sokrypton / sokrypton/ColabFold

Index out of range during the display of 3D structure.

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Dominant language
Jupyter Notebook
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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*
    image
    image

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 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

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