RosettaCommons / RosettaCommons/foundry
Virtual atoms remain superimposed on C-alpha
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- Dominant language
- Python
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Description
Hello,
I've noticed that in a fair amount of structures output by rfd3 (for motif scaffolding) there are residues where it looks like the virtual atoms didn't get removed, resulting in very badly-scoring files (cart_bonded ~ 10,000 REU). In these cases it looks like a glycine in pymol, but the .pdb file will list atoms CB onward as having the same xyz coordinates. Is there a way to cleanup virtual atoms/filter for residues where there are huge steric clashes from virtual atoms remaining on top of the C-alpha?
Thanks!
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Research direction
Start by reproducing the issue with structures output by rfd3 and inspect the .pdb files in PyMOL, focusing on residues whose CB and later atoms share the C-alpha coordinates. Determine where virtual atoms remain superimposed and verify that cleanup or filtering removes those residues and prevents the reported cart_bonded steric clashes.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100