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Molecular replacement with MOLREP
International Tables for Crystallography (2012). Vol. F, ch. 13.5, pp. 364-366 [ doi:10.1107/97809553602060000843 ]
... MOLREP is an automated program for molecular replacement that utilizes a number of original approaches to rotational and translational search and ... Since the first publication describing the program, MOLREP has acquired a variety of features that include weighting of the X-ray ... models, and rigid-body refinement. The program can run in a fully automatic mode using optimized parameters calculated from the ...
Atomic resolution structures
International Tables for Crystallography (2012). Vol. F, Section 21.2.4, p. 673 [ doi:10.1107/97809553602060000880 ]
... is at present too limited to provide sufficient data for a meaningful statistical analysis. In the meantime, atomic resolution protein structures ... contrast, the [omega] torsion angle about the peptide bond exhibits a wider distribution, with a mean of 179.0(56)° compared to 179.6(47)° previously ...
Assessing the quality in specific regions of a model
International Tables for Crystallography (2012). Vol. F, Section 21.2.3.1.3.2, pp. 670-673 [ doi:10.1107/97809553602060000880 ]
Assessing the quality in specific regions of a model 21.2.3.1.3.2. Assessing the quality in specific regions of a model The main purpose for computing the four local quality ... Density correlation (Table 21.2.3.3), is to identify problem regions in a model. In order to do this effectively, it is ...
[more results from section 21.2.3 in volume F]
Deviations from standard atomic volumes as a quality measure for protein crystal structures
International Tables for Crystallography (2012). Vol. F, Section 21.2.2.2.3, pp. 664-665 [ doi:10.1107/97809553602060000880 ]
Deviations from standard atomic volumes as a quality measure for protein crystal structures 21.2.2.2.3. Deviations from standard atomic volumes as a quality measure for protein crystal structures The observations that protein ... found that the packing values of the NMR models displayed a much larger scatter than those of the corresponding crystal ...
[more results from section 21.2.2 in volume F]
Introduction
International Tables for Crystallography (2012). Vol. F, Section 21.2.1, p. 662 [ doi:10.1107/97809553602060000880 ]
... of high enough resolution to define the atomic positions of a macromolecule with sufficient precision. Deriving the atomic models from the ... methods for evaluating the quality of these structures has become a very important requirement. A variety of validation procedures have been proposed by many ...
Assessing the quality of macromolecular structures
International Tables for Crystallography (2012). Vol. F, ch. 21.2, pp. 662-676 [ doi:10.1107/97809553602060000880 ]
... illustrated in some detail and the package SFCHECK, which combines a set of criteria for evaluating the quality of the experimental ... of high enough resolution to define the atomic positions of a macromolecule with sufficient precision. Deriving the atomic models from the ... methods for evaluating the quality of these structures has become a very important requirement. A variety of validation procedures have ...
Distribution
International Tables for Crystallography (2012). Vol. F, Section 13.5.9, p. 366 [ doi:10.1107/97809553602060000843 ]
... and Windows. It is available free to academic users as a standalone version or as part of the CCP4 suite. The ... All inquiries about the program should be addressed to Alexei Vagin (alexei@ysbl.york.ac.uk). References International Tables for Crystallography (2012). ...
Fitting the model into electron density
International Tables for Crystallography (2012). Vol. F, Section 13.5.8, p. 366 [ doi:10.1107/97809553602060000843 ]
... data (multiple isomorphous replacement or multiwavelength anomalous diffraction) or from a partial MR solution, e.g. when one domain of a multi-domain protein has been located in the unit cell. Positioning a model into electron density (or into an EM reconstruction) ...
Multi-copy search
International Tables for Crystallography (2012). Vol. F, Section 13.5.7, pp. 365-366 [ doi:10.1107/97809553602060000843 ]
... Multi-copy search The MR method has been extended to a simultaneous search for multiple copies of the macromolecule in the unit cell (Vagin & Teplyakov, 2000). The central point of this approach is the construction of a dimer search model from the properly oriented monomers using ...
Positional search
International Tables for Crystallography (2012). Vol. F, Section 13.5.6, p. 365 [ doi:10.1107/97809553602060000843 ]
Positional search 13.5.6. Positional search The full-symmetry TF (Vagin, 1989) originates from the T2 function of Crowther & Blow (1967 ... 1981). It simultaneously uses all symmetry operators, resulting in a single peak with an improved signal-to-noise ratio which ... the unit cell. In addition, the TF is coupled with a PF to remove false maxima which correspond to interpenetrating ...
