scipion-em-localrec 2.0

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:

Stable version

Either use the following command

scipion installp -p scipion-em-localrec

or

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

Developer’s version

1. Download repository:

git clone https://github.com/scipion-em/scipion-em-localrec.git

2. Install:

scipion installp -p path_to_scipion-em-localrec --devel

3. Test the plugin:

scipion test localrec.tests.test_protocol_localized_reconstruction

Protocols

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).

Buildbot status

Status devel version:

Status production version:

Acknowledgements

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