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Re: [Imgcif-l] proposed change in first line of imgcif files
- To: imgcif-l@iucr.org
- Subject: Re: [Imgcif-l] proposed change in first line of imgcif files
- From: "James Hester" <jamesrhester@gmail.com>
- Date: Thu, 18 Sep 2008 14:41:23 +1000
- In-Reply-To: <20080826195337.H76753@epsilon.pair.com>
- References: <20080826195337.H76753@epsilon.pair.com>
Dear imgCIFers, My apologies for missing the conclusion of the informal meeting in Osaka - I was sidetracked by other CIF discussions in the hallways. My only potential concern with the special header proposal would have been that information not available in the CIF proper was going to appear in the header comment or the repository website. However, I think Herbert makes clear that the purpose of this header is simply to make available in a more digestible form information that is derivable from the CIF proper, and so I for one don't have a problem with it. We do need to address the issue of why this alternative presentation of missing tag information is needed. Correct me if I'm wrong, but I believe it is because imgCIF files can be enormous and the overhead of reading through the entire file to determine missing tags is prohibitive. Would it be possible to fix this with a DDL attribute that dictionary writers could use to indicate that a data item should appear at the 'beginning' of a data block? This attribute would work as follows: it could take values 'beginning', 'middle' and 'end', with 'middle' being the default. An imgCIF dictionary would specify certain data values as occuring at the 'beginning' (ie in the header) and input programs such as MOSFLM would then need only to read until they found a data value that was not specified as belonging to the 'beginning' (or alternatively, until they found a data value belonging to the 'end'.) This attribute would actually be used quite rarely in the CIF world as I don't think there is a general need for this sort of control of order within a datablock. Note that using multiple dictionaries (eg mmCIF and imgCIF) would not introduce ambiguity about positioning, as the order within the beginning/middle/end zones would still be arbitrary. I'd be interested to hear whether or not such a scheme would remove the need for a special header comment (I'm looking particularly at Harry and Herbert here), and if the response is positive, I will take it to COMCIFS for discussion. James. On Wed, Aug 27, 2008 at 10:35 AM, Herbert J. Bernstein <yaya@bernstein-plus-sons.com> wrote: > > There was an informal meeting to discuss imgCIF at the IUCr > Congress in Osaka on 26 August 2008. Details of the > discussion will follow in future nessages. This message > will summarize a proposal for a change in the first line > of all CBF/imgCIF files that are not fully populated > with all the imgCIF tags needed for processing by mosflm > and adxv. > > 1. What problem is being solve?. As the use of imgCIF > has increased, two very distinct sets of files have appeared: > the "miniCBFs" used for the Pilatus 6m detector and > more fully populated imgCIF files, such as the ones > produced for ADSC detectors. While the information > necessary for processing can be discovered from context > in handling a miniCBF, it may be necessary to read fairly > far into the file to discover that the file is indeed a > miniCBF, complicating the design of reading software. > > 2. The proposed solution. Currently CBF files begin > with a magic number comment line > 1 2 3 4 5 > 12345678901234567890123456789012345678901234567890 > ###CBF: VERSION n.m > > We propose to extend the magic number comment line with > two optional fields to read > > 1 2 3 4 5 > 12345678901234567890123456789012345678901234567890 > ###CBF: VERSION n.m style style_version > > where "style" is a unique CBF style identifier left > justified as a single word in columns 25-34 and > "style_version" is a left justified integer in > columns 35-44. > > Each style will be registered in a central repository > along with information on the tags that will be > carried forthat stye and a template of the tags > that would be needed to fully populate the file. > > More details will follow on this list and on the > CBFlib wiki after the Osaka meeting is over. > ===================================================== > 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 > ===================================================== > _______________________________________________ > imgcif-l mailing list > imgcif-l@iucr.org > http://scripts.iucr.org/mailman/listinfo/imgcif-l -- T +61 (02) 9717 9907 F +61 (02) 9717 3145 M +61 (04) 0249 4148 _______________________________________________ imgcif-l mailing list imgcif-l@iucr.org http://scripts.iucr.org/mailman/listinfo/imgcif-l
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