Crystallographic Information Framework

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Image dictionary (imgCIF) version 1.3.2

Category AXIS



   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)
                    /       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.


Example 1 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
        _axis.vector[1] _axis.vector[2] _axis.vector[3]
        omega rotation goniometer     .    1        0        0
        kappa rotation goniometer omega    -.64279  0       -.76604
        phi   rotation goniometer kappa    1        0        0

Example 2 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.
        _axis.vector[1] _axis.vector[2] _axis.vector[3]
        _axis.offset[1] _axis.offset[2] _axis.offset[3]
        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

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Mandatory category: no