Metadata-Version: 1.1
Name: scipion-em-chimera
Version: 3.3.5
Summary: Plugin to use chimera programs within the Scipion framework
Home-page: https://github.com/scipion-em/scipion-em-chimera
Author: Marta Martinez, Roberto Marabini
Author-email: scipion@cnb.csic.es
License: UNKNOWN
Description: ======================
        Chimera scipion plugin
        ======================
        
        This plugin allows to use chimeraX commands within the Scipion framework.
        
        Chimera  is a program for interactive visualization and analysis of molecular structures and related data. It is developed by the Resource for Biocomputing, Visualization, and Informatics (see `ChimeraX home page <https://www.cgl.ucsf.edu/chimerax/>`_ for details).
        
        
        ===================
        Install this plugin
        ===================
        
        You will need to use `3.0.0 <https://scipion-em.github.io/docs/release-3.0.0/>`_ version of Scipion to run these protocols. To install the plugin, you have two options:
        
        - **Stable version**  
        
        .. code-block:: 
        
              scipion3 installp -p scipion-em-chimera
              
        OR
        
          - 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-chimera.git
        
        2. Install:
        
        .. code-block::
        
                    scipion3 installp -p path_to_scipion-em-chimera --devel
        
        - **Binary files**
        
        Chimera binaries could be installed automatically with the plugin after accepting ChimeraX licence terms,
        but you can also link an existing installation. Default installation path assumed is *software/em/chimerax-1.0,
        if you want to change it, set *CHIMERA_HOME* in *scipion.conf* file to the folder where ChimeraX is installed
        or link your chimerax folder to *software/em/chimerax-1.0*.
        
        - **Tests**
        
        Tested with ChimeraX version: 1.0.
        
        To check the installation, simply run the following Scipion tests: 
        
        * scipion test chimera.tests.test_protocol_chimera_operate
        * scipion test chimera.tests.test_protocol_chimera_fit
        * scipion test chimera.tests.test_protocol_modeller_search
        * scipion test chimera.tests.test_protocol_contact
        * scipion test chimera.tests.test_protocol_chimera_map_subtraction
        
        - **Supported versions of ChimeraX**
        
        1.0, 1.1, 1.2 and 1.3
        
        
        =========
        Protocols
        =========
        
        * rigit fit: Fits an atomic structure (PDB/CIF) to a 3D map using a rigid fit algorithm.
        * model from template: Models three-dimensional structures of proteins using `Modeller <https://salilab.org/modeller/manual/node7.html>`_.
        * contacts: Identifies interatomic `clashes and contacts <https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>`_ based on van der Waals radii. 
        * operate: Provides access to Chimera and allows to save the result in Scipion framework.
        * restore: This protocol opens Chimera and restores the session previously saved with commands *scipionwrite* or *scipionss*. 
        * map subtraction: Protocol to identify remnant densities in a density map by subtracting two maps or masking one of them.
        * alphafold prediction: finds and retrieves existing models from the AlphaFold Database, runs new AlphaFold predictions using Google Colab, executes a local implementation of alphafold. 
        
        
        ========
        Examples
        ========
        
        See `Model Building Tutorial <https://scipion-em.github.io/docs/release-3.0.0/docs/user/user-documentation.html#model-building>`_
        
        ===
        FAQ
        ===
        
         check the FAQ <https://github.com/scipion-em/scipion-em-chimera/blob/devel/FAQ.rst> for known problems
        
        
        ===============
        Buildbot status
        ===============
        
        Status devel version:
        
        .. image:: http://scipion-test.cnb.csic.es:9980/badges/chimera_devel.svg
        
        ..
            Status production version: 
        
        .. 
            image:: http://scipion-test.cnb.csic.es:9980/badges/chimera_prod.svg
        
        
        ======================
        Chimera Extra commands
        ======================
        A set of comamnd to allow interaction between scipion and chimerax has been implemented.
        They may be executed from ChimeraX command line:
          
        * scipionwrite: saves model file
        * scipionss: saves chimera session
        * scipionrs: restores chimera sesion
        * scipioncombine: combines two models [No longer needed since chimerax now implements combine]
        * scipionshell: shows the density of a 3D Map on a spherical shell of the map at a given radius
        * scipionshellcrown: shows a shell of a 3D map between two radii
        * scipion: summary with all scipion related commands
        
Keywords: scipion cryoem imageprocessing scipion-3.0
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python :: 3
