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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: Wed, 22 Jun 2022 17:34:54 +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: <CABcsX24zMJ8yU+JFVKLOxaQKy02cMwE2h5eobWc_4C+NRkxmjw@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>
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.
>>>> --
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>>>> F +61 (02) 9717 3145
>>>> M +61 (04) 0249 4148
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>>>
>>
>> --
>> 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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