Metadata-Version: 1.2
Name: scipion-em-relion
Version: 3.0.1
Summary: Plugin to use Relion programs within the Scipion framework
Home-page: https://github.com/scipion-em/scipion-em-relion
Author: Grigory Sharov, J.M. De la Rosa Trevin, Josue Gomez Blanco
Author-email: gsharov@mrc-lmb.cam.ac.uk, delarosatrevin@scilifelab.se, josue.gomez-blanco@mcgill.ca
License: UNKNOWN
Project-URL: Bug Reports, https://github.com/scipion-em/scipion-em-relion/issues
Project-URL: Source, https://github.com/scipion-em/scipion-em-relion/
Description: =============
        Relion plugin
        =============
        
        This plugin provide wrappers around several programs of `RELION <https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page>`_ software suite.
        
        .. image:: https://img.shields.io/pypi/v/scipion-em-relion.svg
                :target: https://pypi.python.org/pypi/scipion-em-relion
                :alt: PyPI release
        
        .. image:: https://img.shields.io/pypi/l/scipion-em-relion.svg
                :target: https://pypi.python.org/pypi/scipion-em-relion
                :alt: License
        
        .. image:: https://img.shields.io/pypi/pyversions/scipion-em-relion.svg
                :target: https://pypi.python.org/pypi/scipion-em-relion
                :alt: Supported Python versions
        
        .. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-relion?server=https%3A%2F%2Fsonarcloud.io
                :target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-relion
                :alt: SonarCloud quality gate
        
        .. image:: https://img.shields.io/pypi/dm/scipion-em-relion
                :target: https://pypi.python.org/pypi/scipion-em-relion
                :alt: Downloads
        
        
        +--------------+----------------+--------------------+
        | prod: |prod| | devel: |devel| | support: |support| |
        +--------------+----------------+--------------------+
        
        .. |prod| image:: http://scipion-test.cnb.csic.es:9980/badges/relion_prod.svg
        .. |devel| image:: http://scipion-test.cnb.csic.es:9980/badges/relion_devel.svg
        .. |support| image:: http://scipion-test.cnb.csic.es:9980/badges/relion_support.svg
        
        **IMPORTANT!**
        
            If you have imported movies with a gain file in **DM4** format, you need to **flip the gain reference upside-down** in the motion correction protocol! (`bug details <https://github.com/I2PC/xmippCore/issues/39>`_)
        
        
        Installation
        ------------
        
        You will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have two options:
        
        a) Stable version
        
           .. code-block::
        
              scipion installp -p scipion-em-relion
        
        b) Developer's version
        
           * download repository
        
           .. code-block::
        
              git clone https://github.com/scipion-em/scipion-em-relion.git
        
           * install
        
           .. code-block::
        
              scipion installp -p path_to_scipion-em-relion --devel
        
        RELION sources will be downloaded and compiled automatically with the plugin, but you can also link an existing installation. Default installation path assumed is ``software/em/relion-3.1.1``, if you want to change it, set *RELION_HOME* in ``scipion.conf`` file to the folder where the RELION is installed. If you need to use CUDA different from the one used during Scipion installation (defined by *CUDA_LIB*), you can add *RELION_CUDA_LIB* variable to the config file. Moreover, if you have to use a MPI for Relion different from Scipion MPI, you can set *RELION_MPI_BIN* and *RELION_MPI_LIB* variables in the config file.
        
        To check the installation, simply run one of the tests. A complete list of tests can be displayed by executing ``scipion test --show --grep relion``
        
        Supported versions
        ------------------
        
        3.1.0, 3.1.1
        
        **IMPORTANT**: Relion-3.0 can be used with this plugin but we do not officially support it anymore, i.e. there will be no bugfixes for it.
        
        Protocols
        ---------
        
        * 2D classification         
        * 3D auto-refine            
        * 3D classification         
        * 3D initial model          
        * 3D multi-body
        * assign optics group
        * auto-picking              
        * auto-picking LoG          
        * bayesian polishing        
        * center averages
        * compress movies
        * create 3d mask            
        * ctf refinement
        * estimate gain to compress
        * expand symmetry
        * export coordinates
        * export ctf                
        * export particles          
        * local resolution          
        * motion correction
        * particles extraction
        * post-processing           
        * preprocess particles      
        * reconstruct
        * remove preferential views
        * subtract projection
        * symmetrize volume
        
        References
        ----------
        
        1. Scheres et al., JMB, 2012 
        2. Scheres et al., JSB, 2012 
        3. Kimanius et al., eLife, 2016 
        4. Zivanov et al., eLife, 2018
        
Keywords: scipion electron-microscopy cryo-em structural-biology image-processing scipion-3.0
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
