rcsb-pdb-entry-summary

name	rcsb-pdb-entry-summary
description	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.

Purpose

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

1. 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.
2. Review the returned title, resolution, and audit fields.
3. 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