tools-only Structure Modification
Transform coordinates, remove/add entities, modify properties, and build structures programmatically.
Required Imports
from Bio.PDB import PDBParser, PDBIO, StructureBuilder
from Bio.PDB.Structure import Structure
from Bio.PDB.Model import Model
from Bio.PDB.Chain import Chain
from Bio.PDB.Residue import Residue
from Bio.PDB.Atom import Atom
import numpy as np
Transforming Coordinates
from Bio.PDB import PDBParser, PDBIO
import numpy as np
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
# Translate all atoms
translation = np.array([10.0, 0.0, 0.0])
for atom in structure.get_atoms():
atom.coord = atom.coord + translation
# Save transformed structure
io = PDBIO()
io.set_structure(structure)
io.save('translated.pdb')
Rotation Around Axis
from Bio.PDB import PDBParser
from Bio.PDB.vectors import rotaxis
import numpy as np
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
# Rotate around Z axis by 90 degrees
angle = np.radians(90)
axis = np.array([0, 0, 1])
# Get center of mass for rotation origin
coords = np.array([a.coord for a in structure.get_atoms()])
center = coords.mean(axis=0)
# Rotation matrix
cos_a = np.cos(angle)
sin_a = np.sin(angle)
rot_matrix = np.array([
[cos_a, -sin_a, 0],
[sin_a, cos_a, 0],
[0, 0, 1]
])
# Apply rotation around center
for atom in structure.get_atoms():
atom.coord = np.dot(rot_matrix, atom.coord - center) + center
Applying Transformation Matrix
from Bio.PDB import PDBParser
import numpy as np
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
# 4x4 transformation matrix (rotation + translation)
# From superimposition or external source
transform = np.array([
[1.0, 0.0, 0.0, 10.0],
[0.0, 1.0, 0.0, 5.0],
[0.0, 0.0, 1.0, 0.0],
[0.0, 0.0, 0.0, 1.0]
])
rotation = transform[:3, :3]
translation = transform[:3, 3]
for atom in structure.get_atoms():
atom.coord = np.dot(rotation, atom.coord) + translation
Center Structure at Origin
from Bio.PDB import PDBParser
import numpy as np
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
# Calculate center
coords = np.array([a.coord for a in structure.get_atoms()])
center = coords.mean(axis=0)
# Translate to origin
for atom in structure.get_atoms():
atom.coord = atom.coord - center
Removing Atoms
from Bio.PDB import PDBParser, PDBIO
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
# Remove hydrogens
for residue in structure.get_residues():
atoms_to_remove = [a.id for a in residue if a.element == 'H']
for atom_id in atoms_to_remove:
residue.detach_child(atom_id)
io = PDBIO()
io.set_structure(structure)
io.save('no_hydrogens.pdb')
Removing Residues
from Bio.PDB import PDBParser, PDBIO
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
# Remove water molecules
for model in structure:
for chain in model:
residues_to_remove = [r.id for r in chain if r.id[0] == 'W']
for res_id in residues_to_remove:
chain.detach_child(res_id)
io = PDBIO()
io.set_structure(structure)
io.save('no_water.pdb')
Removing a Chain
from Bio.PDB import PDBParser, PDBIO
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
# Remove chain B
model = structure[0]
if model.has_id('B'):
model.detach_child('B')
io = PDBIO()
io.set_structure(structure)
io.save('without_chain_B.pdb')
Modifying B-factors
from Bio.PDB import PDBParser, PDBIO
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
# Set all B-factors to same value
for atom in structure.get_atoms():
atom.bfactor = 20.0
# Or set based on residue property (e.g., conservation score)
conservation_scores = {100: 9.0, 101: 5.0, 102: 3.0} # resnum -> score
for residue in structure.get_residues():
resnum = residue.id[1]
score = conservation_scores.get(resnum, 5.0)
for atom in residue:
atom.bfactor = score * 10 # Scale to B-factor range
io = PDBIO()
io.set_structure(structure)
io.save('modified_bfactor.pdb')
Modifying Occupancy
from Bio.PDB import PDBParser, PDBIO
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
# Set occupancy for specific chain
for atom in structure[0]['A'].get_atoms():
atom.occupancy = 0.5
io = PDBIO()
io.set_structure(structure)
io.save('modified_occupancy.pdb')
Renumbering Residues
from Bio.PDB import PDBParser, PDBIO
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
chain = structure[0]['A']
# Renumber sequentially starting from 1
new_residues = []
for i, residue in enumerate(chain, start=1):
hetfield, _, icode = residue.id
new_id = (hetfield, i, icode)
residue.id = new_id
new_residues.append(residue)
io = PDBIO()
io.set_structure(structure)
