sokrypton / sokrypton/ColabFold

Custom templates not used, but same template is used if searched for using API

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Jupyter Notebook
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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

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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

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