[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Reply to: [list | sender only]
Re: CIF 2.0 syntax proposal for retaining backwards CIF 1.xcompatibility. .
- To: "Discussion list of the IUCr Committee for the Maintenance of the CIF Standard (COMCIFS)" <firstname.lastname@example.org>
- Subject: Re: CIF 2.0 syntax proposal for retaining backwards CIF 1.xcompatibility. .
- From: yayahjb <email@example.com>
- Date: Tue, 17 Sep 2013 18:56:04 -0400
- DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113;h=message-id:date:from:user-agent:mime-version:to:cc:subject:references:in-reply-to:content-type:content-transfer-encoding;bh=9rkbUfDt3SntecwvZDkcsqcLAri3+e/Q9uzUPYJol6Q=;b=otUbg4AW2wHu7plQF4ga0hhxdZSWJEtwdbcOZI7kvlMN4BeM64qjV/qpIjwJ4hyW7plkshUNUhf3irgqG4T1pa6xJdzjeuGMf+HwiMtzBXFpxAuYaJasKGHh98p6//QZwXwY0n43GEye5BbqSTCZe3PrvtLsvvDLNkPOCNU/JLYMCMt0iyqp1vGeelDriL1XQDg5kORwh9V5hVFAvzk6NHw5a/W6UN5/TjR3nlPcpkIKudS8R5/rxV/R1ZxL4wlGCxcQMW9YB4cIpUUjLBN4Qpb/Tyqo1w7dtXRaPkK0LUA241M/TxtLiqVMBzezVF+FYolUGZ2UTBG+rKBW+RH1lA==
- In-Reply-To: <8F77913624F7524AACD2A92EAF3BFA5473F54BD830@11.stjude.org>
- References: <521F284F.firstname.lastname@example.org> <CAM+dB2dy=iTD_RyYJHHSpCqRrvkBBWqyGuu2Ev9hM+fZgyfJuA@mail.gmail.com><8F77913624F7524AACD2A92EAF3BFA5473F54BD830@11.stjude.org>
Dear Coleagues, The real issue here is not what CIF 2 will be. That is settled. The real issue is how CIF 1 will adapt to the new constructs introduced with DDLm and dREL. It is appears that the PDB intends to keep the macromolecular community files in the CIF 1 world, even if the dictionaries move up to DDLm, and we have committed to keeping all the core-cif CIF 1 files not only readable, but validatible against the new DDLm dictionaries. The reality is that, in such a world, people are going to carry things back and forth between CIF 1 and CIF 2. If we don't recommend mappings, we are going to end up with a lot of different ones and a lot of confusion and mismapped data. The missing elements to keep CIF 1 viable in this context seem to be: 1. Handling UTF8 2. Handling bracketed constructs 3. Handling the different quoting and white-space conventions In each case what is needed is a faithful translation from the relevant CIF 2 constructs to valid CIF 1 and a faithful translation from CIF 1 constructs to valid CIF2. With that available, those who wish to use CIF 1 tools with CIF 2 files can work, as can those who wish to use CIF 2 tools against CIF 1 files. 1. Handling UTF8. Most UTF8 files are ASCII files, so almost any of the common encoding mechanism will work -- e.g. the HTML approach or the Python approach -- for carrying UTF8 characters in CIF1 files. The other direction is a non-problem. 2. Handling bracketed constructs. Almost any quoting scheme will allow a bracketed construct to be carried as an opaque value in a CIF 1 file. I propose that we carry CIF 2 bracketed constructs in CIF 1 files as semicolon delimited quoted text, beginning either with \n;$\n (newline, semicolonm dollar, newline) for non-line-folded versions or with \n;\\$\n (newline, semicolon, backslash, dollar, newline) for line-folded versions 3. Handling the different quoting and white-space conventions. This will require aggressive use of both the CIF 1 and CIF 2 quoting mechanisms, but should be doable. Regards, Herbert On 9/17/13 1:21 PM, Bollinger, John C wrote: > On Sunday, September 15, 2013 9:59 PM, James Hester wrote: > >> Reply to Saulius's suggestions of altered syntax. >> =================================== >> > [...] > >> incompatibility with CIF1 is not, in itself, news and is not >> sufficient to justify changes to a syntax that has been sweated over >> for many years. >> > [...] > >> It is to avoid such contortions that we agreed to allow >> incompatibility between CIF1 and CIF2. >> >> We need to avoid any further major syntax changes in CIF2. Closing >> the book on syntax changes results in a precise understanding of >> the differences between CIF1 and CIF2, so we can meaningfully explore >> managing CIF1-CIF2 transitions in alternative ways, e.g. through >> documentation and policy. >> > > The fundamental question Saulius raises is whether a new, backwards-incompatible version of CIF is relevant or desirable. Are the costs of dropping backwards compatibility too high for the benefits we hope to gain? From a higher perspective, those costs may include some or all of the following: > > - Loss of developer good will > - Lack of community acceptance > - Technical issues at various levels arising from confusing one format with the other > - User confusion > > As James observed, COMCIFS and the DDLm-WG's position has been that those potential costs and any others are indeed worth the benefits, so the threshold issue here is whether Saulius has given us sufficient reason to revisit *that* judgment. I take James's and Herbert's responses to Saulius's proposal as "no" answers to that question. Myself, I am undecided, though any way around I am not eager to reopen the syntax for changes. > > Supposing that we proceed with backward-incompatible CIF 2, as appears to be the momentum, perhaps we should consider ways to reduce the above costs / risks. One of the main approaches that occur to me is to take all reasonable steps to position CIF 2 as an improved *alternative* to CIF 1 (as James describes it to be), as opposed to an advancement of it. This would be mostly a promotion and labeling effort. Steps along that path might include > - relabeling the "Changes" document and the language therein to replace "changes" with "differences", > - making sure to promote CIF 2 as an alternative rather than an evolutionary development when we talk about it with colleagues and in publications, > - emphasizing that CIF1 and CIF2 are expected to coexist for an indeterminate time, and > - promoting a different filename convention for CIF 2 files, such as extension ".cif2" instead of plain ".cif". > > Does it make sense to do something like that? > > > John > > -- > John C. Bollinger, Ph.D. > Computing and X-Ray Scientist > Department of Structural Biology > St. Jude Children's Research Hospital > > > Email Disclaimer: www.stjude.org/emaildisclaimer > Consultation Disclaimer: www.stjude.org/consultationdisclaimer > _______________________________________________ > comcifs mailing list > email@example.com > http://mailman.iucr.org/mailman/listinfo/comcifs > _______________________________________________ comcifs mailing list firstname.lastname@example.org http://mailman.iucr.org/mailman/listinfo/comcifs
Reply to: [list | sender only]
- CIF 2.0 syntax proposal for retaining backwards CIF 1.x compatibility (=?windows-1252?Q?Saulius_Gra=9Eulis?=)
- Re: CIF 2.0 syntax proposal for retaining backwards CIF 1.xcompatibility (James Hester)
- RE: CIF 2.0 syntax proposal for retaining backwards CIF 1.xcompatibility. . (Bollinger, John C)
- Prev by Date: RE: CIF 2.0 syntax proposal for retaining backwards CIF 1.xcompatibility. .
- Next by Date: Re: CIF 2.0 syntax proposal for retaining backwards CIF 1.xcompatibility. .
- Prev by thread: RE: CIF 2.0 syntax proposal for retaining backwards CIF 1.xcompatibility. .
- Next by thread: Re: CIF 2.0 syntax proposal for retaining backwards CIF 1.xcompatibility. .