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Automated MAD and MIR structure solution
International Tables for Crystallography (2012). Vol. F, ch. 14.3, pp. 379-383 [ doi:10.1107/97809553602060000846 ]
... straightforward, though often lengthy, process. The recently developed Solve software (Terwilliger & Berendzen, 1999b) is designed to fully automate this class of ... the conversion of MAD data to a pseudo-SIRAS form (Terwilliger, 1994b) that allows much more rapid analysis than one involving ... of difference Patterson functions or by semi-automated analysis (e.g. Terwilliger et al., 1987; Chang & Lewis, 1994; Vagin & Teplyakov, 1998) ...
Conclusions
International Tables for Crystallography (2012). Vol. F, Section 14.3.9, p. 382 [ doi:10.1107/97809553602060000846 ]
... as 56 selenium atoms in the asymmetric unit (W. Smith & C. Janson, personal communication). From the user's point of ...
Generation of model X-ray data sets
International Tables for Crystallography (2012). Vol. F, Section 14.3.8, p. 382 [ doi:10.1107/97809553602060000846 ]
... trial solution onto the (known) correct solution. References Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). Protein data bank: computer-based ...
Automated MIR and MAD structure determination
International Tables for Crystallography (2012). Vol. F, Section 14.3.7, pp. 381-382 [ doi:10.1107/97809553602060000846 ]
... basis for local scaling of each individual data set [see Terwilliger & Berendzen (1999b) for additional details]. Once MIR data have ... estimate of the Patterson function for the anomalously scattering atoms (Terwilliger, 1994a). An automated search of the Patterson function is ... replacement and anomalous scattering measurements. Acta Cryst. A31, 480-487. Terwilliger, T. C. (1994a). MAD phasing: Bayesian estimates of ...
Scoring of trial heavy-atom solutions
International Tables for Crystallography (2012). Vol. F, Section 14.3.6, pp. 380-381 [ doi:10.1107/97809553602060000846 ]
... heavy-atom sites in the trial solution. The weighting factor (Terwilliger & Berendzen, 1999b) is adjusted so that if two solutions have ... the quality of phasing despite its susceptibility to systematic error (Terwilliger & Berendzen, 1999b). The overall figure of merit is essentially ... in Solve is carried out using origin-removed Patterson refinement (Terwilliger & Eisenberg, 1983), occupancies of heavy-atom sites are relatively ...
Conversion of MAD data to a pseudo-SIRAS form
International Tables for Crystallography (2012). Vol. F, Section 14.3.5, pp. 379-380 [ doi:10.1107/97809553602060000846 ]
... wavelength (), and an anomalous difference () at the same standard wavelength (Terwilliger, 1994b). It is easy to see that these three ... structure factor replaced by , and the anomalous difference replaced by (Terwilliger, 1994b). This is the approach taken by Solve. In ... a function of X-ray wavelength. We can therefore write (Terwilliger, 1994b) where is an X-ray wavelength arbitrarily defined ...
The need for rapid refinement and phasing during automated structure solution
International Tables for Crystallography (2012). Vol. F, Section 14.3.4, p. 379 [ doi:10.1107/97809553602060000846 ]
... method chosen on this basis was origin-removed Patterson refinement (Terwilliger & Eisenberg, 1983), which treats each derivative in an MIR data ... used for MIR data thoughout Solve is Bayesian correlated phasing (Terwilliger & Berendzen, 1996; Terwilliger & Eisenberg, 1987), which takes into account the correlation of ...
Decision making and structure solution
International Tables for Crystallography (2012). Vol. F, Section 14.3.3, p. 379 [ doi:10.1107/97809553602060000846 ]
Decision making and structure solution 14.3.3. Decision making and structure solution The process of structure solution can be thought of largely as a decision-making process. In the early stages of solution, a crystallographer must choose which of several potential trial solutions may be worth pursuing. At a later stage, the ...
MAD and MIR structure solution
International Tables for Crystallography (2012). Vol. F, Section 14.3.2, p. 379 [ doi:10.1107/97809553602060000846 ]
... of difference Patterson functions or by semi-automated analysis (e.g. Terwilliger et al., 1987; Chang & Lewis, 1994; Vagin & Teplyakov, 1998). ... Acta Cryst. D50, 667-674. Dickerson, R. E., Kendrew, J. C. & Strandberg, B. E. (1961). The crystal structure of myoglobin ... 1195. Miller, R., Gallo, S. M., Khalak, H. G. & Weeks, C. M. (1994). SnB: crystal structure determination via shake- ...
Introduction
International Tables for Crystallography (2012). Vol. F, Section 14.3.1, p. 379 [ doi:10.1107/97809553602060000846 ]
... straightforward, though often lengthy, process. The recently developed Solve software (Terwilliger & Berendzen, 1999b) is designed to fully automate this class of ... the conversion of MAD data to a pseudo-SIRAS form (Terwilliger, 1994b) that allows much more rapid analysis than one involving the full MAD data set. References Terwilliger, T. C. (1994b). MAD phasing: treatment of dispersive ...
