Individual skill
tooluniverse-electron-microscopy
Search and analyze electron microscopy data — cryo-EM density maps (EMDB), fitted atomic models (PDB), raw micrograph datasets (EMPIAR), and cryo-electron tomography volumes (CryoET Data Portal). Use for finding 3D structural data on a protein/complex, comparing experimental EM resolution to AlphaFold confidence, and accessing raw EM data for re-processing.
plugins/tooluniverse/skills/tooluniverse-electron-microscopy/SKILL.md
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# Electron Microscopy Structure Analysis
Pipeline for discovering and analyzing electron microscopy data across the full resolution spectrum: from 3D density maps (EMDB) to fitted atomic models (PDB), raw micrograph datasets (EMPIAR), and cryo-electron tomography volumes (CryoET Data Portal). Connects EM data to structural biology context via PDB and AlphaFold.
**Guiding principles**:
1. **Resolution awareness** -- always report and interpret map resolution; sub-4A enables atomic modeling, 4-8A enables domain fitting, >8A is shape-level
2. **Map before model** -- the density map is the primary experimental data; fitted models are interpretations
3. **Method matters** -- single particle analysis, tomography, 2D crystallography, and helical reconstruction have different strengths and limitations
4. **Raw data value** -- EMPIAR raw data enables reprocessing with newer algorithms; always note availability
5. **Cross-reference structures** -- connect EMDB maps to PDB entries and AlphaFold predictions for completeness
6. **English-first queries** -- use English terms in tool calls
EM resolution determines what you can see. TEM resolves individual protein complexes (~2nm). Cryo-EM achieves near-atomic resolution (<4Å) for large complexes. SEM shows surface topology. Choose the right EM modality for the question.
