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rcsb-pdb-skill

Submit compact RCSB PDB requests for core metadata, Search API queries, and FASTA downloads. Use when a user wants concise RCSB summaries; save raw JSON or FASTA only on request.

Stars
1,305
Source
openai/plugins
Updated
2026-05-30
Slug
openai--plugins--rcsb-pdb-skill
View on GitHubRaw SKILL.md

// install — copy + paste into any project

mkdir -p .claude/skills && curl -fsSL https://raw.githubusercontent.com/openai/plugins/HEAD/plugins/life-science-research/skills/rcsb-pdb-skill/SKILL.md -o .claude/skills/rcsb-pdb-skill.md

Drops the SKILL.md into .claude/skills/rcsb-pdb-skill.md. Works with Claude Code, Cursor, and any agent that loads SKILL.md files from .claude/skills/.

Operating rules

  • Use scripts/rest_request.py for all RCSB PDB and Search API calls.
  • Use base_url=https://data.rcsb.org/rest/v1 for core metadata, https://search.rcsb.org/rcsbsearch/v2 for Search API, and https://www.rcsb.org for FASTA downloads.
  • Core entry or assembly lookups usually do not need max_items; Search API results are better with query pager rows around 10 and max_items=10.
  • Re-run requests in long conversations instead of relying on older tool output.
  • Treat displayed ... in tool previews as UI truncation, not literal request content.

Execution behavior

  • Return concise markdown summaries from the script JSON by default.
  • Prefer core metadata endpoints for focused lookups and Search API POST requests for discovery.
  • For FASTA downloads, use response_format=text so the script returns a short text_head unless raw output is requested.

Input

  • Read one JSON object from stdin.
  • Required fields: base_url, path
  • Optional fields: method, params, headers, json_body, form_body, record_path, response_format, max_items, max_depth, timeout_sec, save_raw, raw_output_path
  • Common RCSB patterns:
    • {"base_url":"https://data.rcsb.org/rest/v1","path":"core/entry/4hhb"}
    • {"base_url":"https://search.rcsb.org/rcsbsearch/v2","path":"query","method":"POST","json_body":{"query":{"type":"terminal","service":"full_text","parameters":{"value":"hemoglobin"}},"return_type":"entry","request_options":{"pager":{"start":0,"rows":10}}},"record_path":"result_set","max_items":10}
    • {"base_url":"https://www.rcsb.org","path":"fasta/entry/4HHB/download","response_format":"text"}

Output

  • Success returns ok, source, path, method, status_code, warnings, and either compact records, a compact summary, or text_head.
  • Use raw_output_path when save_raw=true.
  • Failure returns ok=false with error.code and error.message.

Execution

echo '{"base_url":"https://data.rcsb.org/rest/v1","path":"core/entry/4hhb"}' | python scripts/rest_request.py

References

  • No additional runtime references are required; keep the import package limited to this file and scripts/rest_request.py.