Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.
npxskills add davila7/claude-code-templates--skill pdb-databaseLoading…
RCSB PDB is the worldwide repository for 3D structural data of biological macromolecules. Search for structures, retrieve coordinates and metadata, perform sequence and structure similarity searches across 200,000+ experimentally determined structures and computed models.
This skill should be used when:
Find PDB entries using various search criteria:
Text Search: Search by protein name, keywords, or descriptions
from rcsbapi.search import TextQuery
query = TextQuery("hemoglobin")
results = list(query())
print(f"Found {len(results)} structures")
Attribute Search: Query specific properties (organism, resolution, method, etc.)
from rcsbapi.search import AttributeQuery
from rcsbapi.search.attrs import rcsb_entity_source_organism
# Find human protein structures
query = AttributeQuery(
attribute=rcsb_entity_source_organism.scientific_name,
operator="exact_match",
value="Homo sapiens"
)
results = list(query())
Sequence Similarity: Find structures similar to a given sequence
from rcsbapi.search import SequenceQuery
query = SequenceQuery(
value="MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEKMSKDGKKKKKKSKTKCVIM",
evalue_cutoff=0.1,
identity_cutoff=0.9
)
results = list(query())
Structure Similarity: Find structures with similar 3D geometry
from rcsbapi.search import StructSimilarityQuery
query = StructSimilarityQuery(
structure_search_type="entry",
entry_id="4HHB" # Hemoglobin
)
results = list(query())
Combining Queries: Use logical operators to build complex searches
from rcsbapi.search import TextQuery, AttributeQuery
from rcsbapi.search.attrs import rcsb_entry_info
# High-resolution human proteins
query1 = AttributeQuery(
attribute=rcsb_entity_source_organism.scientific_name,
operator="exact_match",
value="Homo sapiens"
)
query2 = AttributeQuery(
attribute=rcsb_entry_info.resolution_combined,
operator="less",
value=2.0
)
combined_query = query1 & query2 # AND operation
results = list(combined_query())
Access detailed information about specific PDB entries:
Basic Entry Information:
from rcsbapi.data import Schema, fetch
# Get entry-level data
entry_data = fetch("4HHB", schema=Schema.ENTRY)
print(entry_data["struct"]["title"])
print(entry_data["exptl"][0]["method"])
Polymer Entity Information:
# Get protein/nucleic acid information
entity_data = fetch("4HHB_1", schema=Schema.POLYMER_ENTITY)
print(entity_data["entity_poly"]["pdbx_seq_one_letter_code"])
Using GraphQL for Flexible Queries:
from rcsbapi.data import fetch
# Custom GraphQL query
query = """
{
entry(entry_id: "4HHB") {
struct {
title
}
exptl {
method
}
rcsb_entry_info {
resolution_combined
deposited_atom_count
}
}
}
"""
data = fetch(query_type="graphql", query=query)
Retrieve coordinate files in various formats:
Download Methods:
https://files.rcsb.org/download/{PDB_ID}.pdbhttps://files.rcsb.org/download/{PDB_ID}.cifhttps://files.rcsb.org/download/{PDB_ID}.pdb1 (for assembly 1)Example Download:
import requests
pdb_id = "4HHB"
# Download PDB format
pdb_url = f"https://files.rcsb.org/download/{pdb_id}.pdb"
response = requests.get(pdb_url)
with open(f"{pdb_id}.pdb", "w") as f:
f.write(response.text)
# Download mmCIF format
cif_url = f"https://files.rcsb.org/download/{pdb_id}.cif"
response = requests.get(cif_url)
with open(f"{pdb_id}.cif", "w") as f:
f.write(response.text)
Common operations with retrieved structures:
Parse and Analyze Coordinates: Use BioPython or other structural biology libraries to work with downloaded files:
from Bio.PDB import PDBParser
parser = PDBParser()
structure = parser.get_structure("protein", "4HHB.pdb")
# Iterate through atoms
for model in structure:
for chain in model:
for residue in chain:
for atom in residue:
print(atom.get_coord())
Extract Metadata:
from rcsbapi.data import fetch, Schema
# Get experimental details
data = fetch("4HHB", schema=Schema.ENTRY)
resolution = data.get("rcsb_entry_info", {}).get("resolution_combined")
method = data.get("exptl", [{}])[0].get("method")
deposition_date = data.get("rcsb_accession_info", {}).get("deposit_date")
print(f"Resolution: {resolution} Å")
print(f"Method: {method}")
print(f"Deposited: {deposition_date}")
Process multiple structures efficiently:
from rcsbapi.data import fetch, Schema
pdb_ids = ["4HHB", "1MBN", "1GZX"] # Hemoglobin, myoglobin, etc.
results = {}
for pdb_id in pdb_ids:
try:
data = fetch(pdb_id, schema=Schema.ENTRY)
results[pdb_id] = {
"title": data["struct"]["title"],
"resolution": data.get("rcsb_entry_info", {}).get("resolution_combined"),
"organism": data.get("rcsb_entity_source_organism", [{}])[0].get("scientific_name")
}
except Exception as e:
print(f"Error fetching {pdb_id}: {e}")
# Display results
for pdb_id, info in results.items():
print(f"\n{pdb_id}: {info['title']}")
print(f" Resolution: {info['resolution']} Å")
print(f" Organism: {info['organism']}")
Install the official RCSB PDB Python API client:
# Current recommended package
uv pip install rcsb-api
# For legacy code (deprecated, use rcsb-api instead)
uv pip install rcsbsearchapi
The rcsb-api package provides unified access to both Search and Data APIs through the rcsbapi.search and rcsbapi.data modules.
PDB ID: Unique 4-character identifier (e.g., "4HHB") for each structure entry. AlphaFold and ModelArchive entries start with "AF_" or "MA_" prefixes.
mmCIF/PDBx: Modern file format that uses key-value structure, replacing legacy PDB format for large structures.
Biological Assembly: The functional form of a macromolecule, which may contain multiple copies of chains from the asymmetric unit.
Resolution: Measure of detail in crystallographic structures (lower values = higher detail). Typical range: 1.5-3.5 Å for high-quality structures.
Entity: A unique molecular component in a structure (protein chain, DNA, ligand, etc.).
This skill includes reference documentation in the references/ directory:
Comprehensive API documentation covering:
Use this reference when you need in-depth information about API capabilities, complex query construction, or detailed data schema information.
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Set up and use 1Password CLI (op). Use when installing the CLI, enabling desktop app integration, signing in (single or multi-account), or reading/injecting/running secrets via op.
CLI to manage emails via IMAP/SMTP. Use `himalaya` to list, read, write, reply, forward, search, and organize emails from the terminal. Supports multiple accounts and message composition with MML (MIME Meta Language).