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Re: [ddlm-group] CIF2 semantics

Dear Herbert,

On Wednesday, August 10, 2011 2:05 PM, you wrote:

>   I have been discussing the meaning of a string that looks like a
>number in the absence of a dictionary, saying that that string should
>be treated as something other than a number.  When we were writing
>the CIF 1.1 spec we did not intend to change the well-established
>CIF rule that such a string should be treated as a number.  If
>you have found an error in the CIF 1.1 spec which leads to a reading
>saying something else, then you should propose a correction to the
>CIF 1.1 spec to conform to the well-established CIF rule, just
>as I have proposed fixing the error in the CIF 1.1 spec to require
>the terminal whitespace at the end of a text field.

I cannot in good faith characterize my complaint as an error in the CIF 1.1 specifications.  I think it fairer to describe the problem as a design choice having been made for CIF 1.1 that had unfortunate, unnecessary, and possibly unforeseen consequences.  There is an opportunity to make a different, I claim better, choice for CIF 2.0 without unduly compromising de facto backwards compatibility.  It appears that there is no support for that change.  That leaves me disappointed, but it's all part of the nature of collaborative specification processes such as the one we are engaged in.

>   I don't see any problem to be solved in the example you gave.
>If the 2 CIFs are intended to be processed without a dictionary,
>they are equivalent.  If one or the other is intended to be
>processed with a dictionary, they may or may not be equivalent
>depending on what the dictionaries say.  How is that a problem?

In my view it is inherently problematic that CIF does not definitively answer the question of whether they are equivalent.  I find it deeply unsatisfactory that CIF 1.1's answer is "it depends what you do with them," especially given CIF 1.0's conflicting answer that they are indeed equivalent.  CIF 2.0 *could* answer the question better, but if I have not already persuaded you that that would be worthwhile then I can think of nothing else to say that might do so.



John C. Bollinger, Ph.D.
Department of Structural Biology
St. Jude Children's Research Hospital

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