The generated proteins from the motif scaffolding example are bad

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
45/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Quiet
Tech stack
python
Domain
bioinformatics, machine-learning

Research direction

Start by rerunning the motif scaffolding command from the issue with configs/search_motif_local_pipeline.yaml and task 1YCR_AA, then inspect the resulting protein structures. Trace the configuration and generation path to identify why most outputs are poorly folded; done means the cause is reproducible and a correction or clear explanation is provided.

Written by the indexing model from the issue text.

Description

Hi,

Now I am trying the motif scaffolding example in the tutorial:

complexa design configs/search_motif_local_pipeline.yaml
++run_name=motif_test
++generation.task_name=1YCR_AA

But the generated proteins are very bad, most of them are even not well folded:

Image

Could you help double check to see what is going on? Thanks.

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Python
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Merged PRs (30d)
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