sokrypton / sokrypton/ColabFold
Online colabfold can use PDB-s as templates, local cannot
Nobody has claimed this yet.
- Dominant language
- Jupyter Notebook
- Stars
- 2.9k
- Forks
- 747
- PR merge metrics
- No merged PRs in 30d
Description
Hi,
I am trying to repeat a run that I did online, with the local version of ColabFold. Online, I can use PDB-s as inputs, but locally it contains that it cannot find cif files.
I used the following flags:
--msa-mode single_sequence --templates --custom-template-path $outdir/template
Am I doing sth wrong or this is not a feature of the local version?
Thank you,
Julia
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 run with --templates, --custom-template-path, and --msa-mode single_sequence using the reported PDB inputs. Compare the local and online template-input behavior, then determine whether local ColabFold should accept PDB files; done means the local workflow supports the same input or the limitation is clearly established.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100