How to align two PDB structures using the Bio.PDB module in Biopython

align.py

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import Bio.PDB

# Select what residues numbers you wish to align
# and put them in a list
start_id = 1
end_id   = 70
atoms_to_be_aligned = range(start_id, end_id + 1)

# Start the parser
pdb_parser = Bio.PDB.PDBParser(QUIET = True)

# Get the structures
ref_structure = pdb_parser.get_structure("reference", "1D3Z.pdb")
sample_structure = pdb_parser.get_structure("samle", "1UBQ.pdb")

# Use the first model in the pdb-files for alignment
# Change the number 0 if you want to align to another structure
ref_model    = ref_structure[0]
sample_model = sample_structure[0]

# Make a list of the atoms (in the structures) you wish to align.
# In this case we use CA atoms whose index is in the specified range
ref_atoms = []
sample_atoms = []

# Iterate of all chains in the model in order to find all residues
for ref_chain in ref_model:
  # Iterate of all residues in each model in order to find proper atoms
  for ref_res in ref_chain:
    # Check if residue number ( .get_id() ) is in the list
    if ref_res.get_id()[1] in atoms_to_be_aligned:
      # Append CA atom to list
      ref_atoms.append(ref_res['CA'])

# Do the same for the sample structure
for sample_chain in sample_model:
  for sample_res in sample_chain:
    if sample_res.get_id()[1] in atoms_to_be_aligned:
      sample_atoms.append(sample_res['CA'])

# Now we initiate the superimposer:
super_imposer = Bio.PDB.Superimposer()
super_imposer.set_atoms(ref_atoms, sample_atoms)
super_imposer.apply(sample_model.get_atoms())

# Print RMSD:
print super_imposer.rms

# Save the aligned version of 1UBQ.pdb
io = Bio.PDB.PDBIO()
io.set_structure(sample_structure) 
io.save("1UBQ_aligned.pdb")

Hi, I'm trying to apply your code and I've found that changing the reference and the sample it doesn't work. It just superimposes the output pdb with the sample, but not with the reference.

I tried just changing:

ref_structure = pdb_parser.get_structure("reference", "1D3Z.pdb")
sample_structure = pdb_parser.get_structure("samle", "1UBQ.pdb")

by:

ref_structure = pdb_parser.get_structure("reference", "1UBQ.pdb")
sample_structure = pdb_parser.get_structure("samle", "1D3Z.pdb")

Is there something that can be done? Thanks.

I am trying this 👍

import Bio.PDB

Select what residues numbers you wish to align

and put them in a list

start_id = 1
end_id = 70
atoms_to_be_aligned = range(start_id, end_id + 1)

Start the parser

pdb_parser = Bio.PDB.PDBParser(QUIET = True)

Get the structures

ref_structure = pdb_parser.get_structure("reference", "1bbh.pdb")
sample_structure = pdb_parser.get_structure("sample", "5gyr.pdb")

Use the first model in the pdb-files for alignment

Change the number 0 if you want to align to another structure

ref_model = ref_structure[0]
sample_model = sample_structure[0]

Make a list of the atoms (in the structures) you wish to align.

In this case we use CA atoms whose index is in the specified range

ref_atoms = []
sample_atoms = []

Iterate of all chains in the model in order to find all residues

for ref_chain in ref_model:

Iterate of all residues in each model in order to find proper atoms

for ref_res in ref_chain:
# Check if residue number ( .get_id() ) is in the list
if ref_res.get_id()[1] in atoms_to_be_aligned:
# Append CA atom to list
ref_atoms.append(ref_res['CA'])

Do the same for the sample structure

for sample_chain in sample_model:
for sample_res in sample_chain:
if sample_res.get_id()[1] in atoms_to_be_aligned:
sample_atoms.append(sample_res['CA'])

Now we initiate the superimposer:

super_imposer = Bio.PDB.Superimposer()
super_imposer.set_atoms(ref_atoms, sample_atoms)
super_imposer.apply(sample_model.get_atoms())

Print RMSD:

print (super_imposer.rms)

Save the aligned version of 1UBQ.pdb

io = Bio.PDB.PDBIO()
io.set_structure(sample_structure)
io.save("2_aligned.pdb")

but is giving me the following error :
PDBException: Fixed and moving atom lists differ in size