sokrypton / sokrypton/ColabFold
PDB files are missing a HEADER and a CRYST1 record and PDBx sequence
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Description
Expected Behavior
output PDB files are compatible with other downstream software
Current Behavior
PDB files are not compatible with e.g. Alphafill (https://alphafill.eu/). The PDB files currently are missing a HEADER, a CRYST1 record and a pdbx_poly_seq_scheme, i.e. the amino acid sequence is missing.
Steps to Reproduce (for bugs)
Please make sure to reproduce the issue after a "Factory Reset" in Colab.
If running locally ypdate you local installation colabfold_batch to the newest version.
Please provide your input if you can share it.
ColabFold Output (for bugs)
Please make sure to also post the complete ColabFold output. You can use gist.github.com for large output.
Context
Providing context helps us come up with a solution and improve our documentation for the future.
Your Environment
Include as many relevant details about the environment you experienced the bug in.
- Git commit used
- If you run it on a local system. Please add the server specifications
- Operating system and version:
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 generated PDB output after a Factory Reset in Colab, or after updating the local colabfold_batch installation. Compare the files with the records required by downstream software such as Alphafill: HEADER, CRYST1, and pdbx_poly_seq_scheme. Done means the output includes these records and is accepted by the downstream workflow.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100