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Conclusions
International Tables for Crystallography (2012). Vol. F, Section 18.6.10, p. 517 [ doi:10.1107/97809553602060000860 ]
Conclusions 18.6.10. Conclusions CNS is a general system for structure determination by X-ray crystallography and solution NMR. It covers the whole spectrum of methods used to solve X-ray or solution NMR structures. The multi-layer architecture allows use of the system with different levels of expertise. The HTML interface ...
Refinement bias
International Tables for Crystallography (2012). Vol. F, Section 15.2.8, p. 405 [ doi:10.1107/97809553602060000848 ]
... Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, ...
Difference-map coefficients
International Tables for Crystallography (2012). Vol. F, Section 15.2.7, p. 405 [ doi:10.1107/97809553602060000848 ]
... map coefficients 15.2.7. Difference-map coefficients The computer program SIGMAA (Read, 1986) has been developed to implement the results described here. ... et al., 2005). References Afonine, P. V., Grosse-Kunstleve, R. W. & Adams, P. D. (2005). CCP4 Newsletter, No. 42 ... contribution 8. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Refinement of macromolecular structures by the maximum- ...
Estimation of overall coordinate error
International Tables for Crystallography (2012). Vol. F, Section 15.2.6, pp. 404-405 [ doi:10.1107/97809553602060000848 ]
... coordinate errors are consistent with a particular distribution of amplitudes (Read, 1990). If the simplifying assumption is made that all ... is Gaussian: the Luzzati plot (Luzzati, 1952) and the plot (Read, 1986). Unfortunately, the central assumption is not justified; atoms ... effects that cause the Luzzati and plots to give underestimates (Read, 1990). Chief among these are the correlation of ...
Model bias in combined phase maps
International Tables for Crystallography (2012). Vol. F, Section 15.2.5.2, p. 404 [ doi:10.1107/97809553602060000848 ]
Model bias in combined phase maps 15.2.5.2. Model bias in combined phase maps When model phase information is combined with, for instance, multiple isomorphous replacement (MIR) phase information, there will still be model bias in the acentric map coefficients, to the extent that the model influences the final phases. However, it ...
[more results from section 15.2.5 in volume F]
Figure-of-merit weighting for model phases
International Tables for Crystallography (2012). Vol. F, Section 15.2.4, p. 404 [ doi:10.1107/97809553602060000848 ]
Figure-of-merit weighting for model phases 15.2.4. Figure-of-merit weighting for model phases Blow & Crick (1959) and Sim (1959) showed that the electron-density map with the least r.m.s. error is calculated from centroid structure factors. This conclusion follows from Parseval's theorem, because the centroid structure factor (its ...
Accounting for measurement errors
International Tables for Crystallography (2012). Vol. F, Section 15.2.3.5, p. 403 [ doi:10.1107/97809553602060000848 ]
... in measuring the observed intensities or amplitudes can be neglected (Read, 1986). As the model improves, the effect of measurement ... amplitudes, and then increase the variance of this Gaussian (Pannu & Read, 1996). Finally, the convolution of the likelihood function (expressed ... error can be evaluated by using a series approximation (Pannu & Read, 1996). This has the benefit that it allows ...
[more results from section 15.2.3 in volume F]
Parseval's theorem
International Tables for Crystallography (2012). Vol. F, Section 15.2.2.1, p. 401 [ doi:10.1107/97809553602060000848 ]
... the true map than a featureless map. References Wilson, A. J. C. (1949). The probability distribution of X-ray intensities. ...
[more results from section 15.2.2 in volume F]
Introduction
International Tables for Crystallography (2012). Vol. F, Section 15.2.1, p. 401 [ doi:10.1107/97809553602060000848 ]
Introduction 15.2.1. Introduction The intensities of X-ray diffraction spots measured from a crystal give us only the amplitudes of the diffracted waves. To reconstruct a map of the electron density in the crystal, the unmeasured phase information is also required. In fact, the phases are much more important to the ...
Model phases: probabilities, bias and maps
International Tables for Crystallography (2012). Vol. F, ch. 15.2, pp. 401-406 [ doi:10.1107/97809553602060000848 ]
... with two-dimensional Fourier transforms of photographs (Oppenheim & Lim, 1981; Read, 1997) showed that the phases of one completely overwhelmed the ... many protein crystals display noncrystallographic symmetry; as discussed elsewhere (Vellieux & Read, 1997; Kleywegt & Read, 1997), the resulting relationships among structure factors are exploited ...
