Usage of --omit_AA_jsonl

[Cookiemaster33]

          Thank you so much. Should have looked more closely in the scripts folder. Sorry about that. I was able to adapt the script and it runs perfectly fine. When I run my main script however, it gives me the message "omit_AA_jsonl is no NOT loaded". Not sure what I am doing wrong. This is the command I am using:

python ~/Programs/ProteinMPNN/protein_mpnn_run.py
--jsonl_path $path_for_parsed_chains
--chain_id_jsonl $path_for_assigned_chains
--fixed_positions_jsonl $path_for_fixed_positions
--out_folder $output_dir
--num_seq_per_target 1000
--backbone_noise $noise
--sampling_temp $temperature
--seed 6
--batch_size 100
--tied_positions_jsonl $path_for_tied_positions
--omit_AA_jsonl 'inputs/omit_AA.jsonl'

Thanks for your help.

Best
Toby

Originally posted by @Cookiemaster33 in #65 (comment)