sokrypton / sokrypton/ColabFold
Custom templates not used, but same template is used if searched for using API
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Description
I am trying to fold 1QYS to test out the impact of templating.
If I directly upload the 1QYS template via:
wget https://files.rcsb.org/download/1qys.pdb
and supply that as a custom template to colabfold, it doesn't find it:
2023-03-22 14:32:43,098 Sequence 0 found no templates
But if I do a pdb search using the API, these templates are returned:
2023-03-22 14:41:50,137 Sequence 0 found templates: ['2n4e_A', '2mra_A', '2mbm_A', '1qys_A', '4kyz_B', '2gjh_B', '1qys_A', '2n4e_A', '2mbm_A', '4kyz_B']
^and this clearly includes 1qys! So why doesnt it accept the template if provided to it directly?
I've tested this both on a local installation of colabfold and the Colab notebook.
I am running colabfold 1.5
Contributor guide
First steps
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- Open a pull request that references the issue number.
Research direction
Reproduce the difference between supplying 1qys.pdb as a custom template and finding 1qys_A through the API, using both the local ColabFold installation and the Colab notebook. Trace the custom-template and API template lookup entry points; done means the direct template path consistently recognizes the same 1qys template returned by the API.
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
- Mostly clear
- Newbie friendliness
- 32/100