sokrypton / sokrypton/ColabFold

My mmCIF contains no mentioned error but the parsing still doesn't work

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Jupyter Notebook
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Description

Expected Behavior

Successful parsing of 9 mmCIF files.

Current Behavior

Returning error hit.name did not start with PDBID_chain

Steps to Reproduce (for bugs)

Custom import of mmCIF template will always return error no matter how many resets

ColabFold Output (for bugs)

Traceback (most recent call last):
File "/content/colabfold/batch.py", line 1465, in run
= get_msa_and_templates(jobname, query_sequence, a3m_lines, result_dir, msa_mode, use_templates,
File "/content/colabfold/batch.py", line 792, in get_msa_and_templates
template_feature = mk_template(
File "/content/colabfold/batch.py", line 138, in mk_template
templates_result = template_featurizer.get_templates(
File "/content/alphafold/data/templates.py", line 883, in get_templates
result = _process_single_hit(
File "/content/alphafold/data/templates.py", line 686, in _process_single_hit
hit_pdb_code, hit_chain_id = _get_pdb_id_and_chain(hit)
File "/content/alphafold/data/templates.py", line 103, in _get_pdb_id_and_chain
raise ValueError(f'hit.name did not start with PDBID_chain: {hit.name}')
ValueError: hit.name did not start with PDBID_chain: AF-P00750-F1-model_v4_A

Context

I've read previous resolved issues and my file comply with the fixes but resetting the runtime will always return the error. I'm not too familiar with PDB and mmCIF files and I interpreted the error as unadded chain name. However I did found label_asym_id and the chain label so I'm quite confused. The file is also an AlphaFold output of tissue-type Plasminogen Activator on UniProt. The file is
tPAmmCIF.zip

Your Environment

The ColabFold notebook with A100 GPU as accelerator.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the failure with the attached tPAmmCIF.zip in the ColabFold notebook, then trace the reported call from batch.py through alphafold/data/templates.py, especially _process_single_hit and _get_pdb_id_and_chain. Compare the input hit names with the parser's expected format. Done means all 9 mmCIF files parse successfully without the reported ValueError.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook, python
Domain
bioinformatics
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
30/100

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