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Re: [Imgcif-l] imgCIF X axis

  • To: "Herbert J. Bernstein" <yayahjb@gmail.com>
  • Subject: Re: [Imgcif-l] imgCIF X axis
  • From: James H via imgcif-l <imgcif-l@iucr.org>
  • Date: Thu, 23 Jun 2022 00:36:37 +1000
  • Cc: James H <jamesrhester@gmail.com>, The Crystallographic Binary File and its imgCIF application to image data<imgcif-l@iucr.org>
  • In-Reply-To: <CABcsX24roBmnZ5wtsqXctbgoF5EmxTkEYAaMKHGL7wQDOZKt6g@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>
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_im
g_1.8.4.html#_axis.type>
>         _axis.equipment <http://www.bernstein-plus-sons.com/software/CBF/doc/c
if_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/c
if_img_1.8.4.html#_axis.vector[1]> _axis.vector[2] <http://www.bernstein-plus-so
ns.com/software/CBF/doc/cif_img_1.8.4.html#_axis.vector[2]> _axis.vector[3] <htt
p://www.bernstein-plus-sons.com/software/CBF/doc/cif_img_1.8.4.html#_axis.vector
[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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