======================
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
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