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, p. 312   | 1 | 2 |

Table 15.1.2.1 

K. Y. J. Zhang,a K. D. Cowtanb* and P. Mainc

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
Correspondence e-mail:  cowtan+email@ysbl.york.ac.uk

Table 15.1.2.1 | top | pdf |
Constraints used in density modification

Constraints Use Effectiveness and limitation
(1) Solvent flatness Solvent flattening Works best at medium resolution. Relatively resolution insensitive. Good for phase refinement. Weak on phase extension.
(2) Ideal electron-density distribution Histogram matching Works at a wide range of resolutions. More effective at higher resolution. Very effective for phase extension.
(3) Equal molecules Molecular averaging Works better at low to medium resolution. Its phasing power increases with the number of molecules in the asymmetric unit.
(4) Protein backbone connectivity Skeletonization Requires near atomic resolution to work.
(5) Local shape of electron density Sayre's equation The equation is exact at atomic resolution. It can be used at non-atomic resolution by choosing an appropriate shape function. Its phasing power increases quickly with resolution. Very powerful for phase extension.
(6) Atomicity Atomization If the initial map is good enough, iteration could lead to a final model.
(7) Structure-factor amplitudes Sim weighting Can be used to estimate the reliability of the calculated phases after density modification. It assumes the random distribution of errors that caused the discrepancy between the calculated and observed structure-factor amplitudes.
(8) Experimental phases Phase combination This can be used to filter out the incorrect component of the estimated phases. Most phase-combination procedures assume independence between the calculated and observed phases.