Operating rules

Use scripts/rest_request.py for all AlphaFold API calls.
Use base_url=https://alphafold.ebi.ac.uk/api.
The script accepts max_items, but set it explicitly only when trimming array-heavy responses; single-entry lookups usually do not need it.
For sequence/summary or annotations, start around max_items=3 to 5.
Re-run the request if the conversation is long instead of trusting older tool output.
Treat displayed ... in tool previews as UI truncation, not part of the real request.
If the user asks for full JSON, set save_raw=true and report the saved file path instead of pasting the payload into chat.

Execution behavior

Return concise markdown summaries from the script JSON by default.
Return the script JSON verbatim only if the user explicitly asks for machine-readable output.
Prefer these paths: prediction/<qualifier>, uniprot/summary/<qualifier>.json, sequence/summary, and annotations/<qualifier>.json.
Keep sequence-style inputs compact and prefer rerunning instead of copying prior output back into context.