When running alphafold model the peptide tries to connect to mhc

[rhinowarrior]

The alphafold models can run using swiftTCR but the only problem is that it tries to connect the peptide to the MHC when viewed in PyMol. This is because of this line
command = "pdb_tidy {} | pdb_selchain -A,B,C | pdb_chain -A | pdb_reres -1 > {}".format(str(p_rec), receptor_name)

We can fix this by changing it to this:

  command = (
    "pdb_tidy {} | "  
    "pdb_selchain -A,B | pdb_chain -A | pdb_reres -1000 > mhc.pdb; "  
    "pdb_tidy {} | "  
    "pdb_selchain -C | pdb_chain -A | pdb_reres -1 > pep.pdb; "  
    "pdb_merge pep.pdb mhc.pdb | pdb_tidy > {}; " 
    "rm mhc.pdb pep.pdb"  
    ).format(str(p_rec), str(p_rec), receptor_name)

But this crashes the program because it gives problems in pairwise_rmsd.py so we should really change that code.

[JanAarts]

Yes, rewriting pairwise_rmsd.py would solve a lot of the problems we experience.