Version Compatibility
Reference examples tested with: BioPython 1.83+, scanpy 1.10+
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package> then help(module.function) to check signatures
If code throws ImportError, AttributeError, or TypeError, introspect the installed
package and adapt the example to match the actual API rather than retrying.
Structure I/O
"Read a PDB file" → Parse protein structure files (PDB, mmCIF, MMTF), download from RCSB PDB, and write structures to various formats.
- Python:
Bio.PDB.PDBParser().get_structure('id', 'file.pdb'), Bio.PDB.MMCIFParser()
Parse, download, and write protein structure files in PDB, mmCIF, and MMTF formats.
Required Imports
from Bio.PDB import PDBParser, MMCIFParser, PDBIO, MMCIFIO, PDBList
from Bio.PDB.MMCIF2Dict import MMCIF2Dict
Supported Formats
| Format | Parser | Writer | Description |
|---|
| PDB | PDBParser | PDBIO | Legacy format, limited to 99999 atoms |
| mmCIF | MMCIFParser | MMCIFIO | Modern standard, full metadata |
| MMTF | MMTFParser | - | Compact binary (read-only in Biopython) |
| BinaryCIF | BinaryCIFParser | - | Compact binary, RCSB recommended |
Parsing PDB Files
from Bio.PDB import PDBParser
parser = PDBParser(QUIET=True)
structure = parser.get_structure('1abc', '1abc.pdb')
print(f'Structure ID: {structure.id}')
print(f'Number of models: {len(list(structure.get_models()))}')
print(f'Number of chains: {len(list(structure.get_chains()))}')
print(f'Number of residues: {len(list(structure.get_residues()))}')
print(f'Number of atoms: {len(list(structure.get_atoms()))}')
Parsing mmCIF Files
from Bio.PDB import MMCIFParser
parser = MMCIFParser(QUIET=True)
structure = parser.get_structure('1abc', '1abc.cif')
# mmCIF is the modern standard - use for new workflows
print(f'Structure: {structure.id}')
Parsing MMTF Files
from Bio.PDB.MMTFParser import MMTFParser
parser = MMTFParser()
structure = parser.get_structure('1abc.mmtf')
Parsing BinaryCIF Files
from Bio.PDB import BinaryCIFParser
parser = BinaryCIFParser()
structure = parser.get_structure('1abc', '1abc.bcif')
Downloading from RCSB PDB
from Bio.PDB import PDBList
pdbl = PDBList()
# Download single structure (mmCIF by default)
file_path = pdbl.retrieve_pdb_file('1ABC', pdir='.', file_format='mmCif')
print(f'Downloaded: {file_path}')
# Download as PDB format
file_path = pdbl.retrieve_pdb_file('1ABC', pdir='.', file_format='pdb')
# Download biological assembly
file_path = pdbl.retrieve_pdb_file('1ABC', pdir='.', file_format='mmCif', assembly_num=1)
# Get list of all PDB entries
all_entries = pdbl.get_all_entries()
print(f'Total PDB entries: {len(all_entries)}')
# Get obsolete entries
obsolete = pdbl.get_all_obsolete()
Batch Downloading
from Bio.PDB import PDBList
pdbl = PDBList()
pdb_ids = ['1ABC', '2XYZ', '3DEF']
for pdb_id in pdb_ids:
file_path = pdbl.retrieve_pdb_file(pdb_id, pdir='structures/', file_format='mmCif')
print(f'Downloaded: {pdb_id}')
Writing PDB Files
from Bio.PDB import PDBParser, PDBIO
parser = PDBParser(QUIET=True)
structure = parser.get_structure('1abc', '1abc.pdb')
io = PDBIO()
io.set_structure(structure)
io.save('output.pdb')
Writing mmCIF Files
from Bio.PDB import MMCIFParser, MMCIFIO
parser = MMCIFParser(QUIET=True)
structure = parser.get_structure('1abc', '1abc.cif')
io = MMCIFIO()
io.set_structure(structure)
io.save('output.cif')
Selective Output with Select Class
