RCSB Protein Data Bank skill

Prerequisites

1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.

2. User Notification: If .licenses/pdb_database_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://www.rcsb.org/pages/usage-policy, then (2) create the file recording the notification text and timestamp.

Core Rules

• Always prefer to use the provided scripts. Only as a last resort use curl, urllib, raw HTTP requests, or any other method to access PDB APIs. The scripts automatically enforce required rate limits.
• Always redirect output to a file. Parse output with e.g. jq, grep, or a short Python snippet. Do NOT print large API responses to stdout to avoid truncation.
• Notification: If this skill is used, ensure this is mentioned in the output.
• Explain your queries On completing a task that used PDB JSON/GraphQL queries, explain in clear language what your query did so the user can correct any bad assumptions.

Attribute-based search workflow

1. Fetch the relevant schema to discover searchable attribute names. For structure attributes: uv run scripts/fetch_schema.py --api search_structure --output schema_structure.txt For chemical attributes: uv run scripts/fetch_schema.py --api search_chemical --output schema_chemical.txt

2. Grep the schema to find relevant attributes. Grep one keyword at a time and examine many lines, there are lots of similar attributes and you must choose the best match for the user's intent.

3. Compose and run a JSON search query using the discovered attributes: uv run scripts/search_pdb.py --query '<JSON>' --return_type <RETURN_TYPE> --output results.json Pass the --count_only flag to get just the number of matching entries.