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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 10:39:12 +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: <CABcsX25oGH95vP8RLOET9R=BQZHDoizOu4FDht2ZjbXuYyYw8g@mail.gmail.com>
  • References: <CAM+dB2c5Hv=g03gGkC4==awB_ygVL6Hvdp-vf6R86pVOoRSmYQ@mail.gmail.com><CABcsX25oGH95vP8RLOET9R=BQZHDoizOu4FDht2ZjbXuYyYw8g@mail.gmail.com>
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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