| name | rcsb_database |
| description | 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). |
| license | Unknown |
| metadata | {"skill-author":"VenusFactory2."} |
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 60s) | 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.
References
