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RE: Specifying values 'less than something' in CIFs?. .

On Sunday, April 29, 2012 11:02 AM, Nick Spadaccini wrote:

>? means the data value is unknown and the default defined in the dictionary for that data item can be used.
>. means the value has no meaning in the current context, more often used in loops.

At the risk of exhibiting ignorance, that answer seems not entirely consistent with CIF usage as I understand it.  Is it what you meant to say?  Has there been a shift in opinion down in Oz as to how these values should be used?  Does that vary from dictionary to dictionary?

Yes, the value ? is a placeholder representing an unknown value, and yes, . is a placeholder for a value that is undefined or not applicable in context.  But a dictionary-defined default value is not in general a safe estimate for an unknown value; at best, that would depend on the definition of the item in question.

In practice, it is the other place-holder, ., that by CIF convention is overloaded with the meaning "default value".  The canonical example is symmetry codes in the _geom_* categories of Core CIF, such as _geom_bond_site_symmetry_2.  A . as the value of that item is conventionally interpreted as the default value, 1_555.  That particular value should never be recorded as ?, because (1) if the _geom_bond_* packet is in any way meaningful then both site symmetry codes are certainly known, and (2) existing CIF software may rely on . being used to designate the default value in this case.

That does not in any way invalidate the thermal parameter example, however:

>For example if you have a loop of atomic data,
>_id _x _y _z _u11 _u22 _u33 _u12 _u13 _u23
>C1  .5 .4 .6 .03  .02  .03  .001 .002 -.002
>O1  .1 .2 .3 .02  .02  .02  .001 ?    ?
>H1  .5 .4 .8 .    .    .    .    .     .
>In O1 the values u13, u23 are missing and unknown.
>In H1 the values u11-u23 have no meaning because it was isotropically refined OR no thermals were refined.

In the end, how a program should deal with the placeholder values depends on multiple factors, such as the program's purpose, the definition (if any) of the item for which a placeholder value is recorded, and the particular placeholder value used.  For example, a semantic validation program encountering CIF site occupancies given as ? should at least flag them as questionable, a CIF pretty printer ought to accept them and leave them unchanged, and a crystallographic refinement program might choose to substitute a default value such as 1.0.


>Once you are able to include evaluation and validation methods within the domain dictionary most bases are covered.

I look forward to hearing about that.



John C. Bollinger, Ph.D.
Computing and X-Ray Scientist
Department of Structural Biology
St. Jude Children's Research Hospital

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