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Re: Comments on CIF core changes for 2.3

  • To: Multiple recipients of list <coredmg@iucr.org>
  • Subject: Re: Comments on CIF core changes for 2.3
  • From: Howard Flack <Howard.Flack@cryst.unige.ch>
  • Date: Tue, 15 Jul 2003 17:07:02 +0100 (BST)
CH> data_atom_site_refinement_flags_adp

  Curt's comments make good sense to me. I also very much enjoyed going
to dinner with him in a Chinese restaurant in Los Angeles.

CH> What is partial occupancy constraint?  

  Curt: If you look carefully in the revised version that Brian has
circulated, the word 'partial' only occurs just once, in the item
'data_atom_site_refinement_flags' which the _definition says "It is
retained in this dictionary only to provide compatibility with legacy
CIFs". Amongst the corrections Brian implemented on my bequest, was the
removal of the word 'partial' because I could not understand what it
meant either.

CH> data_diffrn_standards_decay_%_lt
CH> I like the concept

   Personally I hate it. If it is difficult to use, it makes another
good reason to ditch it. I see no difficulty in just reporting a value
of zero with its standard uncertainty.
   Is a negative decay an increase in intensity of the standards?

CH> Doesn't c-glide define reflection and if so isn't reflection
>    _example_detail
>             'x,1/2-y,1/2+z'  'c glide reflection through the plane (x,1/4,z)'

Using the wording of ITA page 5 for the defining the symmetry operation,
in full this should be

              'x,1/2-y,1/2+z'  'glide reflection through the plane
(x,1/4,z), with glide vector 1/2 c'

The somewhat cumbersome wording is in part forced by the necessity of
distinguishing between a symmetry operation and the related symmetry
element. So the symmetry operation is 'glide reflection' with the
related symmetry element being a 'glide plane'. In my way of
understanding English, there is no sense of 'reflection through a plane'
associated with 'glide'. 

> I must admit that until I read (or misread) Howard's comments I would have
> made C2/m look like the simpler example.

  The old definition of _symmetry_equiv_pos_as_xyz says

> Symmetry equivalent position in the 'xyz' representation. Except
>    for the space group P1, this data will be repeated in a loop.
>    The format of the data item is as per International Tables for
>    Crystallography, Vol. A. (1987). All equivalent positions should
>    be entered, including those for lattice centring and a centre of
>    symmetry, if present.

  which makes me think that the simpler version is not the good one.
However, ....

> The suggested extended examples could help resolve ambiguities.  Perhaps the
> extended example could also include a non standard setting.   

  That all sounds like very good advice and makes very good sense. I
always look at the examples first and read the definitions afterwards.

> but I do not know how to set it up to give something
> that looks like this. 
  I have the same problem. In principle I know how to do it, in practice
I always get it wrong!


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