Symmetry mode NOT usable for e.g. inpainting a loop?
Nobody has claimed this yet.
Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 35/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- python
- Domain
- bioinformatics
Research direction
No source file or test is identified in the report. Start by tracing the cyclic symmetry mode and comparing it with the nickel design example, then reproduce the loop-generation case to determine whether chain breaks are expected; done means confirming the limitation or documenting a working way to join the symmetric units.
Written by the indexing model from the issue text.
Description
I've tried to use the cyclic symmetric mode to generate a set of symmetric loops between symmetric structural units (e.g. loops to join together helices in a helical bundle with cyclic symmetry).
However, while this kind of operation works to generate non-symmetric loops, when switching to use of symmetry it acts to always assume chain-breaks after the newly generated loops, such that they are never positioned so as to actually join the e.g. helices of the symmetric helical bundle.
Based on the text in the nickel design example, which says that chain breaks don't strictly need to be given the contigs when using symmetry, it seems this might be a known limitation of the symmetry mode. Is this true? Is it possible to circumvent this limiation?
- Dominant language
- Python
- Stars
- 3.1k
- Forks
- 644
- PR merge metrics
- No merged PRs in 30d
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