Plugin to use chimera programs within the Scipion framework
Project 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 for details).
Install this plugin
You will need to use 2.0.0 version of Scipion to run these protocols. To install the plugin, you have two options:
Stable version
scipion installp -p scipion-em-chimera
OR
through the plugin manager GUI by launching Scipion and following Configuration >> Plugins
Developer’s version
Download repository:
git clone https://github.com/scipion-em/scipion-em-chimera.git
Install:
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.
contacts: Identifies interatomic clashes and contacts 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
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