RosettaCommons / RosettaCommons/foundry
[QUEST] Inpainting residues with RFD3 only gives glycines
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- Dominant language
- Python
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Description
I run the example in "models/rfd3/docs/tutorials/enzyme_tutorial_files/rfd3_enzyme_tutorial.json" and I noticed that the inpainted residues (in this case "select_unfixed_sequence": "A579,A581") are always output as glycine by RFD3. Is there a way to change this behaviour so that the whole sequence space is explored?
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First steps
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Research direction
Start by running the example in models/rfd3/docs/tutorials/enzyme_tutorial_files/rfd3_enzyme_tutorial.json and inspect the output for select_unfixed_sequence values A579,A581. Trace how RFD3 handles these inpainted residues; done would mean the behavior is understood and the requested sequence-space exploration is supported or clearly documented.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, machine-learning
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100