International Tables for Crystallography (2012). Vol. F, ch. 14.3, pp. 379-383 [ doi:10.1107/97809553602060000846 ]
... straightforward, though often lengthy, process. The recently developed Solve software (Terwilliger & Berendzen, 1999b) is designed to fully automate this class of ... the conversion of MAD data to a pseudo-SIRAS form (Terwilliger, 1994b) that allows much more rapid analysis than one involving ... of difference Patterson functions or by semi-automated analysis (e.g. Terwilliger et al., 1987; Chang & Lewis, 1994; Vagin & Teplyakov, 1998) ...
Conclusions
International Tables for Crystallography (2012). Vol. F, Section 14.3.9, p. 382 [ doi:10.1107/97809553602060000846 ]
... as 56 selenium atoms in the asymmetric unit (W. Smith & C. Janson, personal communication). From the user's point of ...
Generation of model X-ray data sets
International Tables for Crystallography (2012). Vol. F, Section 14.3.8, p. 382 [ doi:10.1107/97809553602060000846 ]
... trial solution onto the (known) correct solution. References Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). Protein data bank: computer-based ...
Automated MIR and MAD structure determination
International Tables for Crystallography (2012). Vol. F, Section 14.3.7, pp. 381-382 [ doi:10.1107/97809553602060000846 ]
... basis for local scaling of each individual data set [see Terwilliger & Berendzen (1999b) for additional details]. Once MIR data have ... estimate of the Patterson function for the anomalously scattering atoms (Terwilliger, 1994a). An automated search of the Patterson function is ... replacement and anomalous scattering measurements. Acta Cryst. A31, 480-487. Terwilliger, T. C. (1994a). MAD phasing: Bayesian estimates of ...
Scoring of trial heavy-atom solutions
International Tables for Crystallography (2012). Vol. F, Section 14.3.6, pp. 380-381 [ doi:10.1107/97809553602060000846 ]
... heavy-atom sites in the trial solution. The weighting factor (Terwilliger & Berendzen, 1999b) is adjusted so that if two solutions have ... the quality of phasing despite its susceptibility to systematic error (Terwilliger & Berendzen, 1999b). The overall figure of merit is essentially ... in Solve is carried out using origin-removed Patterson refinement (Terwilliger & Eisenberg, 1983), occupancies of heavy-atom sites are relatively ...
Conversion of MAD data to a pseudo-SIRAS form
International Tables for Crystallography (2012). Vol. F, Section 14.3.5, pp. 379-380 [ doi:10.1107/97809553602060000846 ]
... wavelength (), and an anomalous difference () at the same standard wavelength (Terwilliger, 1994b). It is easy to see that these three ... structure factor replaced by , and the anomalous difference replaced by (Terwilliger, 1994b). This is the approach taken by Solve. In ... a function of X-ray wavelength. We can therefore write (Terwilliger, 1994b) where is an X-ray wavelength arbitrarily defined ...
The need for rapid refinement and phasing during automated structure solution
International Tables for Crystallography (2012). Vol. F, Section 14.3.4, p. 379 [ doi:10.1107/97809553602060000846 ]
... method chosen on this basis was origin-removed Patterson refinement (Terwilliger & Eisenberg, 1983), which treats each derivative in an MIR data ... used for MIR data thoughout Solve is Bayesian correlated phasing (Terwilliger & Berendzen, 1996; Terwilliger & Eisenberg, 1987), which takes into account the correlation of ...
Decision making and structure solution
International Tables for Crystallography (2012). Vol. F, Section 14.3.3, p. 379 [ doi:10.1107/97809553602060000846 ]
Decision making and structure solution 14.3.3. Decision making and structure solution The process of structure solution can be thought of largely as a decision-making process. In the early stages of solution, a crystallographer must choose which of several potential trial solutions may be worth pursuing. At a later stage, the ...
MAD and MIR structure solution
International Tables for Crystallography (2012). Vol. F, Section 14.3.2, p. 379 [ doi:10.1107/97809553602060000846 ]
... of difference Patterson functions or by semi-automated analysis (e.g. Terwilliger et al., 1987; Chang & Lewis, 1994; Vagin & Teplyakov, 1998). ... Acta Cryst. D50, 667-674. Dickerson, R. E., Kendrew, J. C. & Strandberg, B. E. (1961). The crystal structure of myoglobin ... 1195. Miller, R., Gallo, S. M., Khalak, H. G. & Weeks, C. M. (1994). SnB: crystal structure determination via shake- ...
Introduction
International Tables for Crystallography (2012). Vol. F, Section 14.3.1, p. 379 [ doi:10.1107/97809553602060000846 ]
... straightforward, though often lengthy, process. The recently developed Solve software (Terwilliger & Berendzen, 1999b) is designed to fully automate this class of ... the conversion of MAD data to a pseudo-SIRAS form (Terwilliger, 1994b) that allows much more rapid analysis than one involving the full MAD data set. References Terwilliger, T. C. (1994b). MAD phasing: treatment of dispersive ...
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