List of Programs

The following is a list of the most relevant tomography-related programs in Relion 3.2.

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.

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.
relion_tomo_refine_mag: estimates relative anisotropic magnification (incomplete)

relion_tomo_reconstruct_tomogram: creates a (typically low-magnification) tomogram.
relion_tomo_import_tomograms: imports new tilt series to create or extend a tomogram set.
relion_tomo_import_particles: imports new particles.
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 maps generated by relion_tomo_reconstruct_particle so they can be used by the different refinement programs more easily.
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 given set of manifolds.
relion_tomo_add_spheres: creates a manifold set from a set of spheres given in .cmm format.