from Bio.PDB import PDBParser, PDBIO, Select
class ChainSelect(Select):
def __init__(self, chain_id):
self.chain_id = chain_id
def accept_chain(self, chain):
return chain.id == self.chain_id
parser = PDBParser(QUIET=True)
structure = parser.get_structure('1abc', '1abc.pdb')
io = PDBIO()
io.set_structure(structure)
io.save('chain_A.pdb', ChainSelect('A'))
Select Class Methods
from Bio.PDB import Select
class CustomSelect(Select):
def accept_model(self, model):
return model.id == 0 # Only first model
def accept_chain(self, chain):
return chain.id in ['A', 'B'] # Only chains A and B
def accept_residue(self, residue):
return residue.id[0] == ' ' # Exclude hetero residues
def accept_atom(self, atom):
return atom.element != 'H' # Exclude hydrogens
Extracting Header Information
from Bio.PDB import PDBParser
parser = PDBParser(QUIET=True)
structure = parser.get_structure('1abc', '1abc.pdb')
header = structure.header
print(f"Name: {header.get('name', 'Unknown')}")
print(f"Resolution: {header.get('resolution', 'N/A')}")
print(f"Structure method: {header.get('structure_method', 'Unknown')}")
print(f"Deposition date: {header.get('deposition_date', 'Unknown')}")
mmCIF Metadata with MMCIF2Dict
from Bio.PDB.MMCIF2Dict import MMCIF2Dict
mmcif_dict = MMCIF2Dict('1abc.cif')
# Access any mmCIF field
print(f"Entry ID: {mmcif_dict['_entry.id']}")
print(f"Resolution: {mmcif_dict.get('_refine.ls_d_res_high', ['N/A'])[0]}")
print(f"Method: {mmcif_dict.get('_exptl.method', ['Unknown'])[0]}")
# List all available fields
print(f"Available fields: {len(mmcif_dict.keys())}")
Quick Structure Inspection
from Bio.PDB import PDBParser
parser = PDBParser(QUIET=True)
structure = parser.get_structure('1abc', '1abc.pdb')
print(f'Models: {[m.id for m in structure]}')
for model in structure:
print(f' Model {model.id}:')
for chain in model:
residues = list(chain.get_residues())
atoms = list(chain.get_atoms())
print(f' Chain {chain.id}: {len(residues)} residues, {len(atoms)} atoms')
Format Conversion
from Bio.PDB import PDBParser, MMCIFParser, PDBIO, MMCIFIO
# PDB to mmCIF
parser = PDBParser(QUIET=True)
structure = parser.get_structure('prot', 'protein.pdb')
io = MMCIFIO()
io.set_structure(structure)
io.save('protein.cif')
# mmCIF to PDB
parser = MMCIFParser(QUIET=True)
structure = parser.get_structure('prot', 'protein.cif')
io = PDBIO()
io.set_structure(structure)
io.save('protein.pdb')
Writing PQR Files
from Bio.PDB import PDBParser, PDBIO
parser = PDBParser(QUIET=True)
structure = parser.get_structure('1abc', '1abc.pdb')
# PQR format includes charge and radius instead of occupancy and B-factor
io = PDBIO(is_pqr=True)
io.set_structure(structure)
io.save('output.pqr')
Handling Parser Warnings
from Bio.PDB import PDBParser
import warnings
# Suppress warnings
parser = PDBParser(QUIET=True)
# Or capture warnings
parser = PDBParser(QUIET=False)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
structure = parser.get_structure('1abc', '1abc.pdb')
if w:
print(f'Warnings: {len(w)}')
for warning in w:
print(f' {warning.message}')
Related Skills
- structure-navigation - Traverse SMCRA hierarchy to access chains, residues, atoms
- geometric-analysis - Measure distances, angles, and superimpose structures
- structure-modification - Modify coordinates and properties before writing
- database-access/entrez-fetch - Fetch structure metadata from NCBI/UniProt