`run_prediction.py` output PDB files do not contain multiple chains

[kamurani]

Hello,

Apologies if I've misunderstood a crucial step in using the TCRdock tool.

I have successfully generated a pdb file of a TCRpMHC complex and wish to compare it to other models I have generated (using run_prediction.py). In order to do this, I need to calculate the torsion angles and coordinate frame vectors as outlined in the README.md, and I believe I can use the parse_tcr_pmhc_pdbfile.py script to generate these values, given a TCRpMHC complex structure.

However, upon running this script on the output I got from running a previous prediction with TCRdock, I get the following error:

AssertionError: MHC-I pdbfile T00000_mhc_peptide_0_model_1_model_2_ptm.pdb should have 4 or 5 chains, see --help message

I'm guessing this is because the output pdb file does not assign residues to separate chains (looking at the PDB file itself there is only one A chain with ~1000 residues).

Not sure if there is an additional step somewhere I've missed, but my understanding is that the predicted structure file can be compared with other predicted structures (and real structures from the Protein Data Bank) using the torsion angle values etc. for clustering analysis.

Thank you in advance for your assistance!