ValueError: ('B', 120) is not in list

[javarianajeeb]

I have a directory of ~1800 pdb files that I am trying to use to generate a large directory of constraints for binder design using make_secstruc_adj.py. This is what I typed: make_secstruc_adj.py --pdb_dir binderpdbstructures/ --out_dir binderconstraints/

It makes about a dozen constraints before it fails with the error given in the subject line. How do I fix this? Thank you.

[joewatchwell]

I think this is probably because there is a residue in the pdb file that has sequence, but isn't resolved in the structure (our parsers typically assume everything is present in the structure). If you just throw out these pdbs (or remove the part of the pdb file where the structure isn't resolved) I think it should work