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Localrec Scipion plugin

Cryogenic electron microscopy (cryoEM) can yield near-atomic resolution structures of highly ordered macromolecular complexes. Often however some subunits bind in a flexible manner, have different symmetry from the rest of the complex, or are present in sub-stoichiometric amounts, limiting the attainable resolution. We have developed a general method for the localized three-dimensional reconstruction of such subunits earlier (Ilca et al 2015 Nature Commun).

In this project we implement Localized Reconstruction as a plugin (Locarec) for Scipion.

If Localized Reconstruction is useful in your work, please cite:

Ilca SL, Kotecha A, Sun X, Poranen MM, Stuart DI & Huiskonen JT (2015). Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes. Nat Commun 6, 8843. doi:10.1038/ncomms9843

Abrishami V, Ilca SL, Gomez-Blanco J, Rissanen I, de la Rosa-Trevín JM, Reddy VS, Carazo JM, Huiskonen JT (2020). Localized reconstruction in Scipion expedites the analysis of symmetry mismatches in cryo-EM data. Prog. Biophys. Mol. Biol. doi:10.1016/j.pbiomolbio.2020.05.004.

Install this plugin

You will need to use 3.0.0 version of Scipion or later to run these protocols.

Stable version

Either use the following command

scipion3 installp -p scipion-em-localrec


Install plugin 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-localrec --devel
  1. Test the plugin:
scipion3 test localrec.tests.test_protocol_localized_reconstruction


The following protocols have been implemented so far

  • localrec - define subparticles: Determines the coordinates, orientations and defocus values of the sub-particles.
  • localrec - filter subparticles: Excludes unwanted sub-particles based on alignment information.
  • localrec - extract subparticles: Extracts sub-particle images from each particle image.
  • localrec - set origin to subvolume: Fits a sub-volume back to it's original volume (larger volume).
  • localrec - particles subset by subparticles: makes a subset of particles for which there is at least one sub-particle.
  • localrec - stitch subvolumes: Assembles a full volume from the sub-volumes generated by localized reconstruction.


  • scipion test localrec.tests.test_protocol_localized_reconstruction

Buildbot status

Status devel version:


Status production version:



The authors acknowledge funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (649053).


Plugin to use Localrec programs within the Scipion framework








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