modify your search
Results for DC.creator="A." AND DC.creator="T." AND DC.creator="Brunger" page 2 of 2 pages. |
Conclusions
International Tables for Crystallography (2012). Vol. F, Section 18.6.10, p. 517 [ doi:10.1107/97809553602060000860 ]
Conclusions 18.6.10. Conclusions CNS is a general system for structure determination by X-ray crystallography and ... allows the novice to perform standard tasks. The interface provides a convenient means of editing complicated task files, even for the ... graphical output are planned in the future. Most operations within a crystallographic algorithm are defined through modules and task files. ...
Conclusions
International Tables for Crystallography (2012). Vol. F, Section 18.2.8, p. 472 [ doi:10.1107/97809553602060000856 ]
... Simulated annealing has dramatically improved the efficiency of crystallographic refinement. A case in point is the combination of torsion-angle molecular ... Burling et al., 1996). Thus, simulated annealing is also a stepping stone towards development of improved models of macromolecules in ... review are implemented in the software suite Crystallography & NMR System (Brunger et al., 1998). A pre-release of the ...
Ensemble models
International Tables for Crystallography (2012). Vol. F, Section 18.2.7, pp. 471-472 [ doi:10.1107/97809553602060000856 ]
... equation (18.2.3.1). Rather, the X-ray diffraction data represent a spatial and temporal average over all conformations that are assumed ... are simultaneously refined against the observed data, may thus be a more appropriate description of the diffraction data. This has been ... nger, 1994; Burling et al., 1996). An advantage of a multi-conformer model is that it directly incorporates many ...
Multi-start refinement and structure-factor averaging
International Tables for Crystallography (2012). Vol. F, Section 18.2.6, p. 471 [ doi:10.1107/97809553602060000856 ]
... computer time is available, multi-start refinement has several advantages. A more optimal single model than that produced by a single simulated-annealing calculation can usually be obtained. Furthermore, each separate model coming from a multi-start refinement fits the data slightly differently. This ...
Examples
International Tables for Crystallography (2012). Vol. F, Section 18.2.5, pp. 470-471 [ doi:10.1107/97809553602060000856 ]
... . In another realistic test case (Adams et al., 1999), a series of models for the aspartic proteinase penicillopepsin were generated ... among these structures ranged from 100% to 25%, thus providing a set of models with increasing coordinate error compared to the ... latter case, phases from single isomorphous replacement (SIR) were used. A very large number of conjugate-gradient cycles were carried ...
An intuitive explanation of simulated annealing
International Tables for Crystallography (2012). Vol. F, Section 18.2.4.4, p. 470 [ doi:10.1107/97809553602060000856 ]
... any optimization problem is to find the global minimum of a target function. In the case of crystallographic refinement, one searches ... reasonable covalent and non-covalent interactions. Simulated-annealing refinement has a much larger radius of convergence than conjugate-gradient minimization (see below). It must, therefore, be able to find a lower minimum of the target E [equation (18.2.3.1)] than ...
[more results from section 18.2.4 in volume F]
A priori chemical information
International Tables for Crystallography (2012). Vol. F, Section 18.2.3.2, p. 468 [ doi:10.1107/97809553602060000856 ]
A priori chemical information 18.2.3.2. A priori chemical information The parameters for the covalent terms in ... derived from the average geometry and (r.m.s.) deviations observed in a small-molecule database. Extensive statistical analyses were undertaken for ...
[more results from section 18.2.3 in volume F]
Cross validation
International Tables for Crystallography (2012). Vol. F, Section 18.2.2, pp. 466-467 [ doi:10.1107/97809553602060000856 ]
... validation 18.2.2. Cross validation Cross validation (Brünger, 1992) plays a fundamental role in the maximum-likelihood target functions described below. A few remarks about this method are therefore warranted (for reviews ... cross validation, the diffraction data are divided into two sets: a large working set (usually comprising 90% of the data) ...
Introduction
International Tables for Crystallography (2012). Vol. F, Section 18.2.1, p. 466 [ doi:10.1107/97809553602060000856 ]
... formulated as the chemically constrained or restrained nonlinear optimization of a target function, which usually measures the agreement between observed diffraction ... of an atomic model with observed diffraction data and with a priori chemical information. The target function used for this optimization ... the number of atoms in the model) gives rise to a very complicated target function. This, in turn, produces what ...
Enhanced macromolecular refinement by simulated annealing
International Tables for Crystallography (2012). Vol. F, ch. 18.2, pp. 466-473 [ doi:10.1107/97809553602060000856 ]
... formulated as the chemically constrained or restrained nonlinear optimization of a target function, which usually measures the agreement between observed diffraction ... of an atomic model with observed diffraction data and with a priori chemical information. Simulated annealing is an optimization technique particularly ... annealing can cross barriers between minima and thus can explore a greater volume of the parameter space to find better ...
