Metadata-Version: 1.1
Name: scipion-em-chimera
Version: 3.0.1
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 chimera 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 `Chimera home page <https://www.cgl.ucsf.edu/chimera/>`_ for details).
        
        
        ===================
        Install this plugin
        ===================
        
        You will need to use `2.0.0 <https://github.com/I2PC/scipion/releases/tag/v2.0>`_ version of Scipion to run these protocols. To install the plugin, you have two options:
        
        - **Stable version**  
        
        .. code-block:: 
        
              scipion 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::
        
                    scipion installp -p path_to_scipion-em-chimera --devel
        
        - **Binary files** 
        
        Chimera binaries will be installed automatically with the plugin, but you can also link an existing installation. 
        Default installation path assumed is *software/em/chimera-1.13.1*, if you want to change it, set *CHIMERA_HOME* in *scipion.conf* file to the folder where Chimera is installed.
        
        - **Tests**
        
        Tested with Chimera version: 1.13.1.
        
        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
        
        - **Supported versions of Chimera**
        
        1.13.1
        
        
        =========
        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*. 
        
        
        ========
        Examples
        ========
        
        See `Model Building Tutorial <https://github.com/I2PC/scipion/wiki/tutorials/tutorial_model_building_basic.pdf>`_
        
        
        ===============
        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
        
        
Keywords: scipion cryoem imageprocessing scipion-3.0
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python :: 3
