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.

LOOK UP, DON'T GUESS

When uncertain about any scientific fact, SEARCH databases first rather than reasoning from memory. A database-verified answer is always more reliable than a guess.