rcsb-pdb-search

name	rcsb-pdb-search
description	Use this skill to search the Protein Data Bank through the official RCSB Search API when you need structure identifiers from a free-text query. Do not use it when you need structure download or coordinate parsing.

Purpose

Run lightweight RCSB PDB entry searches and save the result set as JSON.

When to use

• You need a quick structure search from a protein, ligand, or concept keyword.
• You want PDB entry IDs for downstream structural analysis.

When not to use

• You need mmCIF/PDB coordinate files.
• You need local structural parsing rather than remote search.

Inputs

• Query string
• Optional --rows and --out

Outputs

• Search API JSON containing PDB entry identifiers

Requirements

• Python 3.13+
• Network access to search.rcsb.org

Procedure

1. Run python3 skills/structural-biology/rcsb-pdb-search/scripts/search_rcsb.py --query hemoglobin --rows 3 --out skills/structural-biology/rcsb-pdb-search/assets/hemoglobin_results.json.
2. Review total_count and result_set.

Validation

• Command exits successfully.
• Output JSON contains result_set.
• At least one structure ID is returned for a common query.

Failure modes and fixes

• Empty results: broaden the text query.
• HTTP errors: retry later or reduce result count.

Safety and limits

• This is a metadata search skill, not a molecular modeling workflow.

Examples

• python3 .../search_rcsb.py --query "p53" --rows 2

Provenance

• RCSB Search API docs: https://search.rcsb.org/

Related skills

• ensembl-gene-lookup