International Tables for Crystallography (2012). Vol. F, Section 18.6.10, p. 517 [ doi:10.1107/97809553602060000860 ]
Conclusions 18.6.10. Conclusions CNS is a general system for structure determination by X-ray crystallography and ... allows the novice to perform standard tasks. The interface provides a convenient means of editing complicated task files, even for the ... graphical output are planned in the future. Most operations within a crystallographic algorithm are defined through modules and task files. ...
Conclusions
International Tables for Crystallography (2012). Vol. F, Section 18.2.8, p. 472 [ doi:10.1107/97809553602060000856 ]
... Simulated annealing has dramatically improved the efficiency of crystallographic refinement. A case in point is the combination of torsion-angle molecular ... Burling et al., 1996). Thus, simulated annealing is also a stepping stone towards development of improved models of macromolecules in ... review are implemented in the software suite Crystallography & NMR System (Brunger et al., 1998). A pre-release of the ...
Ensemble models
International Tables for Crystallography (2012). Vol. F, Section 18.2.7, pp. 471-472 [ doi:10.1107/97809553602060000856 ]
... equation (18.2.3.1). Rather, the X-ray diffraction data represent a spatial and temporal average over all conformations that are assumed ... are simultaneously refined against the observed data, may thus be a more appropriate description of the diffraction data. This has been ... nger, 1994; Burling et al., 1996). An advantage of a multi-conformer model is that it directly incorporates many ...
Multi-start refinement and structure-factor averaging
International Tables for Crystallography (2012). Vol. F, Section 18.2.6, p. 471 [ doi:10.1107/97809553602060000856 ]
... computer time is available, multi-start refinement has several advantages. A more optimal single model than that produced by a single simulated-annealing calculation can usually be obtained. Furthermore, each separate model coming from a multi-start refinement fits the data slightly differently. This ...
Examples
International Tables for Crystallography (2012). Vol. F, Section 18.2.5, pp. 470-471 [ doi:10.1107/97809553602060000856 ]
... . In another realistic test case (Adams et al., 1999), a series of models for the aspartic proteinase penicillopepsin were generated ... among these structures ranged from 100% to 25%, thus providing a set of models with increasing coordinate error compared to the ... latter case, phases from single isomorphous replacement (SIR) were used. A very large number of conjugate-gradient cycles were carried ...
An intuitive explanation of simulated annealing
International Tables for Crystallography (2012). Vol. F, Section 18.2.4.4, p. 470 [ doi:10.1107/97809553602060000856 ]
... any optimization problem is to find the global minimum of a target function. In the case of crystallographic refinement, one searches ... reasonable covalent and non-covalent interactions. Simulated-annealing refinement has a much larger radius of convergence than conjugate-gradient minimization (see below). It must, therefore, be able to find a lower minimum of the target E [equation (18.2.3.1)] than ...
[more results from section 18.2.4 in volume F]
A priori chemical information
International Tables for Crystallography (2012). Vol. F, Section 18.2.3.2, p. 468 [ doi:10.1107/97809553602060000856 ]
A priori chemical information 18.2.3.2. A priori chemical information The parameters for the covalent terms in ... derived from the average geometry and (r.m.s.) deviations observed in a small-molecule database. Extensive statistical analyses were undertaken for ...
[more results from section 18.2.3 in volume F]
Cross validation
International Tables for Crystallography (2012). Vol. F, Section 18.2.2, pp. 466-467 [ doi:10.1107/97809553602060000856 ]
... validation 18.2.2. Cross validation Cross validation (Brünger, 1992) plays a fundamental role in the maximum-likelihood target functions described below. A few remarks about this method are therefore warranted (for reviews ... cross validation, the diffraction data are divided into two sets: a large working set (usually comprising 90% of the data) ...
Introduction
International Tables for Crystallography (2012). Vol. F, Section 18.2.1, p. 466 [ doi:10.1107/97809553602060000856 ]
... formulated as the chemically constrained or restrained nonlinear optimization of a target function, which usually measures the agreement between observed diffraction ... of an atomic model with observed diffraction data and with a priori chemical information. The target function used for this optimization ... the number of atoms in the model) gives rise to a very complicated target function. This, in turn, produces what ...
Enhanced macromolecular refinement by simulated annealing
International Tables for Crystallography (2012). Vol. F, ch. 18.2, pp. 466-473 [ doi:10.1107/97809553602060000856 ]
... formulated as the chemically constrained or restrained nonlinear optimization of a target function, which usually measures the agreement between observed diffraction ... of an atomic model with observed diffraction data and with a priori chemical information. Simulated annealing is an optimization technique particularly ... annealing can cross barriers between minima and thus can explore a greater volume of the parameter space to find better ...
Page: Previous 1 2 | powered by |