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 for details).

Install this plugin

You will need to use 3.0.0 version of Scipion to run these protocols. To install the plugin, you have two options:

• Stable version

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:

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

2. Install:

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-1.6, 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-1.6.

• Linking existing chimeraX installations

Since version 1.8, chimeraX do not offer a generic tar file for any linux distribution. Last version we install is 1.6 but other later versions can be linked following the next steps.

1.- create a folder in software/em/chimerax-#.# (being #.# = 1.8 or any chimeraX version you have installed)

2.- create a subfolder under chimerax-#.# called bin

OPTION1: flatpak installations:

F3.- create a text file called ChimeraX with this content in the :

flatpak run edu.ucsf.rbvi.ChimeraX $@

F4.- make it executable (chmod +x ChimeraX)

OPTION2: other linux installations:

L3.- link the existing ChimeraX binary in the bin folder. e.g: ln -s /usr/bin/chimerax ChimeraX

OPTION3: ChimeraX on windows and Scipion on WSL

W3.- link the existing ChimeraX.exe in the bin folder. e.g: ln -s /usr/bin/chimerax ChimeraX

• Tests

Tested with ChimeraX version: 1.X. where X is in the range 0-6

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

NOTE: the fact that chimerax-plugins supports the above mentioned chimerax versions does not mean that chimerax supports your operating system. For example, if you want to install chimerax 1.4 or higher you need at least ubuntu 22 version.

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.
• 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

FAQ

check the FAQ <https://github.com/scipion-em/scipion-em-chimera/blob/devel/FAQ.rst> for known problems

Buildbot status

Status devel version:

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