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Introduction
International Tables for Crystallography (2012). Vol. F, Section 15.3.1, p. 407 [ doi:10.1107/97809553602060000849 ]
Introduction 15.3.1. Introduction 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 ...
DM/DMMULTI software for phase improvement by density modification
International Tables for Crystallography (2012). Vol. F, ch. 15.3, pp. 407-412 [ doi:10.1107/97809553602060000849 ]
... s equation calculation adds another level of complexity, described in Zhang & Main (1990b). Skeletonization imposes the protein histogram and solvent ... from 6 to 1.5Å, according to the method described by Zhang & Main (1990a). The histogram variances should be consistent with ... Institutes of Health for grant support (GM55663). References Abrahams, J. P. (1997). Bias reduction in phase refinement by ...
Example
International Tables for Crystallography (2012). Vol. F, Section 15.1.7, pp. 398-399 [ doi:10.1107/97809553602060000847 ]
... merit and structure-factor amplitude, as a function of resolution (Zhang et al., 1997), This phase correlation over all reflections is ... analysis of 5-carboxymethyl-2-hydroxymuconate isomerase from Escherichia coli. J. Mol. Biol. 210, 881-882. Zhang, K. Y. J., Cowtan, K. D. & Main, P. (1997) ...
Statistical density-modification methods
International Tables for Crystallography (2012). Vol. F, Section 15.1.6, p. 398 [ doi:10.1107/97809553602060000847 ]
Statistical density-modification methods 15.1.6. Statistical density-modification methods Statistical density-modification methods arise from a reinterpretation of the problem of phase improvement in statistical terms, and as a result reduce the problems of bias associated with the classical density-modification methods described above. This is achieved by expressing all information ...
The diagonal approximation
International Tables for Crystallography (2012). Vol. F, Section 15.1.5.2.3, pp. 397-398 [ doi:10.1107/97809553602060000847 ]
The diagonal approximation 15.1.5.2.3. The diagonal approximation The full-matrix solution to equation (15.1.5.4) requires a significant amount of computing, although it can be achieved using FFTs. The diagonal approximation to the normal matrix has been used as an alternative method of solution to the electron-density shift in equation (15.1.5.4 ...
[more results from section 15.1.5 in volume F]
Resolution extrapolation
International Tables for Crystallography (2012). Vol. F, Section 15.1.4.4, pp. 395-396 [ doi:10.1107/97809553602060000847 ]
Resolution extrapolation 15.1.4.4. Resolution extrapolation The Fourier coefficients of the density-modified map include nonzero contributions for reflections that were not present in the original electron-density map. These values are commonly used to restore the values of reflections that were missing from the original data (including low-resolution reflections falling ...
[more results from section 15.1.4 in volume F]
Reciprocal-space interpretation of density modification
International Tables for Crystallography (2012). Vol. F, Section 15.1.3, pp. 393-394 [ doi:10.1107/97809553602060000847 ]
Reciprocal-space interpretation of density modification 15.1.3. Reciprocal-space interpretation of density modification Density modification, although mostly performed in real space for ease of application, can be understood in terms of reciprocal-space constraints on structure-factor amplitudes and phases. Main & Rossmann (1966) showed that the NCS-averaging operation in real ...
Atomization
International Tables for Crystallography (2012). Vol. F, Section 15.1.2.6, pp. 392-393 [ doi:10.1107/97809553602060000847 ]
Atomization 15.1.2.6. Atomization The atomization method uses the fact that the structure underlying the map consists of discrete atoms. It attempts to interpret the map by automatically placing atoms and refining their positions. Agarwal & Isaacs (1977) proposed a method for the extension of phases to higher resolutions by interpreting an electron ...
[more results from section 15.1.2 in volume F]
Introduction
International Tables for Crystallography (2012). Vol. F, Section 15.1.1, p. 385 [ doi:10.1107/97809553602060000847 ]
... macromolecular crystallography. Acta Cryst. D49, 186-192. Hoppe, W. & Gassmann, J. (1968). Phase correction, a new method to solve partially ...
