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Density modification: theory and practice
This lecture was presented as a powerpoint presentation. To view the slides either use the table of contents below or
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Table of Contents
Density modification: theory and practice
Solvent flattening and NCS averaging: real space
Solvent flattening: real and reciprocal space
NCS averaging and solvent flattening: real space
NCS averaging and solvent flattening: reciprocal space
Solvent flipping: the gamma correction
Translational NCS
Solvent flattening at atomic resolution
Sayre's equation
Sayre's equation at low resolution
Histogram matching
Likelihood and density modification
Atomisation
Detecting NCS
Types of NCS
Defining NCS operators
Domain rotation function
Phased translation function
Defining masks for solvent flattening
Defining masks for averaging
Case history: taq polymerase
Case history: pertussis toxin
Real-space MR for pertussis toxin
Local correlation envelope for pertussis toxin
Case history: Shiga-like toxin B-subunit + trisaccharide
Author: Randy J. Read
Email: rjr27@cam.ac.uk
Home Page: http://www-structmed.cimr.cam.ac.uk/xtal/index.html
Acknowledgments
Several of the schematic figures have been adapted from
Kleywegt & Read, cited below.
The figure illustrating histogram matching has been adapted from
Cowtan & Zhang, also cited below.
References
Vellieux, F.M.D. & Read, R.J. "Non-crystallographic symmetry
averaging in phase refinement and extension", Methods Enzymol.
277: 18-53 (1997).
Kleywegt, G.J. & Read, R.J. "Not your average density",
Structure 5: 1557-1569 (1997).
Cowtan, K.D. & Zhang, K.Y.J. "Density modification for macromolecular
phase improvement", Prog. Biophys. Mol. Biol. 72: 245-270
(1999).
© 1999-2005 Randy
J Read, University of Cambridge. All rights reserved.
Last updated:
7 June, 2005