sokrypton / sokrypton/ColabFold

Using custom templates - upload box not present

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Jupyter Notebook
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Description

Expected Behavior

Using custom templates

To predict the structure with a custom template (PDB or mmCIF formatted): (1) change the template_mode to "custom" in the execute cell and (2) wait for an upload box to appear at the end of the "Input Protein" box. Select and upload your templates (multiple choices are possible).

Current Behavior

**The upload box to appear at the end of the "Input Protein" box, doesn't appear **

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

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 issue after a Colab Factory Reset, setting template_mode to "custom" in the execute cell and checking the end of the "Input Protein" box. Compare the custom-template flow with the expected upload-box behavior; the issue is resolved when multiple PDB or mmCIF templates can be selected and uploaded.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook
Domain
bioinformatics
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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