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wrappers for phenix package
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Phenix scipion plugin

This plugin allows to use programs from the PHENIX software suite within the Scipion framework. Current programs implemented:

  • emringer
  • real space refine
  • molprobity
  • superpose pdbs

Install this plugin

You will need to use 2.0.0 version of Scipion to run these protocols. To install the plugin, you have two options:

  • Stable version
scipion installp -p scipion-em-phenix


  • through the plugin manager GUI by launching Scipion and following Configuration >> Plugins
  • Developer's version
  1. Download repository:
git clone
  1. Install:
scipion installp -p path_to_scipion-em-phenix --devel
  • Binary files

PHENIX binaries will NOT be installed automatically with the plugin. The independent installation of PHENIX software suite by the user is required before running the programs. Default installation path assumed is /usr/local/phenix-1.13-2998; this path or any other of your preference has to be set in PHENIX_HOME in scipion.conf file. We recommend to install PHENIX version 1.13-2998.

  • Tests

Tested with PHENIX version: 1.13-2998.

To check the installation, simply run the following Scipion tests:

  • scipion test phenix.tests.test_protocol_emringer
  • scipion test phenix.tests.test_protocol_real_space_refine
  • scipion test phenix.tests.test_protocol_molprobity
  • scipion test phenix.tests.test_protocol_superpose_pdbs
  • Supported versions of PHENIX

Supports Phenix-1.13-2998.


  • emringer: Validates the agreement between the initial map and the derived low-resolution atomic structure. This program samples the density around Chi1 angles of protein sidechains. Electronic density and appropriate rotameric angles must coincide for each residue if the atomic structure backbone has been perfectly fitted to the map.
  • molprobity: Validates the geometry of an atomic structure inferred from an electron density map.
  • real_space_refine: Designed for extensive real-space refinement of an atomic structure against the map provided. The map can be derived from X-ray or neutron crystallography, or cryoEM. The program obtains a model that fits the map as well as possible having appropriate geometry. The model should not show validation outliers, such as Ramachandran plot or rotamer outliers.
  • superpose_pdbs: Superposes two atomic structures so that they optimally match.


See Model Building Tutorial

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Status devel version:

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