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Re: [Imgcif-l] imgCIF Standard Axis definition

Hi All,

I have to agree very strongly with Harry here. This is being used to
record the original raw measurements from a diffraction experiment, so
we should try to avoid cluttering, especially with information which

(1) could very well be wrong
(2) is derived from the experimental results
(3) will almost certainly be NULL at the time of file creation

There are already perfectly good places for storing this elsewhere.

Just my two cents.

Regards,

Graeme

-----Original Message-----
From: imgcif-l-bounces@iucr.org [mailto:imgcif-l-bounces@iucr.org] On
Behalf Of Harry Powell
Sent: 04 May 2007 10:46
To: The Crystallographic Binary File and its imgCIF application to image
data
Cc: s.parsons@ed.ac.uk
Subject: Re: [Imgcif-l] imgCIF Standard Axis definition

Hi folks

I'm more than a little concerned about putting the (any!) crystal
orientation matrix in the imgCIF/CBF (though for an mmCIF containing the
results of solution and refinement this should be included) - for most
users the imgCIF/CBF is part of their raw data, and they won't have
indexed the crystal and hence have no orientation matrix.  Even if the
orientation matrix is there, presumably some symmetry will have been
imposed on this (I'd usually expect at least crystal system
symmetry...), and this may well be in error. I spend quite a bit of time
pointing pointing out to (even experienced) crystalographers that they
have the wrong symmetry for their data processing...

Also, of course, there are multiple definitions of orientation matrices
(e.g. wavelength dependent and independent, UB style, Niggli...)

 > Dear Herbert,
>
> There already seems to be some work on using multiple crystals in more

> conventional crystallography, so I wonder if there is way to re-use 
> those labels? Perhaps I am trying to put a square peg in a round hole 
> here...
>
> Currently there is _diffrn_id in the _diffrn_orient_matrix category, 
> which identifies the diffraction experiment. I would suggest adding a 
> pointer to the category '_exptl_crystal_id' which might also be called

> '_diffrn.crystal_id' in mmCIF? eg, just add:
>
> '_diffrn_orient_matrix.crystal_id'
>
> ...and allow a loop giving a list of orientation matrices all pointing

> at different crystal_id's. This seems to be the 'many crystal' cif 
> category, but I don't quite see how to list several crystals in the 
> same cif file for now (would I have to give all the crystal colors for

> grains buried inside a piece of rock?). After integration the same 
> data for _exptl_crystal_id should then show up in the integrated
reflections as:
>
> _refln_crystal_id
> and/or:
> _diffrn_refln_crystal_id
>
> Somehow it would be useful to distinguish the cases of having several 
> crystals and several structure refinements, or several crystals giving

> a single merged dataset and a single refinement. This would be closely

> related to the existing practices dealing with twins in small molecule

> crystallography. People make a dataset from single twin component in 
> order to solve the strucuture (shelx hklf 4) and then refine it using 
> all the reflections (shelx hklf 5 I think). I've copied this mail to 
> Simon Parsons in case he knows how this is done in cif already.
>
> Then for crystal translations mmCIF already has:
> '_diffrn.crystal_id'
> '_diffrn.crystal_support'
> '_diffrn.crystal_treatment'
>
> How about then adding a category:
> '_diffrn_crystal_translation'
> containing:
> '_diffrn_crystal_translation.x'
> '_diffrn_crystal_translation.y'
> '_diffrn_crystal_translation.z'
> '_diffrn_crystal_translation.diffrn_id'
> '_diffrn_crystal_translation.crystal_id'
>
> These are x, y, z translations of the crystal with respect to the 
> laboratory axes with all goniometer angles set to zero. Units are mm.
> The diffrn_id refers to the diffraction experiment and there must also

> be a matching _diffrn_orient_matrix.diffrn_id entry and a matching 
> crystal_id. The axis x/y/z definition here will match that of the 
> orientation matrix (and therefore the laboratory co-ordinate system) 
> and if the category is absent then these values are assumed to be 
> zero. This category is allowed to _loop over all the crystals in the
sample.
>
> If the orientation_matrix category contains a UB matrix, one should 
> expect to be able to match the unit cell parameters for each crystal 
> to the ones that can be derived from UB (eg (UB)^T.UB is the metric 
> tensor, which in turn gives the unit cell). Since there are many cif 
> files which implicitly assume a single crystal, it seems the default 
> value for crystal_id in any category must be assumed as the first and 
> only entry in _exptl_crystal_id. Otherwise almost all derived data 
> will end up being littered with crystal_id entries. I wonder if 
> orientation matrix should have been:
>
> '_diffrn_crystal_orient_matrix.UB[0][0]' etc
>
> where I've added crystal in the label. The orientation matrix is a 
> property of the crystal in the diffraction experiment and you can't 
> normally find one without mounting your crystal! Is it a bug in mmCIF 
> to have this independent of the crystal?
>
> What are your thoughts? Perhaps a new category would be better if this

> is a mis-use of the intentions of crystal_id
>
> Best,
>
> Jon
>
> PS: Apologies if this mail was sent twice.
>
> Herbert J. Bernstein wrote:
> > Dear Jon,
> >
> >    Your point is a significant one, not a pedantic one -- it comes 
> > down to what should be refined from the images:  the axis 
> > definitions or offsets relative to fixed axis definitions.  Let us 
> > start with the central issue:  where should the origin of the axis 
> > system be?  You are right -- we have a better chance of a stable 
> > axis system against which to measure offsets if we use the 
> > intersection of two mechanically stable axes to set the origin.  
> > Hopefully, the sample will have been mounted so that that mechanical

> > origin is bathed by the center of the beam and so that that origin 
> > is within the sample, so I would proposed the following approach to
axis definition:
> >
> >    1.  The origin of the axis system should, if possible, be defined

> > in terms of mechanically stable axes to be in the beam.  If the 
> > sample goniometer or other sample positioner has two axes the 
> > intersection 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.
> >
> >    2.  It the sample positioning system has a principal axis that 
> > intersects the origin and which forms an angle of more than 22.5 
> > degrees with the beam axis, the X-axis will point from the origin 
> > specified above along the principal axis of the goniometer,
> >
> >    ... and then continue with the definitions as before using either

> > David's simpler approach or the more detailed one suggested on the 
> > web site.
> >
> >    You are also right about the need for multiple orientation
matrices.
> > I think we need to add a GRAIN or SUBSAMPLE category to list the 
> > grains and and then an extra _diffrn_orient_matrix.grain_id or 
> > _diffrn_orient_matrix.subsample_id tag to separate the matrices for 
> > the different grains.  Would you care to suggest the tags for the 
> > GRAIN or SUBSAMPLE category itself?
> >
> >    Regards,
> >      Herbert
> >
> > At 12:47 AM +0200 5/4/07, Jon Wright wrote:
> >> 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.
> >>>>
> >>>>
> >>>  _______________________________________________
> >>>  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
> >
> >
>
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>

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH


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