.. _sec_sta_programs: Subtomogram Averaging ===================== Data Types ---------- The custom data types used in tomography programs in |RELION| are: .. toctree:: Datatypes/tomogram_set Datatypes/particle_set Datatypes/trajectory_set Datatypes/manifold_set Datatypes/optimisation_set Programs -------- These are the most relevant tomography-related programs in |RELION|: .. toctree:: :hidden: Programs/reconstruct_particle Programs/subtomo Programs/align Programs/refine_ctf Programs/local_particle_refine Programs/fit_blobs_3d Programs/reconstruct_tomogram Programs/import_tomograms Programs/import_particles Programs/make_optimisation_set Programs/make_reference Programs/find_fiducials Programs/add_spheres Programs/sample_manifold previousSubtomogram Core programs ::::::::::::: - :ref:`program_tomo_reconstruct_particle` : creates high-resolution 3D maps from a given data set. - :ref:`program_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: - :ref:`program_tomo_align` : aligns the images of a tilt series and estimates beam-induced motion to better fit a set of particles. - :ref:`program_tomo_refine_ctf` : refines the astigmatic defocus, signal intensity (i.e. ice thickness) and higher-order aberrations. - :ref:`program_tomo_local_particle_refine` : offers a rapid way to refine the angles and positions of individual particles. - :ref:`program_tomo_fit_blobs_3d` : fits a set of spherical manifolds representing vesicles to the observed membranes. Utility programs :::::::::::::::: - :ref:`program_tomo_import_tomograms` : imports new tilt series to create or extend a tomogram set. - :ref:`program_tomo_import_particles` : imports new particles. - :ref:`program_tomo_reconstruct_tomogram` : creates a (typically low-magnification) tomogram. - :ref:`program_tomo_make_optimisation_set` : ties a set of disparate data elements into an :ref:`optimisation set `. - :ref:`program_tomo_make_reference` : runs ``relion_postprocess`` on a pair of reference half maps. - :ref:`program_tomo_add_spheres` : creates a :ref:`manifold set ` from a set of spheres given in ``.cmm`` format. - :ref:`program_tomo_find_fiducials` : detects the fiducial markers in a given data set. - :ref:`program_tomo_sample_manifold` : samples a set of particle positions and orientations from a :ref:`set of manifolds `. Previous pipeline ----------------- - :ref:`RELION 1.4 subtomogram averaging pipeline `.