Plugin to use Relion programs for tomography within the Scipion framework
Project description
This plugin provide wrappers around several programs of RELION software suite (version 3.0) for its use in Tomography.
Current development
This plugin is currently in BETA mode.
Installation
You will need to use 3.0 version of Scipion to be able to run these protocols.
Protocols
Extract coordinates from pseudo-subtomograms : Protocol to extract a set of 3D coordinates from a set of pseudo-subtomograms.
Import coordinates 3D from a star file : Protocol to import a set of 3D coordinates from a star file.
Import subtomograms from a star file : Protocol to import a set of subtomograms from a star file.
3D Classification of subtomograms : 3D Classification of subtomograms.
Tomo CTF refine : Tomo CTF refine
De novo 3D initial model : Generate a de novo 3D initial model from the pseudo-subtomograms.
Apply operation to Relion particles : Operate on the particles star file.
Make pseudo-subtomograms : Make pseudo-subtomograms.
Sharpen a 3D reference maps : Sharpen a 3D reference map and estimate the gold-standard FSC curves for subtomogram averaging.
Prepare data for Relion 4 : Prepare data for Relion 4
Reconstruct particle from tilt series : Reconstruct particle from the original tilt series images.
Auto-refinement of subtomograms : Auto-refinement of subtomograms.
Rec. particle averaging subtomograms : This protocol reconstructs a volume using Relion. Reconstruct a volume from a given set of particles. The alignment parameters will be converted to a Relion star file and used as direction projections to reconstruct.
Tomo frame align : Tomo frame align
Reconstruct tomograms from prepare data prot : This protocol reconstructs a single tomogram using Relion. It is very useful to check if the protocol “Prepare data” has been applied correctly (in terms of flip options, for example).
Matching coordinates : Protocol to generate a set of pseudosubtomograms taking into account the intersection of a set of 3D coordinates and a set of pseudosubtomograms as input.
Latest plugin versions
If you want to check the latest version and release history go to CHANGES
Installing the plugin
In order to install the plugin follow these instructions:
scipion installp -p scipion-em-reliontomo
or through the plugin manager by launching Scipion and following Configuration >> Plugins
To install in development mode
Clone or download the plugin repository
git clone https://github.com/scipion-em/scipion-em-reliontomo.git
Install the plugin in developer mode.
scipion installp -p local/path/to/scipion-em-reliontomo --devel
To check the installation, simply run one of the tests. A complete list of tests can be displayed by executing scipion3 tests --grep reliontomo --show
Supported versions
Relion 3.0, 4.0
References
Scheres et al., JMB, 2012
Scheres et al., JSB, 2012
Kimanius et al., eLife, 2016
Zivanov et al., eLife, 2018
Buildbot status
Status devel version:
Status production version:
Project details
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