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Plugin to use chimera programs within the Scipion framework

Project description

Chimera scipion plugin

This plugin allows to use chimeraX commands within the Scipion framework.

Chimera is a program for interactive visualization and analysis of molecular structures and related data. It is developed by the Resource for Biocomputing, Visualization, and Informatics (see ChimeraX home page for details).

Install this plugin

You will need to use 3.0.0 version of Scipion to run these protocols. To install the plugin, you have two options:

  • Stable version
scipion3 installp -p scipion-em-chimera


  • through the plugin manager GUI by launching Scipion and following Configuration >> Plugins
  • Developer’s version
  1. Download repository:
git clone
  1. Install:
scipion3 installp -p path_to_scipion-em-chimera --devel
  • Binary files

Chimera binaries could be installed automatically with the plugin after accepting ChimeraX licence terms, but you can also link an existing installation. Default installation path assumed is software/em/chimerax-1.0, if you want to change it, set *CHIMERA_HOME in scipion.conf file to the folder where ChimeraX is installed or link your chimerax folder to software/em/chimerax-1.0.

  • Tests

Tested with ChimeraX version: 1.0.

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

  • scipion test chimera.tests.test_protocol_chimera_operate
  • scipion test chimera.tests.test_protocol_chimera_fit
  • scipion test chimera.tests.test_protocol_modeller_search
  • scipion test chimera.tests.test_protocol_contact
  • scipion test chimera.tests.test_protocol_chimera_map_subtraction
  • Supported versions of ChimeraX

1.0, 1.1


  • rigit fit: Fits an atomic structure (PDB/CIF) to a 3D map using a rigid fit algorithm.
  • model from template: Models three-dimensional structures of proteins using Modeller.
  • contacts: Identifies interatomic clashes and contacts based on van der Waals radii.
  • operate: Provides access to Chimera and allows to save the result in Scipion framework.
  • restore: This protocol opens Chimera and restores the session previously saved with commands scipionwrite or scipionss.
  • map subtraction: Protocol to identify remnant densities in a density map by subtracting two maps or masking one of them.

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