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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 ...
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 ]
... 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 molecules. Both the TF and PF allow the incorporation of a second model already placed in the cell. The TF ...
Rotational search
International Tables for Crystallography (2012). Vol. F, Section 13.5.5, p. 365 [ doi:10.1107/97809553602060000843 ]
... RF solutions may be refined prior to positional search using a rigid-body technique. The refinement is performed in space group ... outcome is evaluated by the correlation coefficient. References Crowther, R. A. (1972). The Molecular Replacement Method, edited by M. G. ...
Preparation of the X-ray data
International Tables for Crystallography (2012). Vol. F, Section 13.5.4, pp. 364-365 [ doi:10.1107/97809553602060000843 ]
... advantageous when only low-resolution data are available. In such a case, the estimation of the overall B factor (Bover) from ... the weighting scheme for the X-ray data, MOLREP estimates a number of parameters for the search model. Two of them ... the target protein ([Omega]), are translated into the parameters of a low-pass filter and a high-pass filter (Gonzalez & ...
Preparation of the search model
International Tables for Crystallography (2012). Vol. F, Section 13.5.3, p. 364 [ doi:10.1107/97809553602060000843 ]
... MR (Lebedev et al., 2008). The options include (i) a polyalanine model, (ii) a model with modified atomic B factors increased proportionally to the atom accessibility and (iii) a model with the corrected amino-acid sequence according to ...
Program operation
International Tables for Crystallography (2012). Vol. F, Section 13.5.2, p. 364 [ doi:10.1107/97809553602060000843 ]
... 13.5.2. Program operation The philosophy behind MOLREP was to provide a tool such that most if not all of the tasks ... organized so that the user can run the program in a dialogue mode. The prompts appear as self-explanatory questions with a choice of possible answers and a list of keywords ...
Introduction
International Tables for Crystallography (2012). Vol. F, Section 13.5.1, p. 364 [ doi:10.1107/97809553602060000843 ]
... further in the future. Traditionally, MR has been implemented as a three-dimensional rotational search followed by a three-dimensional translational search. With recent advances in computing a combined six-dimensional search is becoming feasible; however, to ...
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 ...
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 ...
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 ]
... 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 molecules. Both the TF and PF allow the incorporation of a second model already placed in the cell. The TF ...
Rotational search
International Tables for Crystallography (2012). Vol. F, Section 13.5.5, p. 365 [ doi:10.1107/97809553602060000843 ]
... RF solutions may be refined prior to positional search using a rigid-body technique. The refinement is performed in space group ... outcome is evaluated by the correlation coefficient. References Crowther, R. A. (1972). The Molecular Replacement Method, edited by M. G. ...
Preparation of the X-ray data
International Tables for Crystallography (2012). Vol. F, Section 13.5.4, pp. 364-365 [ doi:10.1107/97809553602060000843 ]
... advantageous when only low-resolution data are available. In such a case, the estimation of the overall B factor (Bover) from ... the weighting scheme for the X-ray data, MOLREP estimates a number of parameters for the search model. Two of them ... the target protein ([Omega]), are translated into the parameters of a low-pass filter and a high-pass filter (Gonzalez & ...
Preparation of the search model
International Tables for Crystallography (2012). Vol. F, Section 13.5.3, p. 364 [ doi:10.1107/97809553602060000843 ]
... MR (Lebedev et al., 2008). The options include (i) a polyalanine model, (ii) a model with modified atomic B factors increased proportionally to the atom accessibility and (iii) a model with the corrected amino-acid sequence according to ...
Program operation
International Tables for Crystallography (2012). Vol. F, Section 13.5.2, p. 364 [ doi:10.1107/97809553602060000843 ]
... 13.5.2. Program operation The philosophy behind MOLREP was to provide a tool such that most if not all of the tasks ... organized so that the user can run the program in a dialogue mode. The prompts appear as self-explanatory questions with a choice of possible answers and a list of keywords ...
Introduction
International Tables for Crystallography (2012). Vol. F, Section 13.5.1, p. 364 [ doi:10.1107/97809553602060000843 ]
... further in the future. Traditionally, MR has been implemented as a three-dimensional rotational search followed by a three-dimensional translational search. With recent advances in computing a combined six-dimensional search is becoming feasible; however, to ...
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 ...
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