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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

    To list all executables provided by PHENIX, run: $ sbgrid-list phenix Copy to clipboard
  • 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)

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install phenix Copy to clipboard Available operating systems: Linux 64, OS X INTEL
  • Primary Citation*

    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. 2019. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta crystallographica. Section D, Structural biology. 75: 861-877.

    • *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 by pre-processing experimental …

    Read the full story here.
  • Webinars


    Topic: Atomic model, map and model-to-map fit validation
    Part I: Atomic model validation
    Speaker: Pavel Afonine, Berkeley Lab

    Host: Jason Key
    Recorded on April 14, 2020


    Topic: Map Sharpening; Model Building; other cryo-EM tools in Phenix
    Presenter: Dorothee Liebschner, Berkeley Lab

    Hosted by Jason Key
    Recorded on April 7, 2020


    Topic: Atomic model refinement and validation in Phenix
    Presenter: Pavel Afonine, Computational Research Scientist, Berkeley Lab

    Date recorded: April 3, 2020

    Host: Pete Meyer


    Topic: Density Modification and Model Building with cryo-EM maps.
    Presenter: Tom Terwilliger, Laboratory Fellow, Los Alamos National Laboratory

    Recorded on March 31, 2020
    Host: Jason Key

    Link to slides: https://drive.google.com/open?id=1SHQ...

    Phenix-Amber Integration

    Topic: Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix
    Presenter: Nigel Moriarty, Lawrence Berkeley National Labs

    Host: Pete Meyer
    Recorded on: October 8, 2019

    Iota and Prime

    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: 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

    Lecture 17: Cctbx.xfel: New software for serial crystallography

    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

    Phenix-Rosetta Refinement

    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


    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: 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

  • Keywords

    Crystallography, Molecular Replacement

  • Default Versions

    Linux 64:  1.21.1-5286 (9.2 GB)
    OS X INTEL:  1.21.1-5286 (8.4 GB)

  • Other Versions

      Linux 64:

      1.19.2-4158 (6.1 GB) , 1.20.1-4487 (7.7 GB) , 1.20-4459 (7.9 GB) , 1.21-5207 (9.2 GB)
    • OS X INTEL:

      1.19.2-4158 (5.5 GB) , 1.20.1-4487 (6.8 GB) , 1.20-4459 (7.0 GB) , 1.21-5207 (8.4 GB)
  • Developers

    Nat Echols, Paul Adams, Pavel Afonine