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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.

Important Note:
Starting July 2019, the Protein Data Bank requires models to be in mmCIF for crystallographic structures. You should use the latest official release to generate these files for deposition.

Download the latest official release (1.19.2) [First request download password]
Download the latest nightly build or prerelease
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Using PHENIX (release 1.19.2):
- 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:
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
D. Liebschner, P. V. Afonine, M. L. Baker, G. Bunkóczi, V. B. Chen, T. I. Croll, B. Hintze, L.-W. Hung, S. Jain, A. J. McCoy, N. W. Moriarty, R. D. Oeffner, B. K. Poon, M. G. Prisant, R. J. Read, J. S. Richardson, D. C. Richardson, M. D. Sammito, O. V. Sobolev, D. H. Stockwell, T. C. Terwilliger, A. G. Urzhumtsev, L. L. Videau, C. J. Williams, and P. D. Adams
Acta Cryst. (2019). D75, 861-877
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.
Phenix Paper
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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.

Contact Us

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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