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Re: [Cif2-encoding] How we wrap this up
- To: Group for discussing encoding and content validation schemes for CIF2 <cif2-encoding@xxxxxxxx>
- Subject: Re: [Cif2-encoding] How we wrap this up
- From: "Herbert J. Bernstein" <yaya@xxxxxxxxxxxxxxxxxxxxxxx>
- Date: Fri, 24 Sep 2010 17:25:49 -0400 (EDT)
- In-Reply-To: <281388.90819.qm@web87012.mail.ird.yahoo.com>
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Dear Simon, Thank you, very much. You have done the right thing. -- Herbert Regards, Herbert ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== 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 > Of SIMON WESTRIP > >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. > > [...] > > > Email Disclaimer: www.stjude.org/emaildisclaimer > _______________________________________________ > cif2-encoding mailing list > cif2-encoding@iucr.org > http://scripts.iucr.org/mailman/listinfo/cif2-encoding > >
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- References:
- [Cif2-encoding] How we wrap this up (James Hester)
- Re: [Cif2-encoding] How we wrap this up (SIMON WESTRIP)
- Re: [Cif2-encoding] How we wrap this up (Bollinger, John C)
- Re: [Cif2-encoding] How we wrap this up (SIMON WESTRIP)
- Re: [Cif2-encoding] How we wrap this up (Herbert J. Bernstein)
- Re: [Cif2-encoding] How we wrap this up (SIMON WESTRIP)
- Re: [Cif2-encoding] How we wrap this up (Herbert J. Bernstein)
- Re: [Cif2-encoding] How we wrap this up (SIMON WESTRIP)
- Re: [Cif2-encoding] How we wrap this up (Herbert J. Bernstein)
- Re: [Cif2-encoding] How we wrap this up (SIMON WESTRIP)
- Re: [Cif2-encoding] How we wrap this up (Herbert J. Bernstein)
- Re: [Cif2-encoding] How we wrap this up (SIMON WESTRIP)
- Re: [Cif2-encoding] How we wrap this up (Bollinger, John C)
- Re: [Cif2-encoding] How we wrap this up (SIMON WESTRIP)
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