Image dictionary (imgCIF) version 1.3.2
Data items in the AXIS category record the information required to describe the various goniometer, detector, source and other axes needed to specify a data collection. The location of each axis is specified by two vectors: the axis itself, given as a unit vector, and an offset to the base of the unit vector. These vectors are referenced to a right-handed laboratory coordinate system with its origin in the sample or specimen: | Y (to complete right-handed system) | | | | | |________________X / principal goniometer axis / / / / /Z (to source) Axis 1 (X): The X-axis is aligned to the mechanical axis pointing from the sample or specimen along the principal axis of the goniometer. Axis 2 (Y): The Y-axis completes an orthogonal right-handed system defined by the X-axis and the Z-axis (see below). Axis 3 (Z): The Z-axis is derived from the source axis which goes from the sample to the source. The Z-axis is the component of the source axis in the direction of the source orthogonal to the X-axis in the plane defined by the X-axis and the source axis. These axes are based on the goniometer, not on the orientation of the detector, gravity etc. The vectors necessary to specify all other axes are given by sets of three components in the order (X, Y, Z). If the axis involved is a rotation axis, it is right-handed, i.e. as one views the object to be rotated from the origin (the tail) of the unit vector, the rotation is clockwise. If a translation axis is specified, the direction of the unit vector specifies the sense of positive translation. Note: This choice of coordinate system is similar to but significantly different from the choice in MOSFLM (Leslie & Powell, 2004). In MOSFLM, X is along the X-ray beam (the CBF/imgCIF Z axis) and Z is along the rotation axis. All rotations are given in degrees and all translations are given in mm. Axes may be dependent on one another. The X-axis is the only goniometer axis the direction of which is strictly connected to the hardware. All other axes are specified by the positions they would assume when the axes upon which they depend are at their zero points. When specifying detector axes, the axis is given to the beam centre. The location of the beam centre on the detector should be given in the DIFFRN_DETECTOR category in distortion-corrected millimetres from the (0,0) corner of the detector. It should be noted that many different origins arise in the definition of an experiment. In particular, as noted above, it is necessary to specify the location of the beam centre on the detector in terms of the origin of the detector, which is, of course, not coincident with the centre of the sample. Ref: Leslie, A. G. W. & Powell, H. (2004). MOSFLM v6.11. MRC Laboratory of Molecular Biology, Hills Road, Cambridge, England. http://www.CCP4.ac.uk/dist/x-windows/Mosflm/.Examples:
This example shows the axis specification of the axes of a kappa-
geometry goniometer [see Stout, G. H. & Jensen, L. H. (1989). X-ray
structure determination. A practical
guide, 2nd ed. p. 134. New York: Wiley Interscience].
There are three axes specified, and no offsets. The outermost axis,
omega, is pointed along the X axis. The next innermost axis, kappa,
is at a 50 degree angle to the X axis, pointed away from the source.
The innermost axis, phi, aligns with the X axis when omega and
phi are at their zero points. If T-omega, T-kappa and T-phi
are the transformation matrices derived from the axis settings,
the complete transformation would be:
x' = (T-omega) (T-kappa) (T-phi) x
loop_ _axis.id _axis.type _axis.equipment _axis.depends_on _axis.vector _axis.vector _axis.vector omega rotation goniometer . 1 0 0 kappa rotation goniometer omega -.64279 0 -.76604 phi rotation goniometer kappa 1 0 0
This example show the axis specification of the axes of a
detector, source and gravity. The order has been changed as a
reminder that the ordering of presentation of tokens is not
significant. The centre of rotation of the detector has been taken
to be 68 millimetres in the direction away from the source.
loop_ _axis.id _axis.type _axis.equipment _axis.depends_on _axis.vector _axis.vector _axis.vector _axis.offset _axis.offset _axis.offset source . source . 0 0 1 . . . gravity . gravity . 0 -1 0 . . . tranz translation detector rotz 0 0 1 0 0 -68 twotheta rotation detector . 1 0 0 . . . roty rotation detector twotheta 0 1 0 0 0 -68 rotz rotation detector roty 0 0 1 0 0 -68
Mandatory category: no