Boltz-2 support

[shahryary]

This is a really great tool. We recently tested it with Boltz-2, but unfortunately, it didn’t generate any results.
It would be fantastic if you could add support for Boltz-2 in the future.

[young-su-ko]

I've been able to calculate ipsae with Boltz-2 outputs, so I think it is currently supported. What is the error message you are getting?

[colbyford]

I also get an error with the Boltz-2-generated files:

colby@macbook boltz2 % python ipsae.py <my_npz_file>.npz <my_structure>_model_0.cif 10 10
Traceback (most recent call last):
  File "/Users/colby/<my_path>/ipsae.py", line 473, in <module>
    iptm_boltz1[chain1][chain2]=boltz1_chain_pair_iptm_data[str(nchain1)][str(nchain2)]
                                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^
KeyError: '7'

I'm using Boltz version 2.2.1.

[shahryary]

I resolved the issue with Boltz-2 by converting the PDB file to CIF format.

I'm generating structures in PDB format, so to use them with Boltz-2, I convert the PDB files to CIF format using maxit. Here's the command I use for the conversion:

maxit -o 1 -input "$pdb_file" -output "$cif_file"

Additionally, to run IPSAE successfully, it's important to have the confidence_*_model_0.json file alongside the pae_*_model_0.npz file. Here's the command I use to run IPSAE:

python "/ipsae/src/ipsae.py" "pae_*_model_0.npz" "model_0.cif" 10 10

[tomerco4]

I also get an error with the Boltz-2-generated files:

colby@macbook boltz2 % python ipsae.py <my_npz_file>.npz <my_structure>_model_0.cif 10 10
Traceback (most recent call last):
  File "/Users/colby/<my_path>/ipsae.py", line 473, in <module>
    iptm_boltz1[chain1][chain2]=boltz1_chain_pair_iptm_data[str(nchain1)][str(nchain2)]
                                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^
KeyError: '7'

I'm using Boltz version 2.2.1.

This had the exact same Error.
I found out that the reason for that is because "ipsae.py" assumes that the chains are named contiguously as A, B, C…so if you named a chain "H" (for example antibody heavy chain) then it will raise this 'KeyError'.

You can solve this by naming your chains in sequential order (A,B,C...) or by changing the lines in the code to not assume a specific chain order...