scipion-em-reliontomo 4.0.4

Plugin to use reliontomo within the Scipion framework

This plugin provide wrappers around several programs of RELION software suite for its use in Tomography.

Installation

You will need to use 3.0 version of Scipion to be able to run these protocols.

Protocols

VERSION 4.0:

• 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 map : 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).

VERSION 5.0:

• 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 : apply the refinement of the different parameters related to the CTF estimation.

• 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: re-center and duplicates removal.

• Sharpen a 3D reference map : Sharpen a 3D reference map and estimate the gold-standard FSC curves for subtomogram averaging.

• Extract subtomos : extract the subtomograms from the tilt-series.

• Reconstruct particle : generate a reference map from a particle set by averaging the particles using their positions and orientations

• Auto-refinement of subtomograms : Auto-refinement of subtomograms.

• Bayesian polishing : refine the projections that map 3D space onto the images of the tilt series.

• Tomogram reconstruction : reconstruct tomograms.

• Motion correction : motion correction of the angular frame stacks using Relion’s own implementation.

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 4.0, 5.0

References

1. Zivanov et al., eLife, 2022

2. Burt et al., bioRxiv, 2024