1. uv

   : Read the

   uv

   skill and follow its Setup instructions to ensure

   uv

   is installed and on PATH.
2. User Notification: If LICENSE_NOTIFICATION.txt does not already exist in this skill 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.

• 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.

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.

• Entity: A unique molecule found in a structure.
• Instance / Chain: A particular copy of an entity. E.g. if a structure contains two protein chains with the same sequence, they are the same entity but different instances / chains.
• Assembly: A biologically relevant collection of instances / chains. This may be the same as the deposited structure, a subset, or multiple copies.
• Label vs Auth: Polymer instances get letter labels ("A", "B", "AA") and their monomers are numbered. There are author-assigned ("auth") and PDB-internal ("label") schemes. The label scheme is more consistent and is always used in scripts and APIs. However, users and papers may refer to the author scheme (clarify which scheme is being used if necessary).
• Chemical component: A small molecule / monomer, with an ID matching

  [A-Z]{1,3}

• Primary citation: The main publication about a structure. Prefer

  primary_citation

  attributes over

  citation

  attributes.
• Resolution: Frequently used measure of structure quality (lower is better). Usually prefer

  rcsb_entry_info.resolution_combined

  , which accounts for different experimental methods.

uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "full_text", "parameters": { "value": "isopeptide + ( collagen | fibrinogen )" } }' --return_type entry --output results.json

Important: use

full_text

search as a last resort when there's no more precise attribute search available. Consider using the

struct.title

or

rcsb_pubmed_abstract_text

attributes instead.

1. Fetch the schema for the relevant object type. E.g.

   uv run scripts/fetch_schema.py --api data_entry --output schema_entry.txt

2. Grep the schema for relevant fields (one keyword at a time, many lines).
3. Compose and run a GraphQL metadata query:

   uv run scripts/fetch_pdb_metadata.py --query '<GraphQL>' --output results.json