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rhinowarrior / swifttcr

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When running alphafold model the peptide tries to connect to mhc #19

Open rhinowarrior opened 2 weeks ago

rhinowarrior commented 2 weeks ago

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 commented 2 weeks ago

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