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Integration, scaling, space-group assignment and post refinement
International Tables for Crystallography (2012). Vol. F, ch. 11.3, pp. 272-281 [ doi:10.1107/97809553602060000832 ]
... from short differences between the reciprocal-lattice vectors (Howard, 1986; Kabsch, 1988a). As implemented in XDS, a lattice basis is ... kj, li - lj between pairs of neighbouring reciprocal-lattice vectors (Kabsch, 1993). The reciprocal-lattice points can be considered as ... profile fitting has a long tradition (Diamond, 1969; Ford, 1974; Kabsch, 1988b; Otwinowski, 1993). Implementations of the method differ ...
Parallelization of XDS
International Tables for Crystallography (2012). Vol. F, Section 11.6.5, pp. 309-310 [ doi:10.1107/97809553602060000835 ]
Parallelization of XDS 11.6.5. Parallelization of XDS In order to efficiently use modern multiprocessor hardware, a major effort has been undertaken to replace the original code of XDS by routines that can run concurrently with very little need for synchronization. As described above, data processing by XDS is organized into eight ...
XDSCONV
International Tables for Crystallography (2012). Vol. F, Section 11.6.4, p. 309 [ doi:10.1107/97809553602060000835 ]
XDSCONV 11.6.4. XDSCONV XDSCONV accepts reflection-intensity data files as produced by XSCALE or CORRECT and converts them into the format required by software packages for structure determination. XDSCONV estimates structure-factor moduli based on the assumption that the intensity data set obeys Wilson's distribution and uses a Bayesian approach ...
XSCALE
International Tables for Crystallography (2012). Vol. F, Section 11.6.3, pp. 308-309 [ doi:10.1107/97809553602060000835 ]
XSCALE 11.6.3. XSCALE The scaling program XSCALE (i) puts one or more files obtained from data processing with XDS on a common scale and reports the completeness and quality of the data sets; (ii) offers a choice of either combining symmetry-equivalent observations into a single unique reflection or saving the ...
CORRECT
International Tables for Crystallography (2012). Vol. F, Section 11.6.2.8, pp. 307-308 [ doi:10.1107/97809553602060000835 ]
CORRECT 11.6.2.8. CORRECT CORRECT applies correction factors to the intensities and standard deviations of all reflections found in the file INTEGRATE.HKL, determines the space group if unknown and refines the unit-cell parameters, reports the quality and completeness of the data set and saves the final integrated intensities in the file ...
[more results from section 11.6.2 in volume F]
Functional specification
International Tables for Crystallography (2012). Vol. F, Section 11.6.1, p. 304 [ doi:10.1107/97809553602060000835 ]
Functional specification 11.6.1. Functional specification The program package XDS (Kabsch, 1988a,b, 1993; Chapter 11.3 ) was developed for the reduction ... R factor to monitor the progress of structure refinement. References Kabsch, W. (1988a). Automatic indexing of rotation diffraction patterns. J. ...
XDS
International Tables for Crystallography (2012). Vol. F, ch. 11.6, pp. 304-310 [ doi:10.1107/97809553602060000835 ]
... soon after measurement. 11.6.1. Functional specification The program package XDS (Kabsch, 1988a,b, 1993; Chapter 11.3 ) was developed for the reduction ... XPLAN INTEGRATE CORRECT). IDXREF uses the methods described in Kabsch (1993; Chapter 11.3 ) to determine a crystal lattice that explains ... on a recent article published in Acta Crystallographica Section D (Kabsch, 2010). References Bernstein, H. J. & Ellis, P. J. ( ...
Finding possible space groups
International Tables for Crystallography (2012). Vol. F, Section 11.3.6.2, p. 280 [ doi:10.1107/97809553602060000832 ]
Finding possible space groups 11.3.6.2. Finding possible space groups For protein crystals, the absence of parity-changing symmetry operators restricts the number of possible space groups to 65 instead of 230. Moreover, the determination of correction factors for the integrated intensities does not depend onthe presence or absence of any screw ...
[more results from section 11.3.6 in volume F]
Post refinement
International Tables for Crystallography (2012). Vol. F, Section 11.3.5, pp. 277-278 [ doi:10.1107/97809553602060000832 ]
Post refinement 11.3.5. Post refinement The number of fully recorded reflections on each single image rapidly declines for small oscillation ranges and the complete intensities of the partially recorded reflections have to be estimated. This presented a serious obstacle in early structural work on virus crystals, as the crystal had to ...
Scaling
International Tables for Crystallography (2012). Vol. F, Section 11.3.4, p. 277 [ doi:10.1107/97809553602060000832 ]
... procedures (see, for example Evans, 2006; Otwinowski et al., 2003; Kabsch, 1988b) exploit this a priori knowledge to determine a correction ... Hamilton, Rollett and Sparks. Acta Cryst. 20, 886-891. Hamilton, W. C., Rollett, J. S. & Sparks, R. A. (1965). On ... photographs. Acta Cryst. 18, 129-130. Junk, M., Diederichs, K. & Kabsch, W. (2011). Analysis of the alternate convex search ...
