Emdb Tools#

Configuration File: emdb_tools.json Tool Type: Local Tools Count: 7

This page contains all tools defined in the emdb_tools.json configuration file.

Available Tools#

EMDB_get_imaging_info (Type: EMDBRESTTool)#

Get electron microscopy imaging parameters for an EMDB entry including microscope model, detector…

EMDB_get_imaging_info tool specification

Tool Information:

  • Name: EMDB_get_imaging_info

  • Type: EMDBRESTTool

  • Description: Get electron microscopy imaging parameters for an EMDB entry including microscope model, detector type, acceleration voltage, dose rate, total electron dose, defocus range, and data collection strategy. Returns technical details essential for understanding data quality, reproducing experiments, and optimizing imaging protocols. Use this to assess data collection quality or design similar experiments.

Parameters:

  • emdb_id (string) (required) EMDB structure identifier in format ‘EMD-####’ (e.g., ‘EMD-1234’, ‘EMD-0001’). Find IDs via EMDB search or from publications.

Example Usage:

query = {
    "name": "EMDB_get_imaging_info",
    "arguments": {
        "emdb_id": "example_value"
    }
}
result = tu.run(query)

EMDB_get_map_info (Type: EMDBRESTTool)#

Get detailed electron density map information for an EMDB entry including map statistics, contour…

EMDB_get_map_info tool specification

Tool Information:

  • Name: EMDB_get_map_info

  • Type: EMDBRESTTool

  • Description: Get detailed electron density map information for an EMDB entry including map statistics, contour levels, pixel spacing, dimensions, symmetry, and map file download URLs. Returns technical details essential for map visualization, model fitting, and computational analysis. Use this to prepare for structure visualization in tools like ChimeraX, Coot, or PyMOL.

Parameters:

  • emdb_id (string) (required) EMDB structure identifier in format ‘EMD-####’ (e.g., ‘EMD-1234’, ‘EMD-0001’). Find IDs via EMDB search or from publications.

Example Usage:

query = {
    "name": "EMDB_get_map_info",
    "arguments": {
        "emdb_id": "example_value"
    }
}
result = tu.run(query)

EMDB_get_publications (Type: EMDBRESTTool)#

Get publication information for an EMDB entry including journal articles, preprints, and citation…

EMDB_get_publications tool specification

Tool Information:

  • Name: EMDB_get_publications

  • Type: EMDBRESTTool

  • Description: Get publication information for an EMDB entry including journal articles, preprints, and citations that describe the cryo-EM structure. Returns publication titles, authors, journals, DOIs, PubMed IDs, and abstracts. Use this to find the research papers associated with a structure, understand experimental context, or cite the original work. Use EMDB ID from EMDB_search_structures or EMDB_get_structure.

Parameters:

  • emdb_id (string) (required) EMDB structure identifier in format ‘EMD-####’ (e.g., ‘EMD-1234’, ‘EMD-0001’). Find IDs via EMDB search or from publications.

Example Usage:

query = {
    "name": "EMDB_get_publications",
    "arguments": {
        "emdb_id": "example_value"
    }
}
result = tu.run(query)

EMDB_get_sample_info (Type: EMDBRESTTool)#

Get detailed sample preparation information for an EMDB entry including macromolecular compositio…

EMDB_get_sample_info tool specification

Tool Information:

  • Name: EMDB_get_sample_info

  • Type: EMDBRESTTool

  • Description: Get detailed sample preparation information for an EMDB entry including macromolecular composition, organism source, expression system, molecular weight, oligomeric state, and ligands. Returns biological context essential for understanding the structure’s physiological relevance, complex assembly, and binding partners. Use this to understand sample preparation before structural analysis.

Parameters:

  • emdb_id (string) (required) EMDB structure identifier in format ‘EMD-####’ (e.g., ‘EMD-1234’, ‘EMD-0001’). Find IDs via EMDB search or from publications.

Example Usage:

query = {
    "name": "EMDB_get_sample_info",
    "arguments": {
        "emdb_id": "example_value"
    }
}
result = tu.run(query)

EMDB_get_structure (Type: EMDBRESTTool)#

Get 3D electron microscopy (EM) structure data from the Electron Microscopy Data Bank (EMDB). Ret…

EMDB_get_structure tool specification

Tool Information:

  • Name: EMDB_get_structure

  • Type: EMDBRESTTool

  • Description: Get 3D electron microscopy (EM) structure data from the Electron Microscopy Data Bank (EMDB). Returns cryo-EM structure metadata including resolution (in Ångströms), imaging method, organism, molecule details, voxel dimensions, map download URLs, and cross-references to PDB entries. Use this for structural biology research, comparing protein conformations, drug design, and downloading electron density maps for visualization or model fitting.

Parameters:

  • emdb_id (string) (required) EMDB structure identifier in format ‘EMD-####’ (e.g., ‘EMD-1234’, ‘EMD-0001’). Find IDs via EMDB search or from publications.

Example Usage:

query = {
    "name": "EMDB_get_structure",
    "arguments": {
        "emdb_id": "example_value"
    }
}
result = tu.run(query)

EMDB_get_validation (Type: EMDBRESTTool)#

Get validation analysis results for an EMDB entry including FSC curves, resolution estimates, map…

EMDB_get_validation tool specification

Tool Information:

  • Name: EMDB_get_validation

  • Type: EMDBRESTTool

  • Description: Get validation analysis results for an EMDB entry including FSC curves, resolution estimates, map-model correlation, B-factors, geometry validation, and quality scores. Returns comprehensive quality metrics essential for assessing structure reliability, identifying artifacts, and comparing with other structures. Use this to evaluate data quality before using a structure for drug design or mechanistic studies.

Parameters:

  • emdb_id (string) (required) EMDB structure identifier in format ‘EMD-####’ (e.g., ‘EMD-1234’, ‘EMD-0001’). Find IDs via EMDB search or from publications.

Example Usage:

query = {
    "name": "EMDB_get_validation",
    "arguments": {
        "emdb_id": "example_value"
    }
}
result = tu.run(query)

EMDB_search_structures (Type: EMDBRESTTool)#

Search EMDB through the official EBI Search emdb domain with exact hitCount and start/rows pagina…

EMDB_search_structures tool specification

Tool Information:

  • Name: EMDB_search_structures

  • Type: EMDBRESTTool

  • Description: Search EMDB through the official EBI Search emdb domain with exact hitCount and start/rows pagination. The former /emdb/api/search path currently returns HTTP 200 empty arrays for valid common queries. Continue with metadata.next_start; use EMDB_get_structure on returned IDs for full archive metadata.

Parameters:

  • query (string) (required) Search query for EMDB structures. Examples: ‘ribosome’, ‘spike protein’, ‘SARS-CoV-2’, ‘amyloid’, ‘ion channel’. Searches titles, descriptions, and molecule names.

  • rows (integer) (optional) Search results per page (default 10, max 100).

  • start (integer) (optional) Zero-based EBI Search offset. Continue with metadata.next_start.

Example Usage:

query = {
    "name": "EMDB_search_structures",
    "arguments": {
        "query": "example_value"
    }
}
result = tu.run(query)