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

International Tables for Crystallography (2012). Vol. F, ch. 15.3, p. 407   | 1 | 2 |

Section 15.3.1. Introduction

K. D. Cowtan,a* K. Y. J. Zhangb and P. Mainc

aDepartment of Chemistry, University of York, York YO1 5DD, England,bDivision of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Seattle, WA 90109, USA, and cDepartment of Physics, University of York, York YO1 5DD, England
Correspondence e-mail:  cowtan@ysbl.york.ac.uk

15.3.1. Introduction

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DM is an automated procedure for phase improvement by iterated density modification. It is used to obtain a set of improved phases and figures of merit, using as a starting point the observed diffraction amplitudes and some initial poor estimates for the phases and figures of merit. DM improves the phases through an alternate application of two processes: real-space electron-density modification and reciprocal-space phase combination. DM can perform solvent flattening, histogram matching, multi-resolution modification, averaging, skeletonization and Sayre refinement, as well as conventional or reflection-omit phase combination. Solvent and averaging masks may be input by the user or calculated automatically. Averaging operators may be refined within the program. Multiple averaging domains may be averaged using different operators.

DMMULTI is a modified version of the DM software that can perform density modification simultaneously across multiple crystal forms. The procedure is general, handling an arbitrary number of domains appearing in an arbitrary number of crystal forms. Initial phases may be provided for one or more crystal forms; however, improved phases are calculated in every crystal form.

DM and DMMULTI are distributed as a part of the CCP4 suite of software for protein crystallography (Collaborative Computational Project, Number 4, 1994[link]). The theoretical and algorithmic bases for the DM and DMMULTI software suites are reviewed in Chapter 15.1[link] . In this chapter, some specific issues concerning the programs are described, including program oper­ation, data preparation, choices of modes and code description.

References

Collaborative Computational Project, Number 4 (1994). The CCP4 suite: programs for protein crystallography. Acta Cryst. D50, 760–763.








































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