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Python-based Hierarchical ENvironment for Integrated Xtallography
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PHENIX is a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.
 
Download the latest official release (1.9) [First request download password]
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Using PHENIX (release 1.9):
- The PHENIX Graphical User Interface
- Assessing data quality with phenix.xtriage
- Automated structure solution with AutoSol
- Automated molecular replacement with Phaser-MR
- Automated model building and rebuilding with AutoBuild
- Automated ligand fitting with LigandFit
- Structure refinement with phenix.refine
- Generation of ligand coordinates and restraints with eLBOW
 
The PHENIX system also includes SOLVE/RESOLVE, Phaser, the CCI Applications (phenix.xtriage, phenix.refine, elbow and many more), components from MolProbity, and the Computational Crystallography Toolbox in a Python framework.
 
Citing 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).
 
Funding for PHENIX: NIH General Medical Sciences
 
The PHENIX system also can be used for neutron crystallography. NIH funding supports the development of this capability through a grant to Paul Langan (Los Alamos National Laboratory) and Paul Adams. See the Macromolecular Neutron Crystallography Consortium site for more details. Citation for neutron structure refinement in Phenix: Adams PD, Mustyakimov M, Afonine PV, Langan P: Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules. Acta Cryst. 2009, D65:567-573.
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The PHENIX Industrial Consortium

For-profit groups can obtain access to PHENIX through a Consortium agreement. This provides a license to use PHENIX and research funds to develop new features in PHENIX tailored to the needs of commercial users.

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Groups developing PHENIX:
Paul Adams Randy Read Jane & Dave Richardson Tom Terwilliger
Lawrence Berkeley Lab University of Cambridge Duke University Los Alamos National Lab

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