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tooluniverse-electron-microscopy

Search and analyze electron microscopy data across EMDB, EMPIAR, PDB, and CryoET databases.

1.7k|254|Updated Mar 3, 2025
Search Tags:#protein structure#tomography#structural biology#cryo-em#emdb#electron microscopy#empiar
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-electron-microscopy
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-electron-microscopy
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-electron-microscopy
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-electron-microscopy

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Finding and evaluating electron microscopy structural data requires querying multiple disconnected archives (EMDB, EMPIAR, PDB, CryoET Data Portal) and interpreting resolution, fitting quality, and raw data availability. This Skill provides a phased pipeline that discovers EM maps, fitted atomic models, raw micrograph datasets, and tomography volumes for a target protein or complex, then synthesizes an actionable report.

Core Features & Use Cases

  • EM Map Discovery: Search EMDB by keyword, organism, resolution range, and method, with resolution interpretation guidance (atomic, domain, or shape level).
  • Model Fitting & Validation: Cross-reference EMDB entries with fitted PDB models and assess fitting quality via cross-correlation and validation statistics.
  • Raw Data & Tomography Access: Locate EMPIAR raw micrograph datasets for reprocessing and CryoET Data Portal tomograms for in-situ structural context.
  • Use Case: Ask for cryo-EM structures of a target protein and receive a ranked report of available maps, the best fitted atomic model for drug-binding analysis, links to raw EMPIAR data, and AlphaFold comparisons for unresolved regions.

Quick Start

Find all cryo-EM structures of the human ribosome, report their resolutions, and identify which entries have fitted PDB models and raw EMPIAR data.

Frequently Asked Questions about tooluniverse-electron-microscopy

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I find cryo-EM structures for a specific protein?▼

Search EMDB with EMDB_search_structures using the protein name, optionally filtering by resolution range and method. Results include EMDB IDs, resolution, method, and sample details, which can be cross-referenced with fitted PDB models.

What EM resolution do I need for atomic model building?▼

Atomic model building generally requires maps better than 3.5A resolution, where backbone and large side chains are traceable. Maps at 4-8A support domain-level fitting, while maps worse than 8A show only overall shape.

Can I get raw cryo-EM micrograph data for reprocessing?▼

Yes, EMPIAR archives raw micrographs, particle stacks, and tilt series linked to many EMDB entries. Use EMPIAR_search_entries to find datasets, though deposition is not universal and sizes can reach terabytes.

What is the difference between cryo-EM single particle analysis and cryo-ET?▼

Single particle analysis achieves near-atomic resolution on purified samples, while cryo-electron tomography preserves cellular context in situ at lower resolution. The CryoET Data Portal hosts tomographic datasets; EMDB hosts both map types.

Does this skill visualize or reprocess EM maps?▼

No, it retrieves metadata, resolution statistics, and dataset links only. Visualization requires tools like UCSF ChimeraX or IMOD, and reprocessing requires software such as RELION or cryoSPARC.

When should I use light microscopy data instead of electron microscopy?▼

Use the Image Data Resource (IDR) tools when the question concerns published light-microscopy or high-content screening data, such as gene knockdown imaging studies or antibody-stained cell images, rather than EM structural data.

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