sokrypton / sokrypton/ColabFold
AF2 using MMseqs multimer model ranking error?
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Description
A long-running 3-way multimer job had finally reached the end of its prediction run, and was set to do the ranking step (& lightly refine the top model), when the program frustratingly crashed with the following error msg below. This is the first time I've run into this, but I'm unsure about re-launching the whole enchilada if the job will crash again, hours down the line. Thx for any clarity & help, cheers, FB
2023-12-03 17:20:01,939 reranking models by 'multimer' metric
ModuleNotFoundError Traceback (most recent call last)
in <cell line: 65>()
63
64 download_alphafold_params(model_type, Path("."))
---> 65 results = run(
66 queries=queries,
67 result_dir=result_dir,
5 frames
/content/alphafold/relax/cleanup.py in
20 import io
21
---> 22 import pdbfixer
23 from openmm import app
24 from openmm.app import element
ModuleNotFoundError: No module named 'pdbfixer'
NOTE: If your import is failing due to a missing package, you can
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Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the Colab dependency setup and alphafold/relax/cleanup.py, where the traceback shows the failing import of pdbfixer. Reproduce the multimer ranking and refinement path in the notebook, then verify that the dependency is available and the run completes past this step.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- bioinformatics, machine-learning
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 25/100