International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F. ch. 11.4, p. 228   | 1 | 2 |

Section 11.4.4.3. Beam–spindle

Z. Otwinowskia* and W. Minorb

a UT Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038, USA, and bDepartment of Molecular Physiology and Biological Physics, University of Virginia, 1300 Jefferson Park Avenue, Charlottesville, VA 22908, USA
Correspondence e-mail:  zbyszek@mix.swmed.edu

11.4.4.3. Beam–spindle

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Until 1998, DENZO supported only a single-axis goniostat and used a beam–spindle coordinate system to define crystal and detector orientation and polarization. Initially, the goniostat spindle axis was assumed to be horizontal, so the direction perpendicular to the beam and spindle was described by the keyword vertical, which in reality may not relate to the gravity direction for some goniostats. The keyword rotx relates to rotation around the spindle axis, roty around the vertical axis and rotz around the beam axis. The definition of the orientation matrix in the communication file between DENZO and SCALEPACK uses an unintuitive convention: the letter y in roty relates to the first element of the vector, x in rotx relates to the second and z in rotz to the third. However, the matrix always has a positive determinant, so this convention has no impact on the handedness of the coordinate system. This unfortunate choice of convention, preserved for backward compatibility reasons, appears only in the communication file and has no significance for anybody who does not inspect the matrix.








































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