI:
   - new interfaces for eLBOW, CIF to MTZ conversion, phenix.find_ncs,  
   - new structure comparison tool (evaluation of multiple related  
   - supports execution of jobs on the Sun Grid Engine queueing system
   - maps for PyMOL now output in (smaller, faster) CCP4 format
   - display of sequence and secondary structure in wizards and  
   - new wide-format windows for wizards and phenix.refine
   - many bug fixes

- Automated model building:
   - phenix.autosol now much faster and improved model-building after  
density modification
   - phenix.phase_and_build (carries out an iterative process of  
building a model as
     rapidly as possible and uses this model in density modification  
to improve the map.
     Up to 10x faster compared to AutoBuild, but model quality is  
nearly as good)
   - phenix.build_one_model (quickly build a single model from a map  
and sequence file,
     or extend an existing model)
   - phenix.assign_sequence (carry out an improved sequence assignment  
of a model that
     you have already built. Uses the new loop libraries available in  
   - phenix.apply_ncs (apply NCS operators to a single copy of a  
protein to create all
     the NCS‐related copies)
   - phenix.find_ncs (now supports identification of NCS operators  
from a density map)
   - phenix.fit_loops (two main algorithms now available - fit short  
gaps using a loop
     library derived from high‐resolution structures in the PDB, or  
build loops directly
     by iterative extension with tripeptides

- phenix.refine:
   - reference model restraints (restraint dihedral angles to a higher  
     reference model)
   - alternate ideal angles for torsion definitions (preserves side  
chain rotameric states)
   - automatic flipping of incorrect N/Q/H rotamers
   - custom planarity restraints
   - hydrogen-bond restraints for Watson-Crick base pairs
   - reflections with Fobs=0 used in refinement
   - automatic optimization of mask parameters
   - map parameters now consistent with phenix.maps
   - new custom_nonbonded_symmetry_exclusions atom selection parameter  
to fine tune
     non-bonded interactions across symmetry axes

- Phasing:
   - Option for Phaser likelihood scoring of substructure solutions in  
   - SOLVE converted to C++; FORTRAN compiler no longer required for  
Phenix compilation

- Other:
   - KiNG kinemage viewer incorporated into Phenix
   - Real space refinement option in ligand fitting
   - B-factor sharpening option for maps

For a full list of changes see:


Please note that there is a new publication that 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  
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  
the generous support of the members of the Phenix Industrial Consortium.

Paul Adams
Deputy Division Director, Physical Biosciences Division, Lawrence  
Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Head, Berkeley Center for Structural Biology

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: Marian Harris [ MSHarris at lbl.gov ] 
[ 1-510-486-6886 ]

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