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Re: [Imgcif-l] imgCIF X axis

  • To: James Hester <james.r.hester@gmail.com>
  • Subject: Re: [Imgcif-l] imgCIF X axis
  • From: "Herbert J. Bernstein via imgcif-l" <imgcif-l@iucr.org>
  • Date: Wed, 22 Jun 2022 10:47:58 -0400
  • Cc: "Herbert J. Bernstein" <yayahjb@gmail.com>, The Crystallographic Binary File and its imgCIF application to image data<imgcif-l@iucr.org>
  • In-Reply-To: <CAM+dB2eub4fzZexSig9cZqBooR+iiVspOyzNy7yfAcZUpm-xrA@mail.gmail.com>
  • References: <CAM+dB2c5Hv=g03gGkC4==awB_ygVL6Hvdp-vf6R86pVOoRSmYQ@mail.gmail.com><CABcsX25oGH95vP8RLOET9R=BQZHDoizOu4FDht2ZjbXuYyYw8g@mail.gmail.com><CAM+dB2cRnOFZA+6RLD4oBEbz769aJ2TU-02NpeSFPUaBUKty0Q@mail.gmail.com><CABcsX24zMJ8yU+JFVKLOxaQKy02cMwE2h5eobWc_4C+NRkxmjw@mail.gmail.com><CAM+dB2dqj7M_PEpftjo3H5zfV98=80XQC6Hf-qDQ2SoUOk-qHg@mail.gmail.com><CABcsX24roBmnZ5wtsqXctbgoF5EmxTkEYAaMKHGL7wQDOZKt6g@mail.gmail.com><CAM+dB2eub4fzZexSig9cZqBooR+iiVspOyzNy7yfAcZUpm-xrA@mail.gmail.com>
Dear James,
  I am used to omega at the bottom, not kappa, so it would be omega on top
of
a translational positioner.  I would expect one of the translational rails
to be
the principal axis.
  Regards,
    Herbert

On Wed, Jun 22, 2022 at 10:36 AM James H <jamesrhester@gmail.com> wrote:

