[phenixbb] Phenix version 1.7 released

Paul Adams PDAdams at lbl.gov
Wed Jan 26 15:05:52 PST 2011

The Phenix developers are pleased to announce that version 1.7 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
- Simplified AutoMR interface for single-component searches.
- Multi-criterion validation kinemage display in KiNG.
- Validation of RNA, isotropic ADPs, occupancies.
- Improved project management interface, which will automatically import old projects to the new format when upgrading from a previous version of Phenix. 
- Integrated help browser on Mac with contextual help buttons embedded in program windows.
- phenix.find_tls_groups available as part of the phenix.refine GUI.
- Improved and expanded documentation for wizard and Phaser GUIs.

Structure refinement
- A new fast real space refinement protocol, which can substantially improve poor starting models.
- A fast method for automated identification of TLS groups (phenix.find_tls_groups).
- Reference model, Ramachandran, and secondary structure restraints to improve refinement at low resolution.
- Automated secondary structure restraint generation for non-Watson-Crick base pairs (using the Saenger classification).
- Automatic support for D-peptides when using standard PDB residue names.

Molecular Replacement
- A new command, phenix.mr_rosetta, which integrates molecular replacement, automated model building and Rosetta model rebuilding for difficult structures.
- A new fast search method in Phaser for efficiently locating multiple copies of the same molecule
- A new program (mr_model_preparation) for preparing models for molecular replacement, which automatically downloads related molecules based on a sequence alignment and runs sculptor.
- Improvements to ensemble generation (phenix.ensembler), with an option to use secondary structure matching (using code from Eugene Krissinel).

Ligand fitting
- New tool for automated ligand fitting using previous structures of related protein/ligand complexes (phenix.guided_ligand_replacement).
- Bug fixes and other improvements to phenix.elbow.

- Multi-criterion kinemages can now handle custom restraints (from a .cif file).
- RNA model validation is now available on the command line (phenix.rna_validate).
- Updates to phenix.model_vs_data, which now generates Sigma-A plots and more detailed ADP statistics.

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
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: Kathleen Moody [ KLMoody at lbl.gov ][ 1-510-495-2506 ]

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