Statistical density modification with non-crystallographic symmetry
- PMID: 12454468
- PMCID: PMC2745884
- DOI: 10.1107/s0907444902016360
Statistical density modification with non-crystallographic symmetry
Abstract
Statistical density modification is a technique for phase improvement through a calculation of the posterior probability of the phases, given experimental phase information and expectations about features of the electron-density map. The technique can take advantage of both estimates of electron density in the map and uncertainties or probability distributions for those estimates. For crystals with non-crystallographic symmetry (NCS), this allows the use of the expected similarity of electron density at NCS-related points without requiring an implicit assumption that these regions are identical.
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References
-
- Abrahams, J. P. & Leslie, A. G. W. (1996). Acta Cryst. D52, 30–42. - PubMed
-
- Bricogne, G. (1974). Acta Cryst. A30, 395–405.
-
- Chen, C. C. H., Kim, A., Zhang, H., Howard, A. J., Sheldrick, G. M., Dunaway-Mariano, D. & Herzberg, O. (2000). Am. Crystallogr. Assoc. Annu. Meet., Abstract 02.06.03.
-
- Cowtan, K. (1998). Acta Cryst. D54, 750–756. - PubMed
-
- Huber, A. H., Nelson, W. J. & Weis, W. I (1997). Cell, 90, 871–882. - PubMed
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