Metadata-Version: 1.0
Name: scipion-em-localrec
Version: 3.0.2
Summary: Localrec ready to use in scipion.
Home-page: https://github.com/scipion-em/scipion-em-localrec
Author: Laboratory of Structural Biology
Author-email: grp-lsb-software@helsinki.fi
License: UNKNOWN
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
        
        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.
        
        ===================
        Install this plugin
        ===================
        
        You will need to use `3.0.0 <https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html>`_ version of Scipion to run these protocols.
        
        **Stable version**  
        
        Either use the following command
        
        .. code-block::
        
            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: 
        
        .. code-block::
        
                    git clone https://github.com/scipion-em/scipion-em-localrec.git
        
        2. Install:
        
        .. code-block::
        
                   scipion installp -p path_to_scipion-em-localrec --devel
        
        3. Test the plugin:
        
        .. code-block::
        
                   scipion test localrec.tests.test_protocol_localized_reconstruction
        
        =========
        Protocols
        =========
        
        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.
        
        =====
        Tests
        =====
        
        * scipion test localrec.tests.test_protocol_localized_reconstruction
        
        ===============
        Buildbot status
        ===============
        Status devel version: 
        
        .. image:: http://arquimedes.cnb.csic.es:9980/badges/ccp4_devel.svg
        
        Status production version: 
        
        .. image:: 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).
        
Keywords: localizedreconstruction cryoem imageprocessing scipion-3.0
Platform: UNKNOWN
