Subtomogram Averaging

Data Types

The custom data types used in tomography programs in relion are:

• Tomogram set
• Particle set
• Trajectory set
• Optimisation set

Programs

These are the most relevant tomography-related programs in relion:

Core programs

• relion_tomo_reconstruct_particle : creates high-resolution 3D maps from a given data set.

• relion_tomo_subtomo : creates pseudo subtomograms that can be fed into relion_refine.

Refinement programs

These programs use an existing particle set and a pair of high-resolution 3D reference maps to estimate or improve different properties:

• relion_tomo_align : aligns the images of a tilt series and estimates beam-induced motion to better fit a set of particles.

• relion_tomo_refine_ctf : refines the astigmatic defocus, signal intensity (i.e. ice thickness) and higher-order aberrations.

• relion_tomo_local_particle_refine : offers a rapid way to refine the angles and positions of individual particles.

• relion_tomo_fit_blobs_3d : fits a set of spherical manifolds representing vesicles to the observed membranes.

Utility programs

• relion_tomo_import_tomograms : imports new tilt series to create or extend a tomogram set.

• relion_tomo_import_particles : imports new particles.

• relion_tomo_reconstruct_tomogram : creates a (typically low-magnification) tomogram.

• relion_tomo_make_optimisation_set : ties a set of disparate data elements into an optimisation set.

• relion_tomo_make_reference : runs relion_postprocess on a pair of reference half maps.

• relion_tomo_add_spheres : creates a manifold set from a set of spheres given in .cmm format.

• relion_tomo_find_fiducials : detects the fiducial markers in a given data set.

• relion_tomo_sample_manifold : samples a set of particle positions and orientations from a set of manifolds.

Previous pipeline

• RELION 1.4 subtomogram averaging pipeline.