rcsb_database

Research

RCSB Protein Data Bank (PDB) — experimentally determined 3D biomolecular structures. Search by full-text/sequence/structure/attribute, fetch entry metadata, download coordinate files (PDB/mmCIF). Use when the user provides a PDB ID, asks for structures of a protein, wants to find similar structures by sequence, or needs experimental (not predicted) coordinates. Don't use for AlphaFold predictions (use alphafold_database).

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RCSB Protein Data Bank

Overview

The RCSB PDB hosts >200K experimentally-determined biomolecular structures (X-ray, cryo-EM, NMR, etc.). This skill exposes 3 download tools and 1 search tool.

Project Tools (VenusFactory2)

Tool	Args	Returns	Description
download_rcsb_search_by_query	`query` (JSON string or dict — Search API v2 query block or full payload), `out_dir` (required), `return_type` (default `"entry"`; `entry` \| `assembly` \| `polymer_entity` \| `non_polymer_entity` \| `polymer_instance` \| `mol_definition`), `page_start`/`rows` (pagination; default = return all hits), `sort_by` (e.g. `score`, `rcsb_accession_info.initial_release_date`), `sort_direction` (`asc` \| `desc`), `count_only` (skip results, return only `total_count`), `timeout` (default `60`s)	JSON: `{status, file_info {file_path → rcsb_search_<return_type>.json}, content_preview (first 25 ids), biological_metadata {return_type, total_count, result_count, page_start, rows, sort_by, search_time_ms}}`	Run an RCSB Search API v2 query (text / sequence / structure / attribute).
download_rcsb_entry_metadata_by_pdb_id	`pdb_id` (required, e.g. `4HHB`), `out_path` (required, JSON path)	rich JSON envelope; saves metadata JSON to `out_path`	Fetch full entry metadata for one PDB ID.
download_rcsb_structure_by_pdb_id	`pdb_id` (required), `out_dir` (required), `file_type` (default `pdb`; `pdb` \| `cif` \| `xml`)	rich JSON envelope; structure file at `file_info.file_path`	Download coordinate file.

When to Use This Skill

User provides a PDB ID and asks for the structure / metadata
"Find structures of X" / "find structures similar to this sequence" → download_rcsb_search_by_query with the right service
Build a workflow that pipes RCSB structures into PyMOL (render_protein_structure) or Foldseek

Search API v2 Query Cookbook

Pass query as a dict / JSON-string of a query block (auto-wrapped into {"query": ...}) or a full request payload.

Full-text:

{"type": "terminal", "service": "full_text", "parameters": {"value": "hemoglobin"}}

By sequence (BLAST-like, fast, e-value cutoff):

{
  "type": "terminal", "service": "sequence",
  "parameters": {
    "evalue_cutoff": 0.1, "identity_cutoff": 0.95,
    "sequence_type": "protein",
    "value": "MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFF..."
  }
}

By attribute (e.g. resolution, organism, year):

{
  "type": "group", "logical_operator": "and",
  "nodes": [
    {"type": "terminal", "service": "text",
     "parameters": {"attribute": "rcsb_entry_info.resolution_combined",
                    "operator": "less", "value": 2.0}},
    {"type": "terminal", "service": "text",
     "parameters": {"attribute": "rcsb_entity_source_organism.taxonomy_lineage.name",
                    "operator": "exact_match", "value": "Homo sapiens"}}
  ]
}

Boolean combination: use {"type": "group", "logical_operator": "and"|"or", "nodes": [...]}.

Return Type → Identifier Shape

return_type	identifier shape
`entry`	`4HHB` (PDB ID)
`assembly`	`4HHB-1`
`polymer_entity`	`4HHB-1` (entity ID)
`polymer_instance`	`4HHB.A` (chain)
`mol_definition`	`HEM` (ligand 3-letter code)

Common Mistakes

Passing a Python query dict expecting URL-encoding: dicts are serialized & url-encoded automatically; pass the dict, not a hand-crafted URL.
Forgetting return_type: defaults to entry (PDB IDs). If you want chain identifiers, pass polymer_instance.
Using count_only=True and then trying to read result_set: count-only mode returns {"total_count": N} only, no result_set.
Sequence searches with identity_cutoff too strict: try lower (e.g. 0.3) if you get few hits.