sokrypton / sokrypton/ColabFold
Would like to force multimer mode : No template found SVD issue - new pdb100 issue.
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Description
I am using ColabFold to create multimeric structures to then annotate in my pipeline.
Unfortunately with rare proteins with no template, I am getting errors. Previously- I believe when you used pdb70, these errors didnt exist.
How might I fix this? Is there a way to increase the number of templates found? or perhaps run without needing a template, or to use the previous true unclustered pdb70 setup?
Best wishes
Chris
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 multimer run described in issue #478 with a rare protein that has no template, focusing on the “No template found SVD” error. Compare behavior with the newer pdb100 setup and the previously used pdb70 setup. Done means identifying a reproducible workaround or documenting whether template-free execution or additional template retrieval is supported.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100