sokrypton / sokrypton/ColabFold
stuck in this process:2023-12-23 15:59:12,285 reranking models by 'plddt' metric 2023-12-23 15:59:14,218 Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
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Description
Expected Behavior
Current Behavior
Steps to Reproduce (for bugs)
Please make sure to reproduce the issue after a "Factory Reset" in Colab.
If running locally ypdate you local installation colabfold_batch to the newest version.
Please provide your input if you can share it.
ColabFold Output (for bugs)
Please make sure to also post the complete ColabFold output. You can use gist.github.com for large output.
Context
Providing context helps us come up with a solution and improve our documentation for the future.
Your Environment
Include as many relevant details about the environment you experienced the bug in.
- Git commit used
- If you run it on a local system. Please add the server specifications
- Operating system and version:
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 by reproducing the run after a Colab Factory Reset, or with the local colabfold_batch installation updated as requested. Review the complete ColabFold output and environment details, including the OpenMM deprecation warning and the point where reranking by pLDDT stops; done means identifying the cause of the stall and confirming a successful run.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100