sokrypton / sokrypton/ColabFold
Using recent pdbs (or a more recent version of pdb70) to search for templates.
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Description
Hi,
I will like to consider in the search for templates very recent structures available on the PDB. However, when I try to use the colabfold_batch (https://github.com/YoshitakaMo/localcolabfold) I only get older PBDs as suggested templates. so my questions are:
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Is there a way to make colabfold_batch to search using a newer version of pdb70? How can I check with one is using?
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If not, how can I build my own database and use it for search locally?
Thanks.
Raul.
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 with the colabfold_batch usage and the linked localcolabfold project, then inspect how template databases are selected and how the active pdb70 version is reported. Compare the documented database configuration with the requested newer PDB search and custom local database workflow; done means the supported options and version-check steps are clear.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, cli
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100