When I execute the parse_multiple_chains.py, it runs without error messages and creates a file in the output location that I expect but the file is empty.
I'm running it on my windows laptop, here is the command I used:
C:\ProteinMPNN\helper_scripts>py parse_multiple_chains.py --input_path "C:\ProteinMPNN\4rjj.pdb" --output_path "C:\ProteinMPNN\myparsedfilesetc\parsed_pdbs.jsonl"
The following command works, but I would like to model it as a homooligomer and fix some residues so I think I need to parse it and then make a tied position dictionary.
py protein_mpnn_run.py --path_to_model_weights "C:\ProteinMPNN\vanilla_model_weights" --pdb_path 4rjj.pdb --pdb_path_chains "A B C D" --out_folder "C:\ProteinMPNN\myoutputs\4rjj" --num_seq_per_target 20 --sampling_temp "0.1 0.2 0.3" --batch_size 1 --omit_AAs='XC'
Saving the input pdb file and putting the output file in the helper scripts folder doesn't fix it either:
C:\ProteinMPNN\helper_scripts>py parse_multiple_chains.py --input_path "4rjj.pdb" --output_path "4rjj_parsed_pdbs.jsonl"
Any help would be much appreciated; thanks in advance!
When I execute the parse_multiple_chains.py, it runs without error messages and creates a file in the output location that I expect but the file is empty.
I'm running it on my windows laptop, here is the command I used:
C:\ProteinMPNN\helper_scripts>py parse_multiple_chains.py --input_path "C:\ProteinMPNN\4rjj.pdb" --output_path "C:\ProteinMPNN\myparsedfilesetc\parsed_pdbs.jsonl"
The following command works, but I would like to model it as a homooligomer and fix some residues so I think I need to parse it and then make a tied position dictionary.
py protein_mpnn_run.py --path_to_model_weights "C:\ProteinMPNN\vanilla_model_weights" --pdb_path 4rjj.pdb --pdb_path_chains "A B C D" --out_folder "C:\ProteinMPNN\myoutputs\4rjj" --num_seq_per_target 20 --sampling_temp "0.1 0.2 0.3" --batch_size 1 --omit_AAs='XC'
Saving the input pdb file and putting the output file in the helper scripts folder doesn't fix it either:
C:\ProteinMPNN\helper_scripts>py parse_multiple_chains.py --input_path "4rjj.pdb" --output_path "4rjj_parsed_pdbs.jsonl"
Any help would be much appreciated; thanks in advance!