Pdb Redo Tools

Configuration File: pdb_redo_tools.json Tool Type: Local Tools Count: 2

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

Available Tools

PDB_REDO_get_structure_quality (Type: BaseRESTTool)

Get re-refined structure quality metrics from PDB-REDO for a given PDB entry. PDB-REDO is a datab…

PDB_REDO_get_structure_quality tool specification

Tool Information:

  • Name: PDB_REDO_get_structure_quality

  • Type: BaseRESTTool

  • Description: Get re-refined structure quality metrics from PDB-REDO for a given PDB entry. PDB-REDO is a databank of optimized macromolecular structures: all PDB X-ray structures are re-refined using the latest crystallographic methods, improving R-factors, geometry, and fit to electron density. Returns 200+ quality metrics including: R-factor (RFIN), R-free (RFFIN), resolution (DATARESH), correlation coefficients (CCFFIN, CCWFIN), Ramachandran Z-score (ZRAMA), packing Z-score (ZPACKING), B-factor average (BAVER), number of backbone/sidechain flips (NBBFLIP/NSCFLIP), space group (SPACEGROUP), and unit cell dimensions. Only available for X-ray crystal structures. Use lowercase PDB IDs.

Parameters:

  • pdb_id (string) (required) PDB entry ID in lowercase. Examples: ‘1cbs’ (cellular retinoic acid binding protein), ‘6lu7’ (SARS-CoV-2 main protease), ‘2hhb’ (hemoglobin). Note: not all PDB entries have PDB-REDO data; mainly X-ray crystal structures.

Example Usage:

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

PDB_REDO_get_version_info (Type: BaseRESTTool)

Get PDB-REDO re-refinement version and provenance metadata for a PDB entry. This is the versions….

PDB_REDO_get_version_info tool specification

Tool Information:

  • Name: PDB_REDO_get_version_info

  • Type: BaseRESTTool

  • Description: Get PDB-REDO re-refinement version and provenance metadata for a PDB entry. This is the versions.json file, separate from the quality-metrics data.json: it reports the pdb-redo pipeline version used, the mmCIF coordinate revision (major/minor), the reflections revision, whether coordinates or reflections were edited, Foldit-player provenance (foldit_used, foldit_id, foldit_player), and the version/used flag of every supporting crystallographic program (mtzdmp, WHAT_CHECK, refmac, etc.). Use lowercase PDB IDs. Only X-ray structures present in PDB-REDO have version info.

Parameters:

  • pdb_id (string) (required) PDB entry ID in lowercase. Examples: ‘1cbs’, ‘6lu7’, ‘2hhb’. Not all PDB entries have PDB-REDO data (mainly X-ray crystal structures).

Example Usage:

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