Metadata-Version: 1.2
Name: scipion-em-reliontomo
Version: 3.4.0
Summary: Plugin to use Relion programs for tomography within the Scipion framework
Home-page: https://github.com/scipion-em/scipion-em-reliontomo
Author: CNB-CSIC
Author-email: jjimenez@cnb.csic.es, scipion-users@lists.sourceforge.net
License: UNKNOWN
Project-URL: Bug Reports, https://github.com/scipion-em/scipion-em-reliontomo/issues
Project-URL: Source, https://github.com/scipion-em/scipion-em-reliontomo/
Description: =================
        Reliontomo plugin
        =================
        
        This plugin provide wrappers around several programs of `RELION <https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page>`_ software suite (version 3.0) for its use in Tomography.
        
        
        
        Installation
        ------------
        
        You will need to use `3.0 <https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html>`_ version of Scipion to be able to run these protocols.
        
        
        
        Protocols
        -----------
        
        * **Extract coordinates from pseudo-subtomograms** : Protocol to extract a set of 3D coordinates from a set of pseudo-subtomograms.
        * **Import coordinates 3D from a star file** : Protocol to import a set of 3D coordinates from a star file.
        * **Import subtomograms from a star file** : Protocol to import a set of subtomograms from a star file.
        * **3D Classification of subtomograms** : 3D Classification of subtomograms.
        * **Tomo CTF refine** : Tomo CTF refine
        * **De novo 3D initial model** : Generate a de novo 3D initial model from the pseudo-subtomograms.
        * **Apply operation to Relion particles** : Operate on the particles star file.
        * **Make pseudo-subtomograms** : Make pseudo-subtomograms.
        * **Sharpen a 3D reference maps** : Sharpen a 3D reference map and estimate the gold-standard FSC curves for subtomogram averaging.
        * **Prepare data for Relion 4** : Prepare data for Relion 4
        * **Reconstruct particle from tilt series** :  Reconstruct particle from the original tilt series images.
        * **Auto-refinement of subtomograms** :  Auto-refinement of subtomograms.
        * **Rec. particle averaging subtomograms** : This protocol reconstructs a volume using Relion. Reconstruct a volume from a given set of particles. The alignment parameters will be converted to a Relion star file and used as direction projections to reconstruct.
        * **Tomo frame align** : Tomo frame align
        * **Reconstruct tomograms from prepare data prot** : This protocol reconstructs a single tomogram using Relion. It is very useful  to check if the protocol "Prepare data" has been applied correctly (in terms of flip  options, for example).
        * **Matching coordinates** : Protocol to generate a set of pseudosubtomograms taking into account the intersection of  a set of 3D coordinates and a set of pseudosubtomograms as input.
        
        **Latest plugin versions**
        ==========================
        
        If you want to check the latest version and release history go to `CHANGES <https://github.com/scipion-em-reliotomo/reliontomo/blob/master/CHANGES.txt>`_
        
        
        **Installing the plugin**
        =========================
        
        In order to install the plugin follow these instructions:
        
        .. code-block::
        
            scipion installp -p scipion-em-reliontomo
        
        
        or through the **plugin manager** by launching Scipion and following **Configuration** >> **Plugins**
        
        
        **To install in development mode**
        
        Clone or download the plugin repository
        
        .. code-block::
        
            git clone https://github.com/scipion-em/scipion-em-reliontomo.git
        
        Install the plugin in developer mode.
        
        .. code-block::
        
            scipion installp -p local/path/to/scipion-em-reliontomo --devel
        
        
        To check the installation, simply run one of the tests. A complete list of tests can be displayed by executing ``scipion3 tests --grep reliontomo --show``
        
        Supported versions
        ------------------
        
        Relion 3.0, 4.0
        
        
        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
        
        
        Buildbot status
        ---------------
        
        Status devel version:
        
        .. image:: http://scipion-test.cnb.csic.es:9980/badges/reliontomo_devel.svg
        
        
        Status production version:
        
        .. image:: http://scipion-test.cnb.csic.es:9980/badges/reliontomo_prod.svg
        
        
Keywords: scipion electron-tomography 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
