International
Tables for
Crystallography
Volume B
Reciprocal space
Edited by U. Shmueli

International Tables for Crystallography (2006). Vol. B, ch. 3.3, p. 375   | 1 | 2 |

Section 3.3.1.5.4. Representation of surfaces by dots

R. Diamonda*

aMRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England
Correspondence e-mail: rd10@cam.ac.uk

3.3.1.5.4. Representation of surfaces by dots

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Connolly (Langridge et al., 1981[link]; Connolly, 1983a[link],b[link]) represents surfaces by placing dots on the surface with an approximately uniform superficial density. Connolly's algorithm was developed to display solvent-accessible surfaces of macromolecules and provides for curved concave portions where surface atoms meet. Pearl & Honegger (1983[link]) have developed a similar algorithm, based on a grid, which generates only convex portions which meet in cusps, but is faster to compute than the Connolly surface. Bash et al. (1983[link]) have produced a van der Waals surface algorithm fast enough to permit real-time changes to the structure without tearing the surface.

It has become customary to use a dot representation to display computed surfaces, such as the surface at a van der Waals radius from atomic centres, and to use lines to represent experimentally determined surfaces, especially density contours.

References

Bash, P. A., Pattabiraman, N., Huang, C., Ferrin, T. E. & Langridge, R. (1983). Van der Waals surfaces in molecular modelling: implementation with real-time computer graphics. Science, 222, 1325–1327.Google Scholar
Connolly, M. L. (1983a). Solvent-accessible surfaces of proteins and nucleic acids. Science, 221, 709–713.Google Scholar
Connolly, M. L. (1983b). Analytical molecular surface calculation. J. Appl. Cryst. 16, 548–558.Google Scholar
Langridge, R., Ferrin, T. E., Kuntz, I. D. & Connolly, M. L. (1981). Real-time color graphics in studies of molecular interactions. Science, 211, 661–666.Google Scholar
Pearl, L. H. & Honegger, A. (1983). Generation of molecular surfaces for graphic display. J. Mol. Graphics, 1, 9–12, C2.Google Scholar








































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