rcsb-pdb-skill

Imported from openai/plugins (plugins/life-science-research/skills/rcsb-pdb-skill/SKILL.md). Install upstream with npx skills add openai/plugins --skill rcsb-pdb-skill. Copyright stays with the author.

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.