> My comments in relation to kappa were simply in response to your apparent
> suggestion that my working principle of the "bottom-most rotation axis"
> being the principal axis might not work very well if a kappa axis is
> sitting on top of translation stages. However, if there is an omega axis
> somewhere underneath the kappa axis, as in the example you just provided,
> then that working principle remains valid.
>
> If we return to your original example of a kappa axis sitting on top of
> translation stages, with no further rotation axes underneath, can you
> please explain what the principal axis must be in this case? The positive
> direction of movement of the bottom-most translation stage perhaps?
>
> I agree that in a few places the documentation both in Vol G and the
> dictionary does need to be improved. In my experience the concept of a
> "principal axis" is not readily understood by the general reader (not just
> me) so should be explained. Your kappa on translation stage example might
> be very illuminating in this case. And emphasising that the direction of X
> matches the direction of the principal axis (not just "aligns") might also
> help.
>
> I would be very surprised if the issues with NSLS and DLS had anything to
> do with the coordinate system as such. The laws of physics are invariant
> against rotation and translation, so I suspect that the problem was more
> likely to be that some axis somewhere was not given the correct components
> relative to the chosen coordinate system.
>
> all the best,
> James.
>
>
> On Wed, 22 Jun 2022 at 22:26, Herbert J. Bernstein <yayahjb@gmail.com>
> wrote:
>
>> Dear James,
>>   Here is an example from the AXIS category i the dictionary:
>>
>>  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*
>> ;
>> ;
>>          loop_
>>         _axis.id <http://www.bernstein-plus-sons.com/software/CBF/doc/cif_img
_1.8.4.html#_axis.id>
>>         _axis.type <http://www.bernstein-plus-sons.com/software/CBF/doc/cif_i
mg_1.8.4.html#_axis.type>
>>         _axis.equipment <http://www.bernstein-plus-sons.com/software/CBF/doc/
cif_img_1.8.4.html#_axis.equipment>
>>         _axis.depends_on <http://www.bernstein-plus-sons.com/software/CBF/doc
/cif_img_1.8.4.html#_axis.depends_on>
>>         _axis.vector[1] <http://www.bernstein-plus-sons.com/software/CBF/doc/
cif_img_1.8.4.html#_axis.vector[1]> _axis.vector[2] <http://www.bernstein-plus-s
ons.com/software/CBF/doc/cif_img_1.8.4.html#_axis.vector[2]> _axis.vector[3] <ht
tp://www.bernstein-plus-sons.com/software/CBF/doc/cif_img_1.8.4.html#_axis.vecto
r[3]>
>>         omega rotation goniometer     .    1        0        0
>>         kappa rotation goniometer omega    -.64279  0       -.76604
>>         phi   rotation goniometer kappa    1        0        0
>> ;
>>
>>
>>
>> Note that it is omega and phi that point along X, not kappa and omega is
>> grounded, so I really
>> did mean omega as the principal axis is this case.  I also do mean to
>> suggest that a
>> translation rail can define X.  Please tell me what in the dictionary you
>> are seeing that
>> says that "kappa axis to be the principal axis, no questions asked".  It
>> comes as a
>> surprise to me.
>>
>> At NSLS-II and DLS the choice of coordinate system has had a definite
>> impact on analysis
>> of the data.  Flipping X messes up handling of the beam center, which
>> leads to one
>> of these annoying hunts through the 8 alternatives which can undo beam
>> center flips.
>>         
>> Please send me a copy of the documentation you are working from.  It
>> sounds like we
>> have some work to do to make sure this is really clear.
>>         
>> Regards,
>>     Herbert
>> On Wed, Jun 22, 2022 at 3:35 AM James H <jamesrhester@gmail.com> wrote:
>>
>>> Thanks Herbert. I assume in your kappa example you mistyped and meant
>>> that kappa (not omega) would be the principal axis according to my working
>>> definition. Meanwhile, you seem to be implying that there may be some
>>> flexibility in the choice of "principal axis" for certain goniometers. That
>>> is, in your example a more intuitive choice of principal axis might be that
>>> of an imaginary omega stage underneath the translation stages, at which
>>> point you have the freedom to choose rotation direction and therefore X
>>> axis orientation. However, my reading of the current definition in the AXIS
>>> category would require the kappa axis to be the principal axis, no
>>> questions asked, so I'm not sure how much freedom there actually is.
>>>
>>> I guess it's worth noting as well that the choice of coordinate system
>>> makes zero difference to the analysis of the data, so ambiguity in the
>>> definition of X is not a major issue. However I do think we need to be
>>> clear if and when this freedom of choice does exist.
>>>
>>> all the best,
>>> James.
>>>
>>> On Wed, 22 Jun 2022 at 11:30, Herbert J. Bernstein <yayahjb@gmail.com>
>>> wrote:
>>>
>>>> Dear James,
>>>>   To be clear, it usually works best to do as you say and to choose a
>>>> goniometer
>>>> axis that does not depend on any other axes, but that may conflict with
>>>> your
>>>> preference for a rotation axis, as when a kappa goniometer is mounted on
>>>> an x,y,z translation stage, which means that one of the translations
>>>> would
>>>> be the one that depends on no other axes.  Then if you choose omega as
>>>> the
>>>> principal axis axis to stick to using a rotation axis you have to
>>>> jigger all your
>>>> software to deal with a variable coordinate frame -- not a terrible
>>>> thing if your
>>>> software is carefully written to follow robotics conventions, but a
>>>> likely source
>>>> of bugs in general.
>>>>   I would leave the wording at "principal axis"
>>>>   Regards,
>>>>     Herbert
>>>>
>>>> On Tue, Jun 21, 2022 at 8:39 PM James H <jamesrhester@gmail.com> wrote:
>>>>       
>>>>> Just to pick up on something else in Herbert's reply: I've noticed
>>>>> some confusion when talking to people as to what exactly "the principal
>>>>> axis of the goniometer" is. My current working definition is "the
>>>>> bottom-most rotation axis of the goniometer".  In terms of the imgCIF AXIS
>>>>> category, this would be the goniometer rotation axis that depends_on no
>>>>> other axis, typically omega on a 4-circle diffractometer, and so by
>>>>> definition of X this axis would have axis vector of [1 0 0] in
>>>>> non-pathological cases. Is my understanding correct? Are there subtleties
>>>>> not covered by my working definition?
>>>>>
>>>>> thanks,
>>>>> James.
>>>>>
>>>>> On Wed, 15 Jun 2022 at 21:34, Herbert J. Bernstein <yayahjb@gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Dear James,
>>>>>>   This is a little tricky.  The relevant rules are:
>>>>>>
>>>>>> "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."
>>>>>>
>>>>>>   "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"
>>>>>>
>>>>>> So, yes the x-axis starts from the sample, but where it point to in
>>>>>> the
>>>>>> goniometer depends on where in the goniometer the "principal"
>>>>>> axis of the goniometer points _and_ in which direction the axis
>>>>>> settings increase and whether the principal axis is a rotation
>>>>>> axis or a translation axis.  The only way I have figured out to
>>>>>> do this is to start from the engineering diagrams (or at least
>>>>>> photos) of the goniometer, and even then, I once screwed up
>>>>>> the x-axis for a beamline at DLS (ask Graeme Winter).
>>>>>>
>>>>>>   Regards,
>>>>>>     Herbert
>>>>>>
>>>>>> On Wed, Jun 15, 2022 at 2:38 AM James H via imgcif-l <
>>>>>> imgcif-l@iucr.org> wrote:
>>>>>>
>>>>>>> Dear imgCIF experts,
>>>>>>>
>>>>>>> Just to double-check, is it correct to say that the imgCIF X axis
>>>>>>> always
>>>>>>> points from the specimen towards the goniometer base? Closely
>>>>>>> parsing the
>>>>>>> dictionary and Volume G suggests that the X axis being "aligned"
>>>>>>> with the
>>>>>>> principal axis could also allow the X axis to point from the
>>>>>>> specimen away
>>>>>>> from the goniometer base, particularly if the sense of rotation of
>>>>>>> the
>>>>>>> principal goniometer axis is taken into account when defining X (is
>>>>>>> it?).
>>>>>>>
>>>>>>> thanks,
>>>>>>> James.
>>>>>>> --
>>>>>>> T +61 (02) 9717 9907
>>>>>>> F +61 (02) 9717 3145
>>>>>>> M +61 (04) 0249 4148
>>>>>>> _______________________________________________
>>>>>>> imgcif-l mailing list
>>>>>>> imgcif-l@iucr.org
>>>>>>> http://mailman.iucr.org/cgi-bin/mailman/listinfo/imgcif-l
>>>>>>>
>>>>>> 
>>>>> 
>>>>> --
>>>>> T +61 (02) 9717 9907
>>>>> F +61 (02) 9717 3145
>>>>> M +61 (04) 0249 4148
>>>>>
>>>>
>>>
>>> --
>>> T +61 (02) 9717 9907
>>> F +61 (02) 9717 3145
>>> M +61 (04) 0249 4148
>>>
>>
>
> --
> T +61 (02) 9717 9907
> F +61 (02) 9717 3145
> M +61 (04) 0249 4148
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