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Re: [Imgcif-l] CBF file templates
- To: The Crystallographic Binary File and its imgCIF application to image data <imgcif-l@iucr.org>
- Subject: Re: [Imgcif-l] CBF file templates
- From: harry powell <harry@mrc-lmb.cam.ac.uk>
- Date: Wed, 30 Sep 2009 11:13:05 +0100
- In-Reply-To: <4854F2500EA8C4478A508D2D92973E52047BE33F@EXCHANGE25.fed.cclrc.ac.uk>
- References: <4854F2500EA8C4478A508D2D92973E52047BE339@EXCHANGE25.fed.cclrc.ac.uk><20090929061322.N74653@epsilon.pair.com><4854F2500EA8C4478A508D2D92973E52047BE33D@EXCHANGE25.fed.cclