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relion

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Validates and executes RELION single-particle cryo-EM refinement and half-map postprocessing. Supports STAR optics/acquisition checks, particle-stack consistency, gold-standard half sets, soft-mask validation, diagnostic Fourier shell correlation, and restart guidance.

skills/relion/SKILL.md

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# 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](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
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