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skill CX Codex GP ChatGPT official · OpenAI

rcsb-pdb-skill — Codex skill: what it does, how to install

This skill sends RCSB PDB requests for metadata, search results, and FASTA. Use it when an agent needs compact structure-data summaries.

Install into Codex · Skills CLI (Vercel) All methods and platforms ↓ 
npx skills add openai/plugins --skill rcsb-pdb-skill -a codex
Open on GitHub

What rcsb-pdb-skill does

rcsb-pdb-skill lets Codex query RCSB PDB. It handles core metadata for entries and assemblies, POST requests to the Search API, and FASTA downloads. By default, the agent returns a concise markdown summary; raw JSON or FASTA is saved only when requested.

The skill includes scripts/rest_request.py. The script reads one JSON object from stdin and accepts request parameters, headers, request bodies, record paths, response formats, and raw-output settings. FASTA requests can return a short text head, while API calls can return compact records or a summary. In a long conversation, repeat requests because earlier tool output may no longer be current.

Install it when your Codex or ChatGPT workflow needs RCSB PDB data. It is a poor fit for sources outside RCSB PDB.

What it helps with

  • look up an RCSB PDB entry by text
  • retrieve entry or assembly metadata
  • download a record's FASTA file
  • summarize a Search API response

Example prompts for the agent

  • Search RCSB PDB for hemoglobin and return 10 results.
  • Get the core metadata for entry 4hhb.
  • Download the FASTA for 4HHB and show its text head.

How to install rcsb-pdb-skill

1Skills CLI (Vercel)

npx skills add openai/plugins --skill rcsb-pdb-skill -a codex

2Manually: put the files in place

.agents/skills/rcsb-pdb-skill/SKILL.md

For all projects use ~/.agents/skills/

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Questions about rcsb-pdb-skill

How do I install rcsb-pdb-skill in Codex?

Run npx skills add openai/plugins --skill rcsb-pdb-skill. The skill file is placed at .agents/skills/rcsb-pdb-skill/SKILL.md.

What does rcsb-pdb-skill do?

It sends RCSB PDB requests and returns concise results for metadata lookups, Search API queries, and FASTA downloads. Raw output is saved only when requested.

Which platforms does rcsb-pdb-skill support?

The skill is intended for Codex and ChatGPT. Its API calls run through scripts/rest_request.py, which reads one JSON object from stdin.

See also

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