[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:
http://phenix-online.org/download/
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,
phenix.superpose_maps
- new structure comparison tool (evaluation of multiple related
structures)
- 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
validation
- 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.fit_loops)
- 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
resolution
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
HySS
- 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:
http://www.phenix-online.org/documentation/CHANGES
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:
http://www.phenix-online.org/documentation/
There is a Phenix bulletin board:
http://www.phenix-online.org/mailman/listinfo/phenixbb/
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
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
http://cci.lbl.gov/paul
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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