International Tables for Crystallography (2012). Vol. F, Section 15.3.1, p. 407 [ doi:10.1107/97809553602060000849 ]
Introduction 15.3.1. Introduction 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 ...
DM/DMMULTI software for phase improvement by density modification
International Tables for Crystallography (2012). Vol. F, ch. 15.3, pp. 407-412 [ doi:10.1107/97809553602060000849 ]
... s equation calculation adds another level of complexity, described in Zhang & Main (1990b). Skeletonization imposes the protein histogram and solvent ... from 6 to 1.5Å, according to the method described by Zhang & Main (1990a). The histogram variances should be consistent with ... Institutes of Health for grant support (GM55663). References Abrahams, J. P. (1997). Bias reduction in phase refinement by ...
Example
International Tables for Crystallography (2012). Vol. F, Section 15.1.7, pp. 398-399 [ doi:10.1107/97809553602060000847 ]
... merit and structure-factor amplitude, as a function of resolution (Zhang et al., 1997), This phase correlation over all reflections is ... analysis of 5-carboxymethyl-2-hydroxymuconate isomerase from Escherichia coli. J. Mol. Biol. 210, 881-882. Zhang, K. Y. J., Cowtan, K. D. & Main, P. (1997) ...
Statistical density-modification methods
International Tables for Crystallography (2012). Vol. F, Section 15.1.6, p. 398 [ doi:10.1107/97809553602060000847 ]
Statistical density-modification methods 15.1.6. Statistical density-modification methods Statistical density-modification methods arise from a reinterpretation of the problem of phase improvement in statistical terms, and as a result reduce the problems of bias associated with the classical density-modification methods described above. This is achieved by expressing all information ...
The diagonal approximation
International Tables for Crystallography (2012). Vol. F, Section 15.1.5.2.3, pp. 397-398 [ doi:10.1107/97809553602060000847 ]
The diagonal approximation 15.1.5.2.3. The diagonal approximation The full-matrix solution to equation (15.1.5.4) requires a significant amount of computing, although it can be achieved using FFTs. The diagonal approximation to the normal matrix has been used as an alternative method of solution to the electron-density shift in equation (15.1.5.4 ...
[more results from section 15.1.5 in volume F]
Resolution extrapolation
International Tables for Crystallography (2012). Vol. F, Section 15.1.4.4, pp. 395-396 [ doi:10.1107/97809553602060000847 ]
Resolution extrapolation 15.1.4.4. Resolution extrapolation The Fourier coefficients of the density-modified map include nonzero contributions for reflections that were not present in the original electron-density map. These values are commonly used to restore the values of reflections that were missing from the original data (including low-resolution reflections falling ...
[more results from section 15.1.4 in volume F]
Reciprocal-space interpretation of density modification
International Tables for Crystallography (2012). Vol. F, Section 15.1.3, pp. 393-394 [ doi:10.1107/97809553602060000847 ]
Reciprocal-space interpretation of density modification 15.1.3. Reciprocal-space interpretation of density modification Density modification, although mostly performed in real space for ease of application, can be understood in terms of reciprocal-space constraints on structure-factor amplitudes and phases. Main & Rossmann (1966) showed that the NCS-averaging operation in real ...
Atomization
International Tables for Crystallography (2012). Vol. F, Section 15.1.2.6, pp. 392-393 [ doi:10.1107/97809553602060000847 ]
Atomization 15.1.2.6. Atomization The atomization method uses the fact that the structure underlying the map consists of discrete atoms. It attempts to interpret the map by automatically placing atoms and refining their positions. Agarwal & Isaacs (1977) proposed a method for the extension of phases to higher resolutions by interpreting an electron ...
[more results from section 15.1.2 in volume F]
Introduction
International Tables for Crystallography (2012). Vol. F, Section 15.1.1, p. 385 [ doi:10.1107/97809553602060000847 ]
... macromolecular crystallography. Acta Cryst. D49, 186-192. Hoppe, W. & Gassmann, J. (1968). Phase correction, a new method to solve partially ...
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