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DENZO and SCALEPACK
Otwinowski, Z., Minor, W., Borek, D. and Cymborowski, M.  International Tables for Crystallography (2012). Vol. F, ch. 11.4, pp. 282-295 [ doi:10.1107/97809553602060000833 ]
... analysis, as performed by the HKL package (Otwinowski, 1993; Otwinowski & Minor, 1997) or similar programs (Rossmann, 1979; Leslie & Tsukihara, 1980; Howard ... the reciprocal lattice tends to be the most reliable (Otwinowski & Minor, 1997; Steller et al., 1997). Autoindexing starts with a ... one of the main sources of difficulties in indexing (Otwinowski & Minor, 1997; Gewirth, 2003). The beam position has to ...

HKL-2000 and HKL-3000
Otwinowski, Z., Minor, W., Borek, D. and Cymborowski, M.  International Tables for Crystallography (2012). Vol. F, Section 11.4.12, pp. 292-294 [ doi:10.1107/97809553602060000833 ]
... the data-collection process by HKL-2000 and HKL-3000 (Minor et al., 2002, 2006), incorporation of methods of structure solution by HKL-3000 (Minor et al., 2006), and storage of critical intermediate results in ... graphics. Acta Cryst. D60, 2126-2132. Chruszcz, M., Wlodawer, A. & Minor, W. (2008). Determination of protein structures - a series ...

Detector diagnostics
Otwinowski, Z., Minor, W., Borek, D. and Cymborowski, M.  International Tables for Crystallography (2012). Vol. F, Section 11.4.11, p. 292 [ doi:10.1107/97809553602060000833 ]
... that can detect possible detector or experimental setup problems (Otwinowski & Minor, 1997; Otwinowski et al., 2003). Visual inspection of the ... of the data-acquisition hardware or software. References Otwinowski, Z. & Minor, W. (1997). Processing of X-ray diffraction data collected ...

Merging and signal validation
Otwinowski, Z., Minor, W., Borek, D. and Cymborowski, M.  International Tables for Crystallography (2012). Vol. F, Section 11.4.10.3, p. 292 [ doi:10.1107/97809553602060000833 ]
... 2007, 2010). References Borek, D., Cymborowski, M., Machius, M., Minor, W. & Otwinowski, Z. (2010). Diffraction data analysis in the presence ... D66, 426-436. Borek, D., Ginell, S. L., Cymborowski, M., Minor, W. & Otwinowski, Z. (2007). The many faces of ...
     [more results from section 11.4.10 in volume F]

Global refinement or post refinement
Otwinowski, Z., Minor, W., Borek, D. and Cymborowski, M.  International Tables for Crystallography (2012). Vol. F, Section 11.4.9, p. 291 [ doi:10.1107/97809553602060000833 ]
Global refinement or post refinement 11.4.9. Global refinement or post refinement The process of refining crystal parameters using the combined reflection intensity measurements is known as global refinement or post refinement (Rossmann, 1979; Evans, 1993). The implementation of this method in SCALEPACK allows for separate refinement of the orientation of ...

Stabilization of scaling parameters based on prior knowledge
Otwinowski, Z., Minor, W., Borek, D. and Cymborowski, M.  International Tables for Crystallography (2012). Vol. F, Section 11.4.8.2, pp. 290-291 [ doi:10.1107/97809553602060000833 ]
Stabilization of scaling parameters based on prior knowledge 11.4.8.2. Stabilization of scaling parameters based on prior knowledge The unknown parameters in equation (11.4.8.4) are estimated with various level of uncertainty depending on the multiplicity of observations and how symmetry-equivalent reflections are related to each other. Potentially, this may result in ...
     [more results from section 11.4.8 in volume F]

Integration of diffraction maxima by profile fitting
Otwinowski, Z., Minor, W., Borek, D. and Cymborowski, M.  International Tables for Crystallography (2012). Vol. F, Section 11.4.7, p. 289 [ doi:10.1107/97809553602060000833 ]
... function defines the value of the profile-fitted intensity (Otwinowski & Minor, 1997): References Otwinowski, Z. & Minor, W. (1997). Processing of X-ray diffraction data collected ...

Detector distortions
Otwinowski, Z., Minor, W., Borek, D. and Cymborowski, M.  International Tables for Crystallography (2012). Vol. F, Section 11.4.6.3, p. 289 [ doi:10.1107/97809553602060000833 ]
... distortion function and its inverse. References Messerschmidt, A. & Pflugrath, J. W. (1987). Crystal orientation and X-ray pattern prediction routines ... in macromolecular crystallography. J. Appl. Cryst. 20, 306-315. Press, W. H., Flannery, B. P., Teukolsky, S. A. & Vetterling, W. T. (1989). Numerical Recipes - the Art of Scientific ...
     [more results from section 11.4.6 in volume F]

Refinement and calibration
Otwinowski, Z., Minor, W., Borek, D. and Cymborowski, M.  International Tables for Crystallography (2012). Vol. F, Section 11.4.5.12, p. 288 [ doi:10.1107/97809553602060000833 ]
Refinement and calibration 11.4.5.12. Refinement and calibration Both the refinement and calibration procedures determine the properties of the instrument. The principal difference between refinement and calibration is that calibration is performed with data not obtained during the current diffraction experiment, and refinement uses data obtained during the current diffraction experiment. DENZO ...
     [more results from section 11.4.5 in volume F]

Beam-2[theta]
Otwinowski, Z., Minor, W., Borek, D. and Cymborowski, M.  International Tables for Crystallography (2012). Vol. F, Section 11.4.4.4, p. 285 [ doi:10.1107/97809553602060000833 ]
Beam-2[theta] 11.4.4.4. Beam-2[theta] The description of generalized multiple-axis goniostats introduced a conceptual change in the DENZO coordinate system. The data-collection axis can be oriented in any direction, so in principle rotx, roty and rotz no longer need to be defined relative to the data-collection ...
     [more results from section 11.4.4 in volume F]

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