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RE: Comments on CIF core changes for 2.3




CH> data_diffrn_standards_decay_%_lt
CH> I like the concept

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

CH Comment >>  

The concept I like is being able to avoid claiming 0% decay.
I agree that it could be difficult to use. I also agree
that a std uncertainty would accomplish this without a new term
I have often wondered about what it meant when I had a decay 
of -3(1)%, perhaps we should be defining a new entry that
would "replace" the current term
 
How about data_diffrn_standards_variation

But I don't really like that either because no standards 
are measured in the typical area detector experiment

How about data_diffrn_stability_variation_%

But I don't really like that either BECAUSE
I am wondering how I get this information in the area detector 
experiment.  Typically data are corrected with some scaling
program ( SCALEPACK, SADABS, MULABS, SORTAV .... ) Do any of these  
programs have the ability to separate out "decay" from other 
corrections?  If not, then what are we accomplishing by asking
scientists to provide a number that they do not have ready access to.
One could argue that the programs should be rewritten to provide 
the info.  This may happen, but the probabilities are not high.  



With respect to symmetry you are right (as usual). I was leaving my 
crystallographers hat on while interpreting the English. It is much 
better to not use c glide in the definition as that immediately makes  
me think crystallographically and then glide (or perhaps more 
accurately glide plane) does imply reflection and translation.

-----Original Message-----
From: Howard Flack [mailto:Howard.Flack@cryst.unige.ch]
Sent: Tuesday, 15 July, 2003 11:07 AM
To: Multiple recipients of list
Subject: Re: Comments on CIF core changes for 2.3


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
redundant?  
>    _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

    _example_detail
              '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!

H.

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