sokrypton / sokrypton/ColabFold
Error when using --save-single or pair-representations argument : NoneType object is not subscriptable
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Description
Hi Everyone. Whenever I try to save embeddings for my protein sequence I get an error suggesting nothing is returned from running the model.
Running the multimer model on a protein complex (in csv file format) does not work:
colabfold_batch --amber --templates --numer_recycle 3 model_type=AlphaFold2-multimer-v2 --save-pair-representations protein_complex.csv output_folder
However, running the simple model on a monomer fasta file works as expected:
colabfold_batch --amber --templates --number_recycle 3 --save-pair-representations monomer.fasta output_folder
Does save-pair-representations or single-representations not work for protein complexes or is there a bug?
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Research direction
Start by reproducing the error with the colabfold_batch command, --save-pair-representations, and the protein-complex CSV described here, then compare it with the working monomer FASTA command. Trace why saving representations receives None; done means the multimer command saves the requested representations without the NoneType error.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 32/100