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Rcsb pdb entry summary

Skill ma-compbio-lab/SkillFoundry/skills/structural-biology/rcsb-pdb-entry-summary

A framework for discovering, compiling, and validating reusable skills for scientific agents.

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

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What its author says it does

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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.md

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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

Related skills

  • ensembl-gene-lookup

Keep looking

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