International Tables for Crystallography (2012). Vol. F, ch. 13.5, pp. 364-366 [ doi:10.1107/97809553602060000843 ]
... MOLREP is an automated program for molecular replacement that utilizes a number of original approaches to rotational and translational search and ... Since the first publication describing the program, MOLREP has acquired a variety of features that include weighting of the X-ray ... models, and rigid-body refinement. The program can run in a fully automatic mode using optimized parameters calculated from the ...
Atomic resolution structures
International Tables for Crystallography (2012). Vol. F, Section 21.2.4, p. 673 [ doi:10.1107/97809553602060000880 ]
... is at present too limited to provide sufficient data for a meaningful statistical analysis. In the meantime, atomic resolution protein structures ... contrast, the [omega] torsion angle about the peptide bond exhibits a wider distribution, with a mean of 179.0(56)° compared to 179.6(47)° previously ...
Assessing the quality in specific regions of a model
International Tables for Crystallography (2012). Vol. F, Section 21.2.3.1.3.2, pp. 670-673 [ doi:10.1107/97809553602060000880 ]
Assessing the quality in specific regions of a model 21.2.3.1.3.2. Assessing the quality in specific regions of a model The main purpose for computing the four local quality ... Density correlation (Table 21.2.3.3), is to identify problem regions in a model. In order to do this effectively, it is ...
[more results from section 21.2.3 in volume F]
Deviations from standard atomic volumes as a quality measure for protein crystal structures
International Tables for Crystallography (2012). Vol. F, Section 21.2.2.2.3, pp. 664-665 [ doi:10.1107/97809553602060000880 ]
Deviations from standard atomic volumes as a quality measure for protein crystal structures 21.2.2.2.3. Deviations from standard atomic volumes as a quality measure for protein crystal structures The observations that protein ... found that the packing values of the NMR models displayed a much larger scatter than those of the corresponding crystal ...
[more results from section 21.2.2 in volume F]
Introduction
International Tables for Crystallography (2012). Vol. F, Section 21.2.1, p. 662 [ doi:10.1107/97809553602060000880 ]
... of high enough resolution to define the atomic positions of a macromolecule with sufficient precision. Deriving the atomic models from the ... methods for evaluating the quality of these structures has become a very important requirement. A variety of validation procedures have been proposed by many ...
Assessing the quality of macromolecular structures
International Tables for Crystallography (2012). Vol. F, ch. 21.2, pp. 662-676 [ doi:10.1107/97809553602060000880 ]
... illustrated in some detail and the package SFCHECK, which combines a set of criteria for evaluating the quality of the experimental ... of high enough resolution to define the atomic positions of a macromolecule with sufficient precision. Deriving the atomic models from the ... methods for evaluating the quality of these structures has become a very important requirement. A variety of validation procedures have ...
Distribution
International Tables for Crystallography (2012). Vol. F, Section 13.5.9, p. 366 [ doi:10.1107/97809553602060000843 ]
... and Windows. It is available free to academic users as a standalone version or as part of the CCP4 suite. The ... All inquiries about the program should be addressed to Alexei Vagin (alexei@ysbl.york.ac.uk). References International Tables for Crystallography (2012). ...
Fitting the model into electron density
International Tables for Crystallography (2012). Vol. F, Section 13.5.8, p. 366 [ doi:10.1107/97809553602060000843 ]
... data (multiple isomorphous replacement or multiwavelength anomalous diffraction) or from a partial MR solution, e.g. when one domain of a multi-domain protein has been located in the unit cell. Positioning a model into electron density (or into an EM reconstruction) ...
Multi-copy search
International Tables for Crystallography (2012). Vol. F, Section 13.5.7, pp. 365-366 [ doi:10.1107/97809553602060000843 ]
... Multi-copy search The MR method has been extended to a simultaneous search for multiple copies of the macromolecule in the unit cell (Vagin & Teplyakov, 2000). The central point of this approach is the construction of a dimer search model from the properly oriented monomers using ...
Positional search
International Tables for Crystallography (2012). Vol. F, Section 13.5.6, p. 365 [ doi:10.1107/97809553602060000843 ]
Positional search 13.5.6. Positional search The full-symmetry TF (Vagin, 1989) originates from the T2 function of Crowther & Blow (1967 ... 1981). It simultaneously uses all symmetry operators, resulting in a single peak with an improved signal-to-noise ratio which ... the unit cell. In addition, the TF is coupled with a PF to remove false maxima which correspond to interpenetrating ...
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