The solvent-flattening procedure

Zhang, K. Y. J.; Cowtan, K. D.; Main, P.

doi:10.1107/97809553602060000687

International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

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International Tables for Crystallography (2006). Vol. F. ch. 15.1, p. 314 | 1 | 2 |

Section 15.1.2.1.3. The solvent-flattening procedure

K. Y. J. Zhang,^a K. D. Cowtan^b ^* and P. Main^c

^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

15.1.2.1.3. The solvent-flattening procedure

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Once the envelope has been determined, solvent flattening is performed by simply setting the density in the solvent region to the expected value, $[\rho_{\rm solv}]$ : $[\rho_{\rm mod} ({\bf x}) = \left\{\matrix{\rho({\bf x}), &\rho_{\rm ave} ({\bf x}) \gt \rho_{\rm cut}\cr \rho_{\rm solv}, &\rho_{\rm ave}({\bf x}) \lt \rho_{\rm cut}\cr}\right.. \eqno(15.1.2.6)]$ If the electron density has not been calculated on an absolute scale, the solvent density may be set to its mean value.

A related method is solvent flipping, developed by Abrahams & Leslie (1996). In this approach, the flattening operation is modified by the introduction of a relaxation factor, γ, where γ is positive, effectively `flipping' the density in the solvent region. $[\rho_{\rm mod} ({\bf x}) = \left\{\matrix{\rho({\bf x}),\hfill &\rho_{\rm ave} ({\bf x}) \gt \rho_{\rm cut}\cr \rho_{\rm solv} - [\gamma/(1 - \gamma)] [\rho({\bf x}) - \rho_{\rm solv}], &\rho_{\rm ave} ({\bf x}) \lt \rho_{\rm cut}\cr}\right.. \eqno(15.1.2.7)]$ The effect of this modification is to correct for the problem of independence in phase combination and is discussed in Section 15.1.4.3.

References

Abrahams, J. P. & Leslie, A. G. W. (1996). Methods used in the structure determination of bovine mitochondrial F₁ ATPase. Acta Cryst. D52, 30–42.Google Scholar

International Tables for Crystallography (2006). Vol. F. ch. 15.1, p. 314