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Re: [Imgcif-l] imgCIF Standard Axis definition

• To: The Crystallographic Binary File and its imgCIF application to image data <imgcif-l@iucr.org>
• Subject: Re: [Imgcif-l] imgCIF Standard Axis definition
• From: Jon Wright <wright@esrf.fr>
• Date: Fri, 04 May 2007 00:47:39 +0200
• In-Reply-To: <Pine.BSF.4.58.0705031617010.105@epsilon.pair.com>
• References: <463A3343.4050907@mcmaster.ca><Pine.BSF.4.58.0705031617010.105@epsilon.pair.com>

Hi Herbert,

> 1.  No matter how the direction of the X-axis is chosen,
> it is important to place the origin of the X-axis in
> the sample, not in the detector.  Otherwise calculations
> of beam centers and detector distances become
> quite difficult.

A pedantic point, but the intersection of the goniometer axes would seem
like a first choice of origin for ImageCIF. If there is only one axis
then the intersection of that axis with the centre of the beam seems 
like a second choice. The finite sized sample would then be the last resort.

Not sure where they go in the current dictionaries; but the Bruker/Saint
practice of refining "crystal translations" during integration are
useful data to be recorded. These same numbers come up in grain mapping
applications, which is a growing business. These definitions really
matter and are usually interesting in terms of an agreed upon laboratory 
co-ordinate system.

I see _diffrn_orient_matrix is in mmCIF (?) We often collect images 
where the sample is a collection of grains, each having their own 
orientation and centre of mass. How should multiple crystals be dealt 
with now, for example with non-merohedral twins?

Best,


Jon



> 
> 2.  If an X-axis is chosen that is different from
> the pricipal axis of the goniometer, it is important
> that it be clearly documented, so that, for example
> the detector axes do not get miss-identified.
> 
> There is a draft of the current proposal prior to
> David's suggestion at
> 
> http://www.bernstein-plus-sons.com/software/CBFlib_0.7.7/doc
> 
> Please do consider what is in the proposal and what
> David has suggested as a modification, and please
> send your comments and suggestions to this list.
> 
>   -- HJB
> 
> =====================================================
>  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 Thu, 3 May 2007, David Brown wrote:
> 
>> A proposal for the definition of a reference axis system in imgCIF (and
>> by inference other CIF dictionaries).
>>
>> By I.David Brown
>>
>> The imgCIF dictionary recognizes that authors will require to use a
>> number of different axis systems to describe, e.g., the crystal
>> orientation, the reciprocal space orientation and the detector.  There
>> is clearly a need to be able to relate these axes to each other.
>>
>> For this purpose imgCIF defines a standard laboratory coordinate system
>> (SLCS) based on directions that can be derived from the diffraction
>> equipment being used.  Two directions are needed to define the SLCS and
>> in the first version of the imgCIF dictionary, these directions are the
>> incident beam and the spatially fixed rotation axis of the goniometer
>> that holds the specimen.  X is defined as lying along the goniometer
>> axis, Z as perpendicular to this and lying in the plane of X and the
>> incident beam, and Y is chosen to complete a right handed rectangular
>> coordinate system.  The origin is placed at the sample.
>>
>> Problems arise if there is no goniometer as may occur, e.g.,  in small
>> angle scattering experiments.  The incident beam will always define one
>> direction, but a second direction is needed to define the X axis.
>>
>> A recent proposal made by Bernstein is to use the principal axis of the
>> detector, defined as the direction in which the detector is most rapidly
>> scanned (for 1- annd 2-dimensional detectors).  An alternative might be
>> the direction of the fixed rotation axis of the detector if one exists.
>> The possibility remains, however, that no unique detector direction can
>> be defined.   In this case Bernstein suggests that the Y axis be chosen
>> in the direction of the gravitational field (down) or, in the case where
>> the incident beam is vertical, the Y axis be chosen to point to the north.
>>
>> While the original definition in the current imgCIF dictionary is simple
>> and covers the majority of cases, if there is no goniometer the choices
>> for the second axis start to multiply and some seem quite bizarre.
>> Taking directions from the diffraction equipment makes sense because the
>> relationship between the goniometer and the detector is relevant to
>> interpreting the results.  But directions such as 'down' and 'north' are
>> not related to the operation of the equipment or the interpretation of
>> the measurements.  Rotating the apparatus while maintaining the
>> relationship between its individual components would change the SLCS but
>> make no difference to the relationship between the different practical
>> axis systems.
>>
>> The sole purpose in defining the SLCS is to allow the relationships
>> between other axis systems to be expressed in a straightforward manner
>> against some common coordinate system.  The way in which the SLCS is
>> defined is irrelevant so long as it is used consistently within a
>> related set of CIFs.  It is easier to interpret the transformation
>> matrices used to define other axis systems if everyone chooses the same
>> SLCS and it is convenient to base this SLCS on the obvious directions
>> defined by the apparatus, but in those cases where the incident beam  is
>> the only natural direction then the choice of the SLCS X axis is
>> arbitrary and there is no reason why everyone need use the same SLCS.
>> Since Bernstein's proposed choice of X axis depends on whether there the
>> sample is mounted on a goniometer, and what kind of detector is in use,
>> whether the incident beam is vertical etc.,  there will no longer be a
>> universal definition applicable to all experiments.
>>
>> PROPOSAL
>> My proposal is to keep the current definition using the fixed axis of
>> the sample goniometer where such a direction exists and otherwise to
>> allow the X axis direction to be chosen arbitrarily by the user with the
>> understanding that it must be used consistently within any set of
>> related CIFs (though it is not obvious that even this restriction is
>> needed since it is only the relationship between the practical units
>> that is ultimately needed).  It is likely that a standard SLCS would be
>> adopted for instruments mounted at a major installation, even for that
>> small subset of experiments that do not involve an identifiable fixed
>> rotation axis for the specimen.   An item should be defined in the
>> dictionary where the user can explain how the X axis has been chosen.
>> This proposal would have the advantage of simplicity without defeating
>> the purpose of the SLCS in those rare cases where the specimen is not
>> mounted on a goniometer.
>>
>>
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