{ "info": { "author": "Laboratory of Structural Biology", "author_email": "grp-lsb-software@helsinki.fi", "bugtrack_url": null, "classifiers": [], "description": "=======================\nLocalrec Scipion plugin\n=======================\n\nCryogenic 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).\n\nIn this project we implement Localized Reconstruction as a plugin (Locarec) for Scipion.\n\nIf Localized Reconstruction is useful in your work, please cite:\n\nIlca 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\n\n\n===================\nInstall this plugin\n===================\n\nYou will need to use `2.0.0 `_ version of Scipion to run these protocols. Two versions of the plugin are available:\n\n**Stable version** \n\nEither use the following command\n\n.. code-block::\n\n scipion installp -p scipion-em-localrec\n\nor\n\nInstall the plugin through the plugin manager GUI by launching Scipion and\nfollowing **Configuration** >> **Plugins**\n\n**Developer's version** \n\n1. Download repository: \n\n.. code-block::\n\n git clone https://github.com/scipion-em/scipion-em-localrec.git\n\n2. Install:\n\n.. code-block::\n\n scipion installp -p path_to_scipion-em-localrec --devel\n\n3. Test the plugin:\n\n.. code-block::\n\n scipion test localrec.tests.test_protocol_localized_reconstruction\n\n=========\nProtocols\n=========\n\nThe following protocols have been implemented so far\n\n* localized subparticles: Calculate the orientations of the subunits of interest and their positions in the original particle images.\n* filter subunits: Filter the subunits (sub-particles) based on spatial distance, angular distance, etc.\n* localized extraction: Extract computed sub-particles from a SetOfParticles.\n* stitch particles: Regenerate a particle (volume) from its sub-particles (sub-volumes). \n\n===============\nBuildbot status\n===============\nStatus devel version: \n\n.. image:: http://arquimedes.cnb.csic.es:9980/badges/ccp4_devel.svg\n\nStatus production version: \n\n.. image:: http://arquimedes.cnb.csic.es:9980/badges/ccp4_prod.svg\n\n\n================\nAcknowledgements\n================\n\nThe authors acknowledge funding from the European Research Council under the 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