limit to number of chains in homooligomers

dauparas / ProteinMPNN

Code for the ProteinMPNN paper

MIT License

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limit to number of chains in homooligomers #69

Open acarbn opened 1 year ago

acarbn commented 1 year ago

What is the limit to number of repeating chains I can design in a homooligomer with PMPNN? I get this error when I tried 9 chains:

  File "/nemo/lab/debenedictise/home/users/acarb/ProteinMPNN/tutorial/ProteinMPNN/protein_mpnn_utils.py", line 354, in tied_featurize
    tied_beta[start_idx+v[0][v_count]-1] = v[1][v_count]
    ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: index 7913 is out of bounds for axis 0 with size 7913

dauparas commented 1 year ago

There is no limit to the number of chains used. It seems that the error is coming from the tied_beta array being of size 7913 so there is no index 7913. This example (https://github.com/dauparas/ProteinMPNN/blob/main/examples/submit_example_6.sh) for the homooligomer design should be helpful in the multi-state design problem.