Error in Local Template Search

We deployed a local pdb database and try to use it as following cmd:

colabfold_batch --num-models 5 \
                --num-recycle 30 \
                --data /ssd/home/xxxx/models/colabfold/af2   \
                --recycle-early-stop-tolerance 0.1 \
                --model-type alphafold2_multimer_v1  \
                --save-recycles \
                --random-seed 5 \
                --num-seeds 1 \
                --max-msa 256:512 \
                --templates \
                --pdb-hit-file seq_8919_pdb100_230517.m8 \
                --local-pdb-path /ssd/home/xxx/database/colabfold/pdb/divided \
                seq_8919.a3m \
                seq_8919_output

Expected Behavior

Finish colabfold batch and get result.

Current Behavior

Following error raised due to read some pdbs failed (4udf, 1ejg, etc), I think colabfold could ignore these pdbs by catching exception

Traceback (most recent call last):
  File "/ssd/home/scw6byf/software/colabfold/1.5.5/bin/colabfold_batch", line 8, in <module>
    sys.exit(main())
  File "/ssd/home/scw6byf/software/colabfold/1.5.5/lib/python3.10/site-packages/colabfold/batch.py", line 2035, in main
    run(
  File "/ssd/home/scw6byf/software/colabfold/1.5.5/lib/python3.10/site-packages/colabfold/batch.py", line 1412, in run
    mk_hhsearch_db(custom_template_path)
  File "/ssd/home/scw6byf/software/colabfold/1.5.5/lib/python3.10/site-packages/colabfold/batch.py", line 240, in mk_hhsearch_db
    structure = parser.get_structure("none", cif_fh)
  File "/ssd/home/scw6byf/software/colabfold/1.5.5/lib/python3.10/site-packages/Bio/PDB/MMCIFParser.py", line 62, in get_structure
    self._build_structure(structure_id)
  File "/ssd/home/scw6byf/software/colabfold/1.5.5/lib/python3.10/site-packages/Bio/PDB/MMCIFParser.py", line 265, in _build_structure
    structure_builder.init_atom(
  File "/ssd/home/scw6byf/software/colabfold/1.5.5/lib/python3.10/site-packages/Bio/PDB/StructureBuilder.py", line 289, in init_atom
    residue.add(self.atom)
  File "/ssd/home/scw6byf/software/colabfold/1.5.5/lib/python3.10/site-packages/Bio/PDB/Residue.py", line 48, in add
    raise PDBConstructionException(
Bio.PDB.PDBExceptions.PDBConstructionException: Atom C defined twice in residue <Residue LYS het=  resseq=91 icode= >

Your Environment

Include as many relevant details about the environment you experienced the bug in.

• python 3.8
• colabfold 1.5.5
• CentOS 7.9
• pdb 20240314

Start with colabfold/batch.py at mk_hhsearch_db, around line 240, and inspect the Bio.PDB parser call shown in the traceback. Run the supplied colabfold_batch command against the local PDB database; done means malformed structures such as 4udf and 1ejg are skipped and the batch completes.