Supported Applications


  • Description

    (Python-based Hierarchical Environment for INtegrated Xtallography) a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.

  • Usage Notes

    If you use PHENIX to solve a structure please cite this publication:

    PHENIX: building new software for automated crystallographic structure determination P.D. Adams, R.W. Grosse-Kunstleve, L.-W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.J. Read, J.C. Sacchettini, N.K. Sauter and T.C. Terwilliger. Acta Cryst. D58, 1948-1954 (2002)

  • Primary Citation*

    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. 2010. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta crystallographica Section D: Biological crystallography. 66(2): 213-221.

    • *Full citation information available through

  • Citation Note

    Citations for all software packages used in a given project can also be generated from within PHENIX.

  • Tales

    Structures Solved Simply

    Structures Solved Simply

    It used to be that to book a trip you'd first need to call every airline to compare flights. Then you'd need to find good hotel deals. Then you'd have to revisit the flights. And so on. The same trial and error approach also used to hold true for structural biology. Frequent failures made scientists all too familiar with square one.

    Now, however, what Orbitz and Expedia have done for travel, Phenix has done for structural biology.

    Phenix helps investigators solve Xray crystal structures using multiple approaches, including molecular replacement and experimental phasing. It makes things easier by streamlining these multi-step procedures programmatically. Experimental data goes in, and a solution comes out.

    Phenix Wizards perform the magic. For instance, the autosol program drives experimental phasing ...

    Read More.
  • Webinars

    Topic: Processing serial crystallographic data using cctbx.xfel and DIALS
    Presenter: Aaron Brewster, Project Scientist, Lawrence Berkeley National Laboratory

    Host: Jason Key
    Recorded on January 10, 2016

    Topic: ERRASER for RNA structure error correction
    Presenter: Steven Lewis, postdoc,Richardson Laboratory, Duke University
    Presenter: Jane Richardson, Professor, Duke University

    Host: Jason Key
    Recorded on May 16, 2013

    Topic: Getting the most out of your XFEL data with IOTA and PRIME
    Presenters: Mona Uervirojnangkoorn, Postdoctoral Associate
    and Art Lyubimov, HHMI Research Specialist
    Axel Brunger's Group, Stanford University

    Host: Jason Key
    Recorded on January 17, 2017

    Topic: Cctbx.xfel: New software for serial crystallography
    Presenter: Nicholas Sauter, Lawrence Berkeley National Laboratory

    Presented as part of:
    SBGrid/NE-CAT 2014: Data Processing in Crystallography
    June 5-6, 2014

    Topic: Extending the reach of molecular replacement in Phaser
    Presenter: Randy Read, Wellcome Trust Principal Research Fellow in the Department of Haematology at University of Cambridge.

    Host: Piotr Sliz
    Recorded on April 23, 2012

    Topic: Phenix: Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution
    Presenter: Jeff Headd, Postdoctoral Fellow at Lawrence Berkeley National Laboratories

    Host: Piotr Sliz
    Recorded on December 12, 2011

    Topic: Refinement of challenging structures with Rosetta and Phenix
    Presenter: Nat Echols, Computational Scientist at Lawrence Berkeley National Labs

    Host: Andrew Morin
    Recorded on May 13th, 2014

  • Keywords

    Crystallography, Molecular Replacement

  • Default Versions

    Linux 64:  1.16-3549
    OS X INTEL:  1.16-3549

  • Other Available Versions

      Linux 64:

      1.15.2-3472, 1.14-3260
    • OS X INTEL:

      1.15.2-3472, 1.14-3260
  • Developers

    Pavel Afonine, Nat Echols, Paul Adams.