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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 ]
... though often lengthy, process. The recently developed Solve software (Terwilliger & Berendzen, 1999b) is designed to fully automate this class of structure ... for MIR data thoughout Solve is Bayesian correlated phasing (Terwilliger & Berendzen, 1996; Terwilliger & Eisenberg, 1987), which takes into account the correlation ... Bayesian calculations of phase probabilities are very slow (e.g. Terwilliger & Berendzen, 1997; de La Fortelle & Bricogne, 1997). Consequently, we ...
Conclusions
International Tables for Crystallography (2012). Vol. F, Section 14.3.9, p. 382 [ doi:10.1107/97809553602060000846 ]
Conclusions 14.3.9. Conclusions The Solve algorithm is very useful for solving macromolecular structures by the MIR and MAD methods. It has been used to solve MAD structures with as many 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 ]
... 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 archival file for macromolecular structures. J. Mol. Biol. 112, 535-542. International Tables for Crystallography ( ...
Automated MIR and MAD structure determination
International Tables for Crystallography (2012). Vol. F, Section 14.3.7, pp. 381-382 [ doi:10.1107/97809553602060000846 ]
... for local scaling of each individual data set [see Terwilliger & Berendzen (1999b) for additional details]. Once MIR data have been ... of . Acta Cryst. D50, 11-16. Terwilliger, T. C. & Berendzen, J. (1999b). Automated MIR and MAD structure solution. Acta ...
Scoring of trial heavy-atom solutions
International Tables for Crystallography (2012). Vol. F, Section 14.3.6, pp. 380-381 [ doi:10.1107/97809553602060000846 ]
... 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 a ... 1990; Xiang et al., 1993; Abrahams et al., 1994; Terwilliger & Berendzen, 1999a,c), and histogram matching of electron densities (Zhang & ...
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 ]
Conversion of MAD data to a pseudo-SIRAS form 14.3.5. Conversion of MAD data to a pseudo-SIRAS form The conversion of MAD data to a pseudo-SIRAS form that has almost the same information content requires two important assumptions. The first assumption is that the structure factor corresponding to anomalously ...
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 ]
... for MIR data thoughout Solve is Bayesian correlated phasing (Terwilliger & Berendzen, 1996; Terwilliger & Eisenberg, 1987), which takes into account the correlation ... Bayesian calculations of phase probabilities are very slow (e.g. Terwilliger & Berendzen, 1997; de La Fortelle & Bricogne, 1997). Consequently, we have ... diffraction methods. Methods Enzymol. 276, 472-494. Terwilliger, T. C. & Berendzen, J. (1996). Correlated phasing of multiple isomorphous replacement ...
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 ]
... sites. Acta Cryst. D50, 667-674. Dickerson, R. E., Kendrew, J. C. & Strandberg, B. E. (1961). The crystal structure of ... 1994). SnB: crystal structure determination via shake-and-bake. J. Appl. Cryst. 27, 613-621. Sheldrick, G. M. (1990). ...
Introduction
International Tables for Crystallography (2012). Vol. F, Section 14.3.1, p. 379 [ doi:10.1107/97809553602060000846 ]
... though often lengthy, process. The recently developed Solve software (Terwilliger & Berendzen, 1999b) is designed to fully automate this class of structure ... replacement information. Acta Cryst. D50, 17-23. Terwilliger, T. C. & Berendzen, J. (1999b). Automated MIR and MAD structure solution. Acta ...
International Tables for Crystallography (2012). Vol. F, ch. 14.3, pp. 379-383 [ doi:10.1107/97809553602060000846 ]
... though often lengthy, process. The recently developed Solve software (Terwilliger & Berendzen, 1999b) is designed to fully automate this class of structure ... for MIR data thoughout Solve is Bayesian correlated phasing (Terwilliger & Berendzen, 1996; Terwilliger & Eisenberg, 1987), which takes into account the correlation ... Bayesian calculations of phase probabilities are very slow (e.g. Terwilliger & Berendzen, 1997; de La Fortelle & Bricogne, 1997). Consequently, we ...
Conclusions
International Tables for Crystallography (2012). Vol. F, Section 14.3.9, p. 382 [ doi:10.1107/97809553602060000846 ]
Conclusions 14.3.9. Conclusions The Solve algorithm is very useful for solving macromolecular structures by the MIR and MAD methods. It has been used to solve MAD structures with as many 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 ]
... 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 archival file for macromolecular structures. J. Mol. Biol. 112, 535-542. International Tables for Crystallography ( ...
Automated MIR and MAD structure determination
International Tables for Crystallography (2012). Vol. F, Section 14.3.7, pp. 381-382 [ doi:10.1107/97809553602060000846 ]
... for local scaling of each individual data set [see Terwilliger & Berendzen (1999b) for additional details]. Once MIR data have been ... of . Acta Cryst. D50, 11-16. Terwilliger, T. C. & Berendzen, J. (1999b). Automated MIR and MAD structure solution. Acta ...
Scoring of trial heavy-atom solutions
International Tables for Crystallography (2012). Vol. F, Section 14.3.6, pp. 380-381 [ doi:10.1107/97809553602060000846 ]
... 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 a ... 1990; Xiang et al., 1993; Abrahams et al., 1994; Terwilliger & Berendzen, 1999a,c), and histogram matching of electron densities (Zhang & ...
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 ]
Conversion of MAD data to a pseudo-SIRAS form 14.3.5. Conversion of MAD data to a pseudo-SIRAS form The conversion of MAD data to a pseudo-SIRAS form that has almost the same information content requires two important assumptions. The first assumption is that the structure factor corresponding to anomalously ...
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 ]
... for MIR data thoughout Solve is Bayesian correlated phasing (Terwilliger & Berendzen, 1996; Terwilliger & Eisenberg, 1987), which takes into account the correlation ... Bayesian calculations of phase probabilities are very slow (e.g. Terwilliger & Berendzen, 1997; de La Fortelle & Bricogne, 1997). Consequently, we have ... diffraction methods. Methods Enzymol. 276, 472-494. Terwilliger, T. C. & Berendzen, J. (1996). Correlated phasing of multiple isomorphous replacement ...
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 ]
... sites. Acta Cryst. D50, 667-674. Dickerson, R. E., Kendrew, J. C. & Strandberg, B. E. (1961). The crystal structure of ... 1994). SnB: crystal structure determination via shake-and-bake. J. Appl. Cryst. 27, 613-621. Sheldrick, G. M. (1990). ...
Introduction
International Tables for Crystallography (2012). Vol. F, Section 14.3.1, p. 379 [ doi:10.1107/97809553602060000846 ]
... though often lengthy, process. The recently developed Solve software (Terwilliger & Berendzen, 1999b) is designed to fully automate this class of structure ... replacement information. Acta Cryst. D50, 17-23. Terwilliger, T. C. & Berendzen, J. (1999b). Automated MIR and MAD structure solution. Acta ...
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