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Localrec ready to use in scipion.

Project description

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
  1. Install:
scipion installp -p path_to_scipion-em-localrec --devel
  1. 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:

http://arquimedes.cnb.csic.es:9980/badges/ccp4_devel.svg

Status production version:

http://arquimedes.cnb.csic.es:9980/badges/ccp4_prod.svg

Acknowledgements

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

Project details


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Files for scipion-em-localrec, version 2.0
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