Localrec ready to use in scipion.
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
Install this plugin
You will need to use 2.0.0 version of Scipion to run these protocols. Two versions of the plugin are available:
Either use the following command
scipion installp -p scipion-em-localrec
Install the plugin through the plugin manager GUI by launching Scipion and following Configuration >> Plugins
- Download repository:
git clone https://github.com/scipion-em/scipion-em-localrec.git
scipion installp -p path_to_scipion-em-localrec --devel
- Test the plugin:
scipion test localrec.tests.test_protocol_localized_reconstruction
The following protocols have been implemented so far
- localized subparticles: Calculate the orientations of the subunits of interest and their positions in the original particle images.
- filter subunits: Filter the subunits (sub-particles) based on spatial distance, angular distance, etc.
- localized extraction: Extract computed sub-particles from a SetOfParticles.
- stitch particles: Regenerate a particle (volume) from its sub-particles (sub-volumes).
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).
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