RosettaCommons / RosettaCommons/RFdiffusion
Oxygen placed in inappropriate angles
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- Dominant language
- Python
- Stars
- 3.1k
- Forks
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Description
RFdiffusion output often contains oxygen that is placed in a inappropriate angle relative to the backbone. These oxygens are hard to fix even with partial diffusion of the whole structure.
Is there a way to fix/prevent this issue aside from relaxing the structure with molecular dynamics?
Contributor guide
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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
The report provides example images but names no source files, tests, or command for reproducing the oxygen-placement problem. Start by reproducing the reported RFdiffusion output, then locate the structure-generation and relaxation entry points; done would require an agreed fix or prevention method validated on the reported cases.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- machine-learning
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100