scipion-em-chimera 2.0.1

Plugin to use chimera programs within the Scipion framework

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

1. Download repository:

git clone https://github.com/scipion-em/scipion-em-chimera.git

2. 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

See Model Building Tutorial

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