International Tables for Crystallography (2012). Vol. F, ch. 11.3, pp. 272-281 [ doi:10.1107/97809553602060000832 ]
... from short differences between the reciprocal-lattice vectors (Howard, 1986; Kabsch, 1988a). As implemented in XDS, a lattice basis is ... kj, li - lj between pairs of neighbouring reciprocal-lattice vectors (Kabsch, 1993). The reciprocal-lattice points can be considered as ... profile fitting has a long tradition (Diamond, 1969; Ford, 1974; Kabsch, 1988b; Otwinowski, 1993). Implementations of the method differ ...
Parallelization of XDS
International Tables for Crystallography (2012). Vol. F, Section 11.6.5, pp. 309-310 [ doi:10.1107/97809553602060000835 ]
Parallelization of XDS 11.6.5. Parallelization of XDS In order to efficiently use modern multiprocessor hardware, a major effort has been undertaken to replace the original code of XDS by routines that can run concurrently with very little need for synchronization. As described above, data processing by XDS is organized into eight ...
XDSCONV
International Tables for Crystallography (2012). Vol. F, Section 11.6.4, p. 309 [ doi:10.1107/97809553602060000835 ]
XDSCONV 11.6.4. XDSCONV XDSCONV accepts reflection-intensity data files as produced by XSCALE or CORRECT and converts them into the format required by software packages for structure determination. XDSCONV estimates structure-factor moduli based on the assumption that the intensity data set obeys Wilson's distribution and uses a Bayesian approach ...
XSCALE
International Tables for Crystallography (2012). Vol. F, Section 11.6.3, pp. 308-309 [ doi:10.1107/97809553602060000835 ]
XSCALE 11.6.3. XSCALE The scaling program XSCALE (i) puts one or more files obtained from data processing with XDS on a common scale and reports the completeness and quality of the data sets; (ii) offers a choice of either combining symmetry-equivalent observations into a single unique reflection or saving the ...
CORRECT
International Tables for Crystallography (2012). Vol. F, Section 11.6.2.8, pp. 307-308 [ doi:10.1107/97809553602060000835 ]
CORRECT 11.6.2.8. CORRECT CORRECT applies correction factors to the intensities and standard deviations of all reflections found in the file INTEGRATE.HKL, determines the space group if unknown and refines the unit-cell parameters, reports the quality and completeness of the data set and saves the final integrated intensities in the file ...
[more results from section 11.6.2 in volume F]
Functional specification
International Tables for Crystallography (2012). Vol. F, Section 11.6.1, p. 304 [ doi:10.1107/97809553602060000835 ]
Functional specification 11.6.1. Functional specification The program package XDS (Kabsch, 1988a,b, 1993; Chapter 11.3 ) was developed for the reduction ... R factor to monitor the progress of structure refinement. References Kabsch, W. (1988a). Automatic indexing of rotation diffraction patterns. J. ...
XDS
International Tables for Crystallography (2012). Vol. F, ch. 11.6, pp. 304-310 [ doi:10.1107/97809553602060000835 ]
... soon after measurement. 11.6.1. Functional specification The program package XDS (Kabsch, 1988a,b, 1993; Chapter 11.3 ) was developed for the reduction ... XPLAN INTEGRATE CORRECT). IDXREF uses the methods described in Kabsch (1993; Chapter 11.3 ) to determine a crystal lattice that explains ... on a recent article published in Acta Crystallographica Section D (Kabsch, 2010). References Bernstein, H. J. & Ellis, P. J. ( ...
Finding possible space groups
International Tables for Crystallography (2012). Vol. F, Section 11.3.6.2, p. 280 [ doi:10.1107/97809553602060000832 ]
Finding possible space groups 11.3.6.2. Finding possible space groups For protein crystals, the absence of parity-changing symmetry operators restricts the number of possible space groups to 65 instead of 230. Moreover, the determination of correction factors for the integrated intensities does not depend onthe presence or absence of any screw ...
[more results from section 11.3.6 in volume F]
Post refinement
International Tables for Crystallography (2012). Vol. F, Section 11.3.5, pp. 277-278 [ doi:10.1107/97809553602060000832 ]
Post refinement 11.3.5. Post refinement The number of fully recorded reflections on each single image rapidly declines for small oscillation ranges and the complete intensities of the partially recorded reflections have to be estimated. This presented a serious obstacle in early structural work on virus crystals, as the crystal had to ...
Scaling
International Tables for Crystallography (2012). Vol. F, Section 11.3.4, p. 277 [ doi:10.1107/97809553602060000832 ]
... procedures (see, for example Evans, 2006; Otwinowski et al., 2003; Kabsch, 1988b) exploit this a priori knowledge to determine a correction ... Hamilton, Rollett and Sparks. Acta Cryst. 20, 886-891. Hamilton, W. C., Rollett, J. S. & Sparks, R. A. (1965). On ... photographs. Acta Cryst. 18, 129-130. Junk, M., Diederichs, K. & Kabsch, W. (2011). Analysis of the alternate convex search ...
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