Bio.PDB.PDBExceptions.PDBException: Fixed and moving atom lists differ in size #341
Description
Hi Martin.
I am designing a peptitde with length from 15-60 aa. The target has A and B chains (391 aa and 407aa).
The json file I used is:
{
"design_path": "/media/user/ALL_USERS/hjd/De_novo/test_E1/",
"binder_name": "TESTE1",
"starting_pdb": "/media/user/ALL_USERS/hjd/De_novo/test_E1/Cleaned_AB.pdb",
"chains": "A",
"target_hotspot_residues": "A91,A226",
"lengths": [15, 50],
"number_of_final_designs": 200
}
The command I used is:
python -u /home/jedi/App/BindCraft/bindcraft.py --settings './test_E1.json' --filters '/home/jedi/App/BindCraft/settings_filters/default_filters.json' --advanced '/home/jedi/App/BindCraft/settings_advanced/default_4stage_multimer.json'
The error message I got is:
Traceback (most recent call last):
File "/home/jedi/App/BindCraft/bindcraft.py", line 150, in
trajectory_target_rmsd = target_pdb_rmsd(trajectory_pdb, target_settings["starting_pdb"], target_settings["chains"])
File "/home/jedi/App/BindCraft/functions/biopython_utils.py", line 82, in target_pdb_rmsd
sup.set_atoms(atoms_starting, atoms_trajectory)
File "/home/jedi/miniconda3/envs/BindCraft/lib/python3.10/site-packages/Bio/PDB/Superimposer.py", line 35, in set_atoms
raise PDBException("Fixed and moving atom lists differ in size")
Bio.PDB.PDBExceptions.PDBException: Fixed and moving atom lists differ in size
There was no problem at all when I ran the demo PDL1. The code works fine, but this protein gives me error. Wish you have a good one. Many thanks!