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RELION cryo-EM refinement checker

Validates RELION cryo-EM particle data and runs refinement, half-map FSC and postprocessing steps

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
4 files

What it does

Once installed, the agent knows how to check RELION single-particle cryo-EM projects before and during 3D refinement. It validates STAR metadata and particle stacks, runs bounded refinement and postprocessing commands, computes a diagnostic Fourier shell correlation between two independent half maps, and gives guidance on restarting jobs. It is aimed at extracted particles that already have CTF estimates and an initial reference, not at the earlier motion correction or picking steps.

Great for

  • Structural biology students or researchers running RELION SPA pilot refinements on extracted particles
  • Lab members who need a checklist for half-map validation and soft-mask postprocessing
  • Developers building validation tooling around RELION STAR files and MRC maps

Skip it if

  • Tomography, helical reconstruction, Blush or heterogeneous-state modelling, which the skill says require other upstream workflows
  • Final publication-grade resolution claims, since the Python FSC is unmasked and the skill says it does not replace mask-corrected FSC; biological interpretation of the map is also outside its scope
  • Users without RELION 5.0.1 and an MPI installation, since the refinement steps cannot run without them and the reference says the sequential executable cannot perform the gold-standard split

Try asking

  • “Validate my particles.star file against the stacks in my project folder before I start refinement”
  • “Run a small CPU pilot refinement with MPI on my extracted particles and a low-pass initial reference”
  • “Compute a diagnostic FSC between my two unfiltered half maps and explain the 0.143 crossing”
  • “Help me restart a RELION refinement job from its optimiser STAR file without losing the random half split”
Step-by-step guide: how to use RELION cryo-EM refinement checkerInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 4 original files, the MIT licence and an attribution note.

    relion.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip relion.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip relion.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Run validate-star first and review its physical-range warnings, but do not overwrite unusual acquisition values by guessing their units
  • Keep the _optimiser.star, model and sampling files together with the particle paths so jobs can be restarted from the original optimiser
  • Treat the Python FSC as a diagnostic only and use RELION's native tools or mask-corrected FSC for reported resolution

What's inside

  • references/acquisition-and-restarts.md
  • references/runtime-and-validation.md
  • scripts/spa_workflow.py
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.