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Re: Seattle Discussions

• To: Multiple recipients of list <imgcif-l@bnl.gov>
• Subject: Re: Seattle Discussions
• From: John Westbrook <jwest@ndbdev.Rutgers.EDU>
• Date: Wed, 18 Sep 1996 07:37:54 -0400 (EDT)

Andy Hammersley wrote:
> Concerning my point 6., John Westbrook wrote:
> 
> > I would be happy to try to translate your CBF definition into
> > a DDL-2 compliant dictionary..
> 
> I think that would be a very useful and appreciated contribution.
> (You'll probably spot some inconsistencies.)
>
Could someone please send me the CBF definition of point me at 
a network site for this document.

 
> I have some questions which maybe could be answered in this context.
> Syd Hall introduced, in his CIF workshop talk, the STAR concept of
> defining dependencies of one data item on another.
> 
> Can this be included, based on the data item values ?
> 
> e.g. If we have the following:
> 
> _array_intensities.linearity linear # Simple linear intensity scaling
> 
> Then no extra data items are needed to define the scaling of pixel
> element values, but if the data item had a different value e.g.
> 
>  scaling_offset # Zero Offset and scale factor
> 
> then two data items would have to be defined (unless default values were
> considered appropriate) e.g.
> 
> _array_intensities.offset 201 # Detector offset value
> _array_intensities.scaling 2 # Double intensity range
> 
> (I think, from talking to Syd, that the answer is yes, but I don't
> know how to do this.)
>
You can define that there is a relationship within the definition
of these three data items, but there is really no way to define a
relationship that is conditional on a value of one members of the group.
So there is no mechanism to specify that if _array_intensities.linearity
= "scaling_offset" then require the specification of an offset and 
and a scaling.   However, you can specify that offset and scaling
are related to/have a functional association with linearity and 
that these items must always be specified as a group.  In the 
case of linearity = "linear", then the values of offset and scaling
would be given the CIF placeholder value, '.', to show that values are
not appropriate for the linear case.  
 
> Similarly, would it be possible to define a strict ordering of certain
> data items. I don't think this occurs in CIF, but it would make writing
> CBF software much easier if certain restrictions on the ordering of data
> items could be imposed. e.g. in the above example the
> '_array_intensities.offset' and '_array_intensities.scaling' could be
> restricted to occur only after the '_array_intensities.linearity' item
> has "introduced" them. Can these sort of restrictions be defined ?
> Or maybe there are better suggestions for how to enbody these requirements
> in a CIF format.

The order of data in a CIF vector or table has no significance.
The easiest way to introduce an order into CIF is to explicitly
add a data item that reflects the order.  There are many examples
in the mmCIF dictionary where indices have been added to tables
for just this purpose.  

******************************************************************
*  John Westbrook                    Ph:  (908) 445-4290         *
*  Department of Chemistry           Fax: (908) 445-4320         *
*  Rutgers University                                            *
*  PO Box 939                     e-mail: jwest@ndb.rutgers.edu  *
*  Piscataway, NJ 08855-0939                                     *
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