International Tables for Crystallography (2012). Vol. F, Section 18.6.10, p. 517 [ doi:10.1107/97809553602060000860 ]
Conclusions 18.6.10. Conclusions CNS is a general system for structure determination by X-ray crystallography and solution NMR. It covers the whole spectrum of methods used to solve X-ray or solution NMR structures. The multi-layer architecture allows use of the system with different levels of expertise. The HTML interface ...
Refinement bias
International Tables for Crystallography (2012). Vol. F, Section 15.2.8, p. 405 [ doi:10.1107/97809553602060000848 ]
... Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, ...
Difference-map coefficients
International Tables for Crystallography (2012). Vol. F, Section 15.2.7, p. 405 [ doi:10.1107/97809553602060000848 ]
... map coefficients 15.2.7. Difference-map coefficients The computer program SIGMAA (Read, 1986) has been developed to implement the results described here. ... et al., 2005). References Afonine, P. V., Grosse-Kunstleve, R. W. & Adams, P. D. (2005). CCP4 Newsletter, No. 42 ... contribution 8. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Refinement of macromolecular structures by the maximum- ...
Estimation of overall coordinate error
International Tables for Crystallography (2012). Vol. F, Section 15.2.6, pp. 404-405 [ doi:10.1107/97809553602060000848 ]
... coordinate errors are consistent with a particular distribution of amplitudes (Read, 1990). If the simplifying assumption is made that all ... is Gaussian: the Luzzati plot (Luzzati, 1952) and the plot (Read, 1986). Unfortunately, the central assumption is not justified; atoms ... effects that cause the Luzzati and plots to give underestimates (Read, 1990). Chief among these are the correlation of ...
Model bias in combined phase maps
International Tables for Crystallography (2012). Vol. F, Section 15.2.5.2, p. 404 [ doi:10.1107/97809553602060000848 ]
Model bias in combined phase maps 15.2.5.2. Model bias in combined phase maps When model phase information is combined with, for instance, multiple isomorphous replacement (MIR) phase information, there will still be model bias in the acentric map coefficients, to the extent that the model influences the final phases. However, it ...
[more results from section 15.2.5 in volume F]
Figure-of-merit weighting for model phases
International Tables for Crystallography (2012). Vol. F, Section 15.2.4, p. 404 [ doi:10.1107/97809553602060000848 ]
Figure-of-merit weighting for model phases 15.2.4. Figure-of-merit weighting for model phases Blow & Crick (1959) and Sim (1959) showed that the electron-density map with the least r.m.s. error is calculated from centroid structure factors. This conclusion follows from Parseval's theorem, because the centroid structure factor (its ...
Accounting for measurement errors
International Tables for Crystallography (2012). Vol. F, Section 15.2.3.5, p. 403 [ doi:10.1107/97809553602060000848 ]
... in measuring the observed intensities or amplitudes can be neglected (Read, 1986). As the model improves, the effect of measurement ... amplitudes, and then increase the variance of this Gaussian (Pannu & Read, 1996). Finally, the convolution of the likelihood function (expressed ... error can be evaluated by using a series approximation (Pannu & Read, 1996). This has the benefit that it allows ...
[more results from section 15.2.3 in volume F]
Parseval's theorem
International Tables for Crystallography (2012). Vol. F, Section 15.2.2.1, p. 401 [ doi:10.1107/97809553602060000848 ]
... the true map than a featureless map. References Wilson, A. J. C. (1949). The probability distribution of X-ray intensities. ...
[more results from section 15.2.2 in volume F]
Introduction
International Tables for Crystallography (2012). Vol. F, Section 15.2.1, p. 401 [ doi:10.1107/97809553602060000848 ]
Introduction 15.2.1. Introduction The intensities of X-ray diffraction spots measured from a crystal give us only the amplitudes of the diffracted waves. To reconstruct a map of the electron density in the crystal, the unmeasured phase information is also required. In fact, the phases are much more important to the ...
Model phases: probabilities, bias and maps
International Tables for Crystallography (2012). Vol. F, ch. 15.2, pp. 401-406 [ doi:10.1107/97809553602060000848 ]
... with two-dimensional Fourier transforms of photographs (Oppenheim & Lim, 1981; Read, 1997) showed that the phases of one completely overwhelmed the ... many protein crystals display noncrystallographic symmetry; as discussed elsewhere (Vellieux & Read, 1997; Kleywegt & Read, 1997), the resulting relationships among structure factors are exploited ...
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