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Re: [Cif2-encoding] How we wrap this up

Dear Simon,

   Thank you, very much.  You have done the right thing. -- Herbert

  Herbert J. Bernstein, Professor of Computer Science
    Dowling College, Kramer Science Center, KSC 121
         Idle Hour Blvd, Oakdale, NY, 11769


On Fri, 24 Sep 2010, SIMON WESTRIP wrote:

> Dear James
> As you may have gathered I have been reconsidering my position on this issue.
> Please forgive me, but I would like to change my vote if that is OK, in favour of the
> 'any encoding' camp.
> This apparent U-turn is not a response to recent contributions; rather it is the
> outcome of a meeting I had this morning
> where I demonstrated some new software to the Managing Editor of IUCr journals.
> By way of explanation:
> I have been developing a new docx template which the IUCr editorial office is shortly
> to release for use by
> authors. The template will be packaged with some tools to extract data from CIFs
> and tabulate them in the Word document, e.g. open an mmCIF, click a button, and
> standard
> tables populated with data from the CIF will be included in the document, acting as
> table templates for the author to edit as appropriate for their manuscript.
> Inclusion of the mmCIF tools is part of an unofficial policy to 'coax' biologists to
> start using/accepting mmCIF
> as a useful medium, rather than as a product of their deposition to the PDB, and to
> encourage them to become comfortable
> with passing mmCIFs between applications, and even to edit the things (in the same way
> as the core-CIF community
> treats CIFs). For example, our perception is that there is no reason why an author
> should not feel free to take an mmCIF
> that has been created by e.g. pdb_extract and populate it using third-party software
> before uploading to the PDB for
> deposition.
> This cause would not be furthered by effectively invalidating an mmCIF if it were not
> to be encoded in one of
> the specified encodings.
> So although I am uneasy about a specification that propogates uncertainty, I'm also
> uneasy about alienating users,
> especially when we are struggling to change their mindset as in the case of the
> biological community
> (my perception of the biological community's attitude to mmCIF is based on feedback
> from authors/coeditors to
> IUCr journals).
> Granted this may not be the most compelling argument in favour of 'any encoding', but
> recognizing the hurdles that
> may have to be overcome once we move beyond ASCII whatever the CIF2 specification, I
> support 'any encoding'
> as 'a means to an end'.
> I will not provide my preferences in terms of the numbered options until you say so;
> afterall, I have already voted and
> all this has to be signed off by COMCIFs in any case.
> Cheers
> Simon
> _______________________________________________________________________________________
> From: "Bollinger, John C" <John.Bollinger@STJUDE.ORG>
> To: Group for discussing encoding and content validation schemes for CIF2
> <cif2-encoding@iucr.org>
> Sent: Friday, 24 September, 2010 14:50:57
> Subject: Re: [Cif2-encoding] How we wrap this up
> Dear Simon,
> It is exactly this sort of issue that drove me to support more permissive encoding
> rules and ultimately to devise the UTF-8 + UTF-16 + local proposal.
> Do please think about the considerations Herb raised.  As you reconsider your votes, I
> urge you also to ask yourself what, *precisely*, a "text file" is, and to consider
> whether your answer is functionally different from my "local".  If you decide not, then
> please consider what that answer implies about CIF2 support of UTF-8 and UTF-16 (which
> evidently you favor) under each option on the table, especially for CIFs containing
> non-ASCII characters.  Whatever you decide about the meaning of "text file", please
> consider whether reasonable people might reach a different conclusion, as I assert they
> might do, and to what extent the standard needs to address that.
> Regards,
> John
> --
> John C. Bollinger, Ph.D.
> Department of Structural Biology
> St. Jude Children's Research Hospital
> >From: cif2-encoding-bounces@iucr.org [mailto:cif2-encoding-bounces@iucr.org] On Behalf
> >Sent: Friday, September 24, 2010 7:53 AM
> >To: Group for discussing encoding and content validation schemes for CIF2
> >Subject: Re: [Cif2-encoding] How we wrap this up. .
> >
> >Dear Herbert
> >
> >Not for the first time, I find your arguement persuasive. Brian's vote and explanation
> have also raised some
> >questions that I would like to look into.
> >
> >I will confirm or otherwise my vote as soon as possible, assuming that is OK with
> James and assuming that
> >this round of votes might wrap this up.
> >
> >Cheers
> >
> >Simon
> >
> >________________________________________
> >From: Herbert J. Bernstein <yaya@bernstein-plus-sons.com>
> >To: Group for discussing encoding and content validation schemes for CIF2
> <cif2-encoding@iucr.org>
> >Sent: Friday, 24 September, 2010 13:17:14
> >Subject: Re: [Cif2-encoding] How we wrap this up
> >
> >If he ignores the standard, in most cases all he has to do to comply with CIF2 is to
> run whatever applications he currently runs to produce CIF1 and, perhaps, in some
> cases, run a minor edit pass at the end, to convert for the minor syntactive
> differences and/or changed tags required to comply with CIF2 and the new dictionaries,
> but he is unlikely to have to do anything to deal with the messy business of whether
> his encoding is really a proper UTF8 encoding or not.
> >The punishment if he tries to comply, is that he has to totally uproot and reconfigure
> the environment in which he produces CIFs from whatever he is currently doing to create
> an enviroment in which he can reliably create and, more importantly, transmit compliant
> UTF8 files.  This can be very tricky if he does only a partial job, say fudging in one
> special application (yet to be written), because if he stays with his old system, all
> kinds of tools will keep trying to transcode whatever he has produced back to whatever
> his system considers a standard. Those of us who have files, applications and tools
> that have lived through several generations of macs are living proof of the problem.
> Macs now have excellent UTF8/16 unicode support, but every once in a while in working
> with a unicode file I find it has been strangely and unexpectedly converted to
> something else, and it can be really tricky to spot when the unaccented roman text part
> has been left untouched but just a few accen
> ted letters have gotten different accents.
> >Mandating UTF8 is simply trying to shift a serious software problem from the central
> handlers of CIF (IUCr, PDB, etc.) to the external users. Most users will probably have
> the good sense to simply ignore the demand and leave the burden just where it is now. 
> A few sophisticated users will probably adapt with no trouble, but the punishment for
> those users who blindly follow orders before we have a complete multiplatform
> supporting infrastructure in place by mandating UTF8 is severe, expensive and
> undeserved.  Until and unless we have developed solid support, we will just be
> alienating people from CIF.  I will continue to oppose such a move.
> [...]
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