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Re: [ddlm-group] The Grazulis eliding proposal: how to incorporateinto CIF?. .. .. .

Dear Herbert,

On Tuesday, June 28, 2011 1:46 PM, Herbert J. Bernstein wrote:

>   I fear we are not comunicating very effectively.

Evidently not.

>  I am
>_not_ comfortable with the current state of the CIF2
>document, and I do not find the current emendation to
>be an improvement.

Your opinions about the document and the proposed change are entirely at your discretion, of course, but it does come as a surprise to me that you think the entire changes document unsatisfactory.  If there are issues with it that you have not previously brought before the group then I would greatly appreciate the opportunity to hear and perhaps comment on them before Madrid.  Even those who will actually be present in Madrid might appreciate the opportunity to consider those issues ahead of time.

As far as I am aware, the only point of CIF 2.0 syntax remaining open for discussion is the (in-)ability of CIF 2.0 to represent arbitrary strings.  Inasmuch as both this working group and COMCIFS already approved the changes document, I would be very reluctant to reopen it for general changes.  Nevertheless, if you have discovered serious flaws in it then better to fix them sooner than later.  Otherwise, it is unproductive to criticize proposals for being based on the only document available to base them on.

>  Much as I would dearly love to have
>the current line-folding protocol in CIF2, I think it
>is much more important to work on making CIF2 into
>something clear and coherent.  I for one find the
>either-or approach to prefixes and line-folding unnecessary
>and confusing.

Line folding and prefixes are compatible.  Saulius pointed this out in his initial description of the protocol, as a group we commented on it in our subsequent discussion, and my formal proposal from earlier today specifically and explicitly provides for them to work together.  I'm not sure how you acquired an impression to the contrary, but if it was from my text then please explain so that I can improve it.

>  When working with old fortran compilers,
>I _need_ the line folding protocol.  If the prefixes
>are bing introduced, I need a way to deal with both the
>prefixes _and_ the line-folding protocol, not have it
>be either-or.  I understand that mose people don't
>see a problem, but I work with software both on new computers
>and very, very old computers (e.g. I just brought an Indigo
>back to life).

I don't see a problem specific to line-folding and prefixes.  Not even for very old compilers.  I do appreciate that some old compilers present issues for text processing in general, and that these manifest in the context of CIF.  I think most of us do, else CIF 2.0 would be different.

>   I repeat my suggestion that we need to meet and talk things
>out.  Maybe then I will understand what the rest of you are trying
>to do, and maybe I will be able to explain what I am trying
>to do.

It was my understanding that there would indeed be opportunities for those who attend Madrid to meet, and I hope that at least one such meeting happens.  It will bear more fruit the better its participants can prepare for it, however.  If I were going to be present, then I would want to have as specific an idea as possible of the topics to be covered.  Bringing those up here, in advance, would have the added advantage of including, at least to some extent, group members who otherwise would be shut out.



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

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