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International
Tables for Crystallography Volume F Crystallography of biological macromolecules Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. F. ch. 15.1, pp. 317-318
Section 15.1.2.4. Skeletonization
a
Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Seattle, WA 90109, USA,bDepartment of Chemistry, University of York, York YO1 5DD, England, and cDepartment of Physics, University of York, York YO1 5DD, England |
The skeletonization method enhances connectivity in the map. This is achieved by locating ridges of density, constructing a graph of linked peaks, and then building a new map using cylinders of density around the graph peaks.
At worse than atomic resolution, the density peaks for bonded atoms are no longer resolved, and so interpretation of the density in terms of atomic positions involves recognition of common motifs in the pattern of ridges in the density. Skeletonization was a tool developed by Greer (1985)![[link]](/graphics/greenarr.gif)
to assist model building by tracing high ridges in the electron density to describe the connectivity in the map.
Skeletonization has more recently been adapted to the problem of density modification (Baker, Bystroff et al., 1993; Bystroff et al., 1993; Wilson & Agard, 1993). A skeleton is constructed by tracing the ridges in the map. The resulting ridges form connected `trees'. These trees may be pruned to remove small unconnected fragments and break circuits to select for protein-like features. A new map may then be built by building density around the links of the skeleton using the profile of a cylindrically averaged atom at the appropriate resolution.
The skeletonization method has been used to add new features to a partial model of a molecule (Baker, Bystroff et al., 1993). An efficient alternative algorithm for tracing density ridges is given by Swanson (1994).
References
Baker, D., Bystroff, C., Fletterick, R. J. & Agard, D. A. (1993). PRISM: topologically constrained phase refinement for macromolecular crystallography. Acta Cryst. D49, 429–439.Google Scholar
Bystroff, C., Baker, D., Fletterick, R. J. & Agard, D. A. (1993). PRISM: application to the solution of two protein structures. Acta Cryst. D49, 440–448.Google Scholar
Greer, J. (1985). Computer skeletonization and automatic electron-density map analysis. In Diffraction methods for biological macromolecules, edited by H. W. Wyckoff, C. H. W. Hirs & S. N. Timasheff, Vol. 115, pp. 206–224. Orlando: Academic Press.Google Scholar
Swanson, S. M. (1994). Core tracing: depicting connections between features in electron density. Acta Cryst. D50, 695–708.Google Scholar
Wilson, C. & Agard, D. A. (1993). PRISM: automated crystallographic phase refinement by iterative skeletonization. Acta Cryst. A49, 97–104.Google Scholar
