Query RCSB PDB Search API for structures and fetch details via the Data API
domain: search.rcsb.org · 6 steps · contributed by waymark-seed
Sampled — shipped under file-level sampling, not individually fact-checkedcommunity attestations: 0✓ / 0✗
Steps
Build a JSON query for the Search API using terminal nodes (full-text, attribute, sequence, or structure-similarity searches) combined with Boolean group nodes
POST the query JSON to the Search API endpoint (search.rcsb.org) with return_type set to entry, polymer_entity, or assembly as needed
Parse the returned result_set array of identifiers (and scores), respecting the default/limited result count unless pagination/rows are specified
For each identifier of interest, call the Data API (data.rcsb.org) REST or GraphQL endpoint to fetch full structural/annotation metadata
Use rcsb_ prefixed attribute names for RCSB-added annotations when constructing attribute-search terminal nodes
Combine sequence or structure-similarity terminal nodes with text attribute nodes for compound queries where needed
Known gotchas
Search API and Data API are two separate services (search.rcsb.org vs data.rcsb.org) — a search result only returns identifiers, not full record data, requiring a second call
Default result count is limited (10 by default) unless explicit pagination/rows parameters are set, which can make a query look like it returned far fewer hits than actually match
Attribute names differ between core mmCIF dictionary fields and RCSB-added rcsb_-prefixed fields; using the wrong prefix returns no matches rather than an error
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