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 https://github.com/dauparas/ProteinMPNN/issues/65#issuecomment-1701736999