[Imgcif-l] Questions of reference frames
Herbert J. Bernstein
yaya at bernstein-plus-sons.com
Tue Feb 16 12:52:29 GMT 2010
Nice question. The current best wording we have is appended.
If we have an intersection between the beam and any part of the
sample, that definition comes close, so what I now would suggest is
If the sample goniometer or other
sample positioner has two axes the intersection of which defines a
unique point at which the sample should be mounted to be bathed
by the beam, that will be the origin of the axis system. If no such
point is defined, then the midpoint of the line of intersection
between the sample and the center of the beam will define the origin.
If the beam does not intersect the sample at the initial settings
if the axes, then the point of closest approach between the
center lins of the beam and the pricipal axis of the goniometer
will define the origin, if that axis is defined and if the
angle between that axis and the center line of the beam is at
least 22.5 degrees.
For this definition the sample positioning system will be set at
its initial reference position for the experiment.
Axis 1 (X): The X-axis is parallel to the mechanical axis pointing
from the sample or specimen along the principal axis of the
goniometer or sample positioning system if the sample positioning
system has an axis has a well-defined point of closest approach
to the center-line of the beam to define the origin as above
and which form an angle of more than 22.5 degrees with the beam axis.
If this is acceptable, I will embed it in the wording below.
========================================================================
THE IMGCIF STANDARD LABORATORY COORDINATE SYSTEM
The imgCIF standard laboratory coordinate system is a right-handed
orthogonal coordinate similar to the MOSFLM coordinate system,
but imgCIF puts Z along the X-ray beam, rather than putting X along
the
X-ray beam as in MOSFLM.
The vectors for the imgCIF standard laboratory coordinate system
form a right-handed Cartesian coordinate system with its origin
in the sample or specimen. The origin of the axis system should,
if possible, be defined in terms of mechanically stable axes to be
be both in the sample and in the beam. If the sample goniometer or
other
sample positioner has two axes the intersection of which defines a
unique point at which the sample should be mounted to be bathed
by the beam, that will be the origin of the axis system. If no such
point is defined, then the midpoint of the line of intersection
between the sample and the center of the beam will define the origin.
For this definition the sample positioning system will be set at
its initial reference position for the experiment.
| 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 or
sample positioning system if the sample positioning system has an
axis
that intersects the origin and which form an angle of more than 22.5
degrees with the beam axis.
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.
If the conditions for the X-axis can be met, the coordinate system
will be based on the goniometer or other sample positioning system
and the beam and 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.
In some experimental techniques, there is no goniometer or the
principal
axis of the goniometer is at a small acute angle with respect to
the source axis. In such cases, other reference axes are needed
to define a useful coordinate system. The order of priority in
defining directions in such cases is to use the detector, then
gravity, then north.
If the X-axis cannot be defined as above, then the
direction (not the origin) of the X-axis should be parallel to the
axis
of the primary detector element corresponding to the most rapidly
varying dimension of that detector element's data array, with its
positive sense corresponding to increasing values of the index for
that dimension. If the detector is such that such a direction cannot
be defined (as with a point detector) or that direction forms an
angle of less than 22.5 degrees with respect to the source axis, then
the X-axis should be chosen so that if the Y-axis is chosen
in the direction of gravity, and the Z-axis is chosen to be along
the source axis, a right-handed orthogonal coordinate system is
chosen.
In the case of a vertical source axis, as a last resort, the
X-axis should be chosen to point North.
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.
The unit cell, reciprocal cell and crystallographic orthogonal
Cartesian coordinate system are defined by the CELL and the matrices
in the ATOM_SITES category.
=====================================================
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
+1-631-244-3035
yaya at dowling.edu
=====================================================
On Tue, 16 Feb 2010, Graeme.Winter at Diamond.ac.uk wrote:
> Hi Folks,
>
> I'm still trying to finish off the details of our CBF template here and
> I have hit what feels like a slight conceptual snag...
>
> The X axis is defined as rigidly the direction of the rotation axis,
> from the sample. Now, historically the sample has been "small" so this
> is pretty clear, but if the sample is "large" (or a normal size, but on
> a uFocus beamline) then we can consider different regions of the sample
> for exposure. A very real possibility is then to offset the rotation
> axis from the direct beam, so that a toroidal region of sample is
> exposed. This then brings a conceptual challenge:
>
> The origin of the coordinate system is defined as the point where the
> rotation axis intersects the direct beam. They do not intersect. Hmmm...
>
> Also, if I do wish to translate the rotation axis, how to I report this?
> The reference frame is "fixed" to this, so in effect I am moving the
> beamline (indeed, the whole world) by the same distance in the opposite
> direction. It would be good to record this, so that an analysis program
> can determine the use of a toroidal (or corkscrew) data collection for
> radiation damage purposes, given the size and placement of the direct
> beam.
>
> Has anyone else figured this out?
>
> Of have I the wrong end of the stick (quite likely!)
>
> Many thanks,
>
> Graeme
>
> Graeme Winter
> Software and MX Support Scientist
> Diamond Light Source
>
> +44 1235 778091 (work)
> +44 7786 662784 (work mobile)
>
>
>
>
>
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