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Reliontomo plugin

This plugin provide wrappers around several programs of RELION software suite (version 3.0) for its use in Tomography.

Current development

This plugin is currently in BETA mode.


You will need to use 3.0 version of Scipion to be able to run these protocols.


  • Extract coordinates from pseudo-subtomograms : Protocol to extract a set of 3D coordinates from a set of pseudo-subtomograms.
  • Import coordinates 3D from a star file : Protocol to import a set of 3D coordinates from a star file.
  • Import subtomograms from a star file : Protocol to import a set of subtomograms from a star file.
  • 3D Classification of subtomograms : 3D Classification of subtomograms.
  • Tomo CTF refine : Tomo CTF refine
  • De novo 3D initial model : Generate a de novo 3D initial model from the pseudo-subtomograms.
  • Apply operation to Relion particles : Operate on the particles star file.
  • Make pseudo-subtomograms : Make pseudo-subtomograms.
  • Sharpen a 3D reference maps : Sharpen a 3D reference map and estimate the gold-standard FSC curves for subtomogram averaging.
  • Prepare data for Relion 4 : Prepare data for Relion 4
  • Reconstruct particle from tilt series : Reconstruct particle from the original tilt series images.
  • Auto-refinement of subtomograms : Auto-refinement of subtomograms.
  • Rec. particle averaging subtomograms : This protocol reconstructs a volume using Relion. Reconstruct a volume from a given set of particles. The alignment parameters will be converted to a Relion star file and used as direction projections to reconstruct.
  • Tomo frame align : Tomo frame align
  • Reconstruct tomograms from prepare data prot : This protocol reconstructs a single tomogram using Relion. It is very useful to check if the protocol "Prepare data" has been applied correctly (in terms of flip options, for example).
  • Matching coordinates : Protocol to generate a set of pseudosubtomograms taking into account the intersection of a set of 3D coordinates and a set of pseudosubtomograms as input.

Latest plugin versions

If you want to check the latest version and release history go to CHANGES

Installing the plugin

In order to install the plugin follow these instructions:

scipion installp -p scipion-em-reliontomo

or through the plugin manager by launching Scipion and following Configuration >> Plugins

To install in development mode

Clone or download the plugin repository

git clone

Install the plugin in developer mode.

scipion installp -p local/path/to/scipion-em-reliontomo --devel

To check the installation, simply run one of the tests. A complete list of tests can be displayed by executing scipion3 tests --grep reliontomo --show

Supported versions

Relion 3.0, 4.0


  1. Scheres et al., JMB, 2012
  2. Scheres et al., JSB, 2012
  3. Kimanius et al., eLife, 2016
  4. Zivanov et al., eLife, 2018

Buildbot status

Status devel version:

Status production version:


Plugin to use Relion tomography programs within the Scipion framework








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Contributors 4