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:
http://phenix-online.org/download/
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
General:
========
- 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
Refinement:
===========
- 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
Miscellaneous:
==============
- 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:
http://www.phenix-online.org/documentation/CHANGES
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:
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:
[log in to unmask] and [log in to unmask]
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
http://cci.lbl.gov/paul
Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 64R0121
Berkeley, CA 94720, USA.
Executive Assistant: Louise Benvenue [ [log in to unmask] ][ 1-510-495-2506 ]
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