Discussion List Archives

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [Imgcif-l] Questions of reference frames

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@dowling.edu
=====================================================

On Tue, 16 Feb 2010, Graeme.Winter@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)
>
>
>
>
>
> -- 
>
> This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.
>
> Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd.
>
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.
>
> Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>
>
>
>
>
>
>
>
>
> _______________________________________________
> imgcif-l mailing list
> imgcif-l@iucr.org
> http://scripts.iucr.org/mailman/listinfo/imgcif-l
>
_______________________________________________
imgcif-l mailing list
imgcif-l@iucr.org
http://scripts.iucr.org/mailman/listinfo/imgcif-l

Reply to: [list | sender only]
International Union of Crystallography

Scientific Union Member of the International Science Council (admitted 1947). Member of CODATA, the ISC Committee on Data. Partner with UNESCO, the United Nations Educational, Scientific and Cultural Organization in the International Year of Crystallography 2014.

International Science Council Scientific Freedom Policy

The IUCr observes the basic policy of non-discrimination and affirms the right and freedom of scientists to associate in international scientific activity without regard to such factors as ethnic origin, religion, citizenship, language, political stance, gender, sex or age, in accordance with the Statutes of the International Council for Science.

Useful links