rcsb-pdb-entry-summary
Use this skill to fetch a canonical RCSB PDB entry record by accession when you need quick structural metadata. Do not use it for search ranking or full structure parsing pipelines.
SKILL.mdskills/structural-biology/rcsb-pdb-entry-summary/SKILL.md
GitHubPurpose
Fetch a structure entry summary from the official RCSB data API using a PDB ID.
When to use
- You already know the PDB accession.
- You want a small, official structural metadata payload.
When not to use
- You need text search across the whole archive.
- You need atom-level coordinate processing.
Inputs
- PDB entry ID
- Optional output path
Outputs
- JSON payload from
data.rcsb.org/rest/v1/core/entry/<id>
Requirements
- Python 3.13+
- Network access to
data.rcsb.org
Procedure
- Run
python3 skills/structural-biology/rcsb-pdb-entry-summary/scripts/fetch_pdb_entry.py --entry-id 4HHB --out skills/structural-biology/rcsb-pdb-entry-summary/assets/4hhb_entry.json. - Review the returned title, resolution, and audit fields.
- Use related RCSB endpoints later for deeper polymer or assembly inspection.
Validation
- Command exits successfully.
- Output includes top-level entry metadata for the requested PDB ID.
Failure modes and fixes
- 404 or empty data: confirm the accession exists and is current.
- Need archive search: use the RCSB search API in a later, separate skill.
Safety and limits
- Metadata lookup only.
- This skill does not download coordinate files or run structural analysis.
Examples
python3 .../fetch_pdb_entry.py --entry-id 1STP
Provenance
- RCSB data API docs: https://data.rcsb.org/redoc/index.html
Related skills
ensembl-gene-lookup