Fix CE-Symm bug with short repeats #1101
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Most are in docstrings. One misspelled public method has been deprecated.
[rcsb/symmetry#118](rcsb/symmetry#118) The problem was actually downstream from CE-Symm in the QuatSymmDetector code used for assigning a symmetry group. The code was re-aligning subunits using CE. This fails for short alignments of <15 residues (two AFP with default settings). Thus no atoms get aligned and an exception was thrown whenever an output format required information about the symmetry group. This fix re-uses the original CE-Symm alignment for the symmetry group detection. This might change CE-Symm and QuatSymm results for proteins with small subunits or borderline scores. Changes: - New `SubunitClustererMethod.MANUAL` enum value - Improve `SymmetryTools.getQuaternarySymmetry`
Better refinement now finds slightly larger helical rotation, moving it from R to H.
Member
|
Thank you, @sbliven! |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This fixes rcsb/symmetry#118.
It switches the determination of the symmetry group and rotation axes to use the CESymm alignment directly. Before it was recomputed using QuatSymmDetector, which failed with short repeats.
A new CE-Symm version will be released after the next biojava release.