I am trying to write a script which automatically picks the subunits for a protein complex. Instead of the PDB I am using the IMGT format which is just different numbering system.
For example for 1KJ3, we have:
By looking at the 1KJ3 you can see there are two similar subunits where chains (Q,I,M) and (P,H,L) interact. What is the best way to get this information directly from the PDB file without needing to look at the structures? Should I calculate distances among chains?
FYI I am using Python & BioPython.