Snippet to map alphafold multi-fragment structures to the reference sequence

alphafold_multifragment_file.py

import prody

# Set fname
fname = 'AF-Q96M86-F13-model_v1.cif.gz'

# Use prody to parse AlphaFold structure in mmCIF format
pdb, header = prody.parseMMCIF(fname, header=True)

# extract coordinates of the fragment in the reference sequence 
# e.g. Uniprot AC Q96M86
# remember, that both PDB and Uniprot start counting from 1

# index of first residue
b = int(header[0].search('_ma_target_ref_db_details.seq_db_align_begin').data[0])

# index of last residue
e = int(header[0].search('_ma_target_ref_db_details.seq_db_align_end').data[0])