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Molecular replacement with MOLREP
Vagin, A. and Teplyakov, A.  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
Wodak, S. J., Vagin, A. A., Richelle, J., Das, U., Pontius, J. and Berman, H. M.  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
Wodak, S. J., Vagin, A. A., Richelle, J., Das, U., Pontius, J. and Berman, H. M.  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
Wodak, S. J., Vagin, A. A., Richelle, J., Das, U., Pontius, J. and Berman, H. M.  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
Wodak, S. J., Vagin, A. A., Richelle, J., Das, U., Pontius, J. and Berman, H. M.  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
Wodak, S. J., Vagin, A. A., Richelle, J., Das, U., Pontius, J. and Berman, H. M.  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
Vagin, A. and Teplyakov, A.  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
Vagin, A. and Teplyakov, A.  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
Vagin, A. and Teplyakov, A.  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
Vagin, A. and Teplyakov, A.  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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