Electron Microscopy Structure Analysis

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.

COMPUTE, DON'T DESCRIBE

When analysis requires computation (statistics, data processing, scoring, enrichment), write and run Python code via Bash. Don't describe what you would do — execute it and report actual results. Use ToolUniverse tools to retrieve data, then Python (pandas, scipy, statsmodels, matplotlib) to analyze it.

When to Use

Typical triggers:

• "Find cryo-EM structures of [protein/complex]"
• "What EMDB maps are available for [target]?"
• "Get raw micrograph data for [structure]"
• "Find tomography datasets for [organelle/cell type]"
• "What is the resolution of [EMDB entry]?"
• "Cross-reference this EM map with PDB models"
• "Find cryo-ET datasets for [sample]"

Not this skill: For X-ray crystallography or NMR structures, use PDB search tools directly. For protein structure prediction, use tooluniverse-protein-structure.

Core Databases

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