How do I use a PSSM with proteinMPNN?

[proteins247]

Hello,

I don't quite understand the examples for using a PSSM. I generated an ASCII PSSM with psi-blast, but that doesn't seem to be the format that is used by the example scripts. There seems to be two helper scripts:

• https://github.com/dauparas/ProteinMPNN/blob/main/helper_scripts/make_pssm_input_dict.py
• https://github.com/dauparas/ProteinMPNN/blob/main/helper_scripts/other_tools/make_pssm_dict.py

In the former, it expects a PSSM in the form of npz files. Could that format be explained, or how can I convert my ASCII PSSM into that format?

In the latter, the script appears to be an example to be modified, since it points to file paths that existed for the creator of the script. Even so, the parse_pssm function within that script doesn't seem to be read my ASCII PSSM. I could adjust my script, but I am feeling like I have the wrong format for that script, as well.