Rcsb pdb entry summary

Skill ma-compbio-lab/SkillFoundry/skills/structural-biology/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.From its SKILL.md

Install

npx -y skills add ma-compbio-lab/SkillFoundry --skill rcsb-pdb-entry-summary

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SKILL.md

1.6 KB, 352 tokens by cl100k_base, as published. Nobody here has run it

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

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

What ships with it: 7 files

35.2 KB alongside SKILL.md, 1 of them executable