Using multiple input structures for a single sequence output about proteinmpnn

[dauparas]

You can build a tied-residue dictionary using this helper script https://github.com/dauparas/ProteinMPNN/blob/main/helper_scripts/make_pos_neg_tied_positions_dict.py (--homooligomer 1 --input_path "my_path_to_input.pdb" --output_path "my_path_to_output.jsonl")And then pass the tied position .jsonl to the main script using this flag --tied_positions_jsonl

[acarbn]

Thanks. It is a monomer, not an oligomer. Would I still need --homooligomer 1?
I tried the following:

python $pmpnn/helper_scripts/make_pos_neg_tied_positions_dict.py --input_path=$path_for_parsed_chains --output_path=$path_for_tied_positions --homooligomer 1 --pos_neg_chain_list="A" --pos_neg_chain_betas "1.0"

It asked me --pos_neg_chain_list and --pos_neg_chain_betas flags to work, that's why I added them (also gave the same chain ID to all structures as A). Now I have a sequence for each structure but only 1 of them is really regenerated, the rest gave the same sequence as input and NaN as scores. Does it mean it considered and used all the structures yet gave only one sequence?