scipion-em-reliontomo 4.0.5

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.

scipion installp -p scipion-em-reliontomo

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

scipion installp -p local/path/to/scipion-em-reliontomo --devel

Supported versions

Relion 4.0, 5.0

References

1. Zivanov et al., eLife, 2022

2. Burt et al., bioRxiv, 2024