io.save('renumbered.pdb')
Changing Chain ID
from Bio.PDB import PDBParser, PDBIO
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
# Rename chain A to X
model = structure[0]
chain = model['A']
chain.id = 'X'
io = PDBIO()
io.set_structure(structure)
io.save('renamed_chain.pdb')
Building Structure from Scratch
from Bio.PDB.Structure import Structure
from Bio.PDB.Model import Model
from Bio.PDB.Chain import Chain
from Bio.PDB.Residue import Residue
from Bio.PDB.Atom import Atom
from Bio.PDB import PDBIO
import numpy as np
# Create hierarchy
structure = Structure('new_struct')
model = Model(0)
chain = Chain('A')
residue = Residue((' ', 1, ' '), 'ALA', '')
# Add atoms
ca = Atom('CA', np.array([0.0, 0.0, 0.0]), 20.0, 1.0, ' ', 'CA', 1, 'C')
cb = Atom('CB', np.array([1.5, 0.0, 0.0]), 20.0, 1.0, ' ', 'CB', 2, 'C')
residue.add(ca)
residue.add(cb)
chain.add(residue)
model.add(chain)
structure.add(model)
io = PDBIO()
io.set_structure(structure)
io.save('new_structure.pdb')
Using StructureBuilder
from Bio.PDB import StructureBuilder, PDBIO
import numpy as np
sb = StructureBuilder.StructureBuilder()
sb.init_structure('built')
sb.init_model(0)
sb.init_chain('A')
sb.init_seg(' ')
# Add residue with atoms
sb.init_residue('ALA', ' ', 1, ' ')
sb.init_atom('N', np.array([-1.0, 0.0, 0.0]), 20.0, 1.0, ' ', 'N', 1, 'N')
sb.init_atom('CA', np.array([0.0, 0.0, 0.0]), 20.0, 1.0, ' ', 'CA', 2, 'C')
sb.init_atom('C', np.array([1.0, 0.0, 0.0]), 20.0, 1.0, ' ', 'C', 3, 'C')
sb.init_atom('O', np.array([1.5, 1.0, 0.0]), 20.0, 1.0, ' ', 'O', 4, 'O')
sb.init_residue('GLY', ' ', 2, ' ')
sb.init_atom('N', np.array([1.5, -1.0, 0.0]), 20.0, 1.0, ' ', 'N', 5, 'N')
sb.init_atom('CA', np.array([2.5, -1.0, 0.0]), 20.0, 1.0, ' ', 'CA', 6, 'C')
sb.init_atom('C', np.array([3.5, -1.0, 0.0]), 20.0, 1.0, ' ', 'C', 7, 'C')
sb.init_atom('O', np.array([4.0, 0.0, 0.0]), 20.0, 1.0, ' ', 'O', 8, 'O')
structure = sb.get_structure()
io = PDBIO()
io.set_structure(structure)
io.save('built_structure.pdb')
Adding a Residue to Existing Chain
from Bio.PDB import PDBParser, PDBIO
from Bio.PDB.Residue import Residue
from Bio.PDB.Atom import Atom
import numpy as np
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
chain = structure[0]['A']
# Create new residue
new_residue = Residue((' ', 999, ' '), 'ALA', '')
ca = Atom('CA', np.array([50.0, 50.0, 50.0]), 20.0, 1.0, ' ', 'CA', 9999, 'C')
new_residue.add(ca)
# Add to chain
chain.add(new_residue)
io = PDBIO()
io.set_structure(structure)
io.save('with_new_residue.pdb')
Copying a Chain
from Bio.PDB import PDBParser, PDBIO
from Bio.PDB.Chain import Chain
from Bio.PDB.Residue import Residue
from Bio.PDB.Atom import Atom
import copy
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
# Deep copy chain A as chain B
original_chain = structure[0]['A']
new_chain = Chain('B')
for residue in original_chain:
new_residue = Residue(residue.id, residue.resname, residue.segid)
for atom in residue:
new_atom = Atom(
atom.name, atom.coord.copy(), atom.bfactor, atom.occupancy,
atom.altloc, atom.fullname, atom.serial_number, atom.element
)
new_residue.add(new_atom)
new_chain.add(new_residue)
structure[0].add(new_chain)
io = PDBIO()
io.set_structure(structure)
io.save('duplicated_chain.pdb')
Extract and Save Specific Residues
from Bio.PDB import PDBParser, PDBIO
from Bio.PDB.Structure import Structure
from Bio.PDB.Model import Model
from Bio.PDB.Chain import Chain
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
# Extract residues 50-100
new_structure = Structure('subset')
new_model = Model(0)
new_chain = Chain('A')
for residue in structure[0]['A']:
if 50 <= residue.id[1] <= 100 and residue.id[0] == ' ':
new_chain.add(residue.copy())
new_model.add(new_chain)
new_structure.add(new_model)
io = PDBIO()
io.set_structure(new_structure)
io.save('residues_50_100.pdb')
Merge Two Structures
from Bio.PDB import PDBParser, PDBIO
parser = PDBParser(QUIET=True)
struct1 = parser.get_structure('s1', 'structure1.pdb')
struct2 = parser.get_structure('s2', 'structure2.pdb')
# Add chains from struct2 to struct1 (rename to avoid conflicts)
for chain in struct2[0]:
new_id = chr(ord(chain.id) + 10) # Offset chain ID
chain.id = new_id
struct1[0].add(chain)
io = PDBIO()
io.set_structure(struct1)
io.save('merged.pdb')
Related Skills
- structure-io - Parse and write structure files
- structure-navigation - Access chains, residues, atoms
- geometric-analysis - Calculate distances, angles, RMSD
- sequence-manipulation/seq-objects - Generate sequences from modified structures