Metadata-Version: 1.2
Name: scipion-em-cistem
Version: 1.0.1
Summary: Plugin to use cisTEM programs within the Scipion framework
Home-page: https://github.com/scipion-em/scipion-em-cistem
Author: Grigory Sharov
Author-email: sharov.grigory@gmail.com
License: UNKNOWN
Project-URL: Bug Reports, https://github.com/scipion-em/scipion-em-cistem/issues
Project-URL: Source, https://github.com/scipion-em/scipion-em-cistem/
Description: =============
        cisTEM plugin
        =============
        
        **ATTENTION: This plugin replaces grigoriefflab plugin. You cannot use both of them simultaneously.**
        
        This plugin provide wrappers around several programs of `cisTEM <https://cistem.org>`_ software suite.
        
        +------------------+------------------+
        | stable: |stable| | devel: | |devel| |
        +------------------+------------------+
        
        .. |stable| image:: http://scipion-test.cnb.csic.es:9980/badges/cistem_sdevel.svg
        .. |devel| image:: http://scipion-test.cnb.csic.es:9980/badges/cistem_sdevel.svg
        
        
        Installation
        ------------
        
        You will need to use `3.0 <https://github.com/I2PC/scipion/releases/tag/V3.0.0>`_ 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-cistem
        
        b) Developer's version
        
            * download repository
        
            .. code-block::
        
                git clone https://github.com/scipion-em/scipion-em-cistem.git
        
            * install
        
            .. code-block::
        
                scipion installp -p path_to_scipion-em-cistem --devel
        
        cisTEM binaries will be installed automatically with the plugin, but you can also link an existing installation.
        
            * Default installation path assumed is ``software/em/cistem-1.0.0-beta``, if you want to change it, set *CISTEM_HOME* in ``scipion.conf`` file pointing to the folder where the cisTEM is installed.
            * It's possible to use CTFFIND4 installed separately from cisTEM by defining *CTFFIND4_HOME* variable in ``scipion.conf``.
        
        To check the installation, simply run one of the following Scipion tests:
        
        .. code-block::
        
           scipion test cistem.tests.test_protocols_cistem_movies.TestUnblur
           scipion test cistem.tests.test_protocols_cistem.TestCtffind4
           scipion test cistem.tests.test_protocols_cistem.TestFindParticles
           scipion test cistem.tests.test_protocols_cistem.TestRefine2D
        
        A complete list of tests can also be seen by executing ``scipion test --show --grep cistem``
        
        Supported versions
        ------------------
        
        1.0.0-beta
        
        
        Protocols
        ---------
        
        * ctffind4
        * unblur
        * find particles
        * classify 2D
        
        References
        ----------
        
        1. Timothy Grant and Alexis Rohou and Nikolaus Grigorieff. (2018) cisTEM, user-friendly software for single-particle image processing. eLife 7:e35383.
        
Keywords: scipion electron-microscopy cryo-em structural-biology image-processing scipion-3.0
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
