RosettaCommons / RosettaCommons/RFdiffusion
Discrepancies in Absolute Coordinates & Missing Side Chains in Output
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- Python
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Description
hi,
I've noticed the following while experimenting with RFdiffusion:
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The absolute coordinates of atoms in the output PDB files differ from those in the reference PDB files, even for regions of the structure that have been fixed.
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Additionally, the output PDB files only contain backbone atoms, with all side chains removed. Given that side chains have degrees of freedom and are essential for accurate structural modeling, shouldn't they also be fixed in the correct orientation? Even though inverse folding models might be able to infer side-chain positions, it seems counterproductive to lose this information during motif scaffolding.
Question: Is there any known workaround or setting that can preserve the absolute coordinates and retain the side chains?
Any guidance or suggestions would be greatly appreciated, thank you!
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Research direction
No source files or tests are named. Start by reproducing motif scaffolding with RFdiffusion, then compare fixed-region coordinates and atom records between the reference and output PDB files; done means establishing whether a documented setting or workaround preserves absolute coordinates and side chains.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics, machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100