sokrypton / sokrypton/ColabFold
Running Alphafold using unpublished Pdb as a custom template
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- Dominant language
- Jupyter Notebook
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Description
Hi,
I am trying to run Alphafold using a custom template. The template I am using as input is not published yet but I have both realspace-refined Pdb and cif files. When I am trying to run Alphafold with the unpublished Pdb, I get an error saying "no templates found”. I am wondering if is it possible to run Alphafold using unpublished Pdb as a custom template.
Regards,
Shashank.
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
The issue names no files, tests, or entry points. Start by reproducing the “no templates found” result with the unpublished PDB and CIF inputs, then inspect how ColabFold discovers and validates custom templates. Done means establishing whether unpublished structures are supported and documenting the required input or limitation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100