sokrypton / sokrypton/ColabFold
Index out of range during the display of 3D structure.
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- Dominant language
- Jupyter Notebook
- Stars
- 2.9k
- Forks
- 747
- PR merge metrics
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Description
Expected Behavior
3D plots should be visible I guess.
Current Behavior
Index out of range
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:
Used the Alpha Fold 2 ipynb
With this protein sequence: LINVLLVDEHELVRAGIRRILEDIKGIKVVGEACCGEDAVKWCRTNAVDVVLMDMNMPGIGGLEATRKIARSTADIKVIMLTVHTENPLPAKVMQAGAAGYLSKGAAPQEVVSAIRSVYSGQRYIASDIAQQMALSQIEPAKTETPFASLSERELQIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNIHGDVELTHLAIRHGLCNAETLTSQ*
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 Alpha Fold 2 ipynb after a Factory Reset, using the supplied protein sequence, and capture the complete ColabFold output. Compare the 3D display step with the current colabfold_batch installation; done means identifying the index failure and confirming that the 3D plot renders successfully.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- bioinformatics, data-visualization
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100