Aligning PDB structures with Biopython

You can use the Bio.PDB module in Biopython to align PDB files. This is how I did it. The code should be pretty much self-explanatory.

In this example I align the crystal structure of Ubiquitin (PDB code: 1UBQ) to the first structure of a corresponding NMR ensemble (PDB code: 1D3Z, see picture below).

	# The MIT License
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	# Copyright (c) 2010-2016 Anders S. Christensen
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	# THE SOFTWARE.
	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")

view raw align.py hosted with ❤ by GitHub