RELION single-particle refinement

Use for a RELION single-particle project, especially extracted particles → homogeneous selected particle subset → gold-standard refinement → half-map validation and postprocessing. The bundled runner starts from CTF-annotated extracted particles and an initial 3D reference. It does not replace motion correction, picking, 2D/3D selection, or a biological interpretation of map quality. For tomography, helical reconstruction, Blush, or heterogeneous-state modeling, use the appropriate upstream workflow rather than forcing those data into this bounded SPA runner.

Preserve acquisition and coordinate conventions

Read references/acquisition-and-restarts.md when starting from movies or resuming jobs. Confirm pixel size in Å/pixel, voltage in kV, spherical aberration in mm, defocus in Å, amplitude contrast as a fraction, and the symmetry justified by the specimen. Do not “correct” a suspicious value by guessing its units.