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Identifying non-crystallographic symmetry in protein electron-density maps: a feature-based approach.
- Source :
- Acta Crystallographica: Section D (Wiley-Blackwell); Sep2006, Vol. 62 Issue 9, p1012-1021, 10p, 1 Diagram, 4 Charts, 6 Graphs
- Publication Year :
- 2006
-
Abstract
- Non-crystallographic symmetry (NCS) averaging is a well known method for improving the quality of an electron-density map and thus aiding structure determination. Prior methods of NCS-operator determination based on estimated heavy-atom positions are prone to errors arising from inaccuracies in these coordinates or differences in the relative orientations of domains between molecules. In this paper, two real-space methods to determine NCS relationships from initial electron-density maps are presented. A brute-force method identifies matching regions in a map by local density correlation. A feature-based algorithm uses rotation-invariant features to reduce the computational time taken by the brute-force algorithm by filtering out regions that are likely to have dissimilar density patterns. This makes the feature-based algorithm faster and as accurate as the brute-force approach. Neither method requires the positions of heavy atoms or any information regarding the protein sequence. Both methods have been tested on a diverse range of experimentally phased maps and the correct NCS relationships were accurately identified for almost all of the test cases. The NCS operators obtained by the feature-based algorithm were used to perform NCS averaging and an improvement in map correlation was observed for some cases. [ABSTRACT FROM AUTHOR]
- Subjects :
- SYMMETRY
MOLECULES
ELECTRON distribution
ELECTRONS
AMINO acid sequence
ATOMS
Subjects
Details
- Language :
- English
- ISSN :
- 09074449
- Volume :
- 62
- Issue :
- 9
- Database :
- Complementary Index
- Journal :
- Acta Crystallographica: Section D (Wiley-Blackwell)
- Publication Type :
- Academic Journal
- Accession number :
- 22146056
- Full Text :
- https://doi.org/10.1107/S0907444906023158