| 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
- 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.
- 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
Related skills
