sokrypton / sokrypton/ColabFold
predicting only one complex using fasta input that includes multiple entries
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Description
Hi,
I am using AlphaFold2_batch (https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/batch/AlphaFold2_batch.ipynb) and placed a fasta file containing multiple pairs of protein:peptide sequences like this
FBP0001
PIAQIHILEGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELASK:FLLKQIEF
FBP0002
PIAQIHILEGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELASK:IEFLKGQLPEAPVI
I did get the results but it only predicted the first entry within the fasta.
Did I get anything wrong in my input fasta?
I did not change any codes.
Anyone coming across the same issue before?
Thanks!
Contributor guide
First steps
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Research direction
Start with the AlphaFold2_batch notebook linked in the issue and reproduce the run using the two-entry FASTA input shown. Trace how multiple FASTA entries are read and determine whether both complexes are processed; done means the notebook handles the documented multi-entry input or clearly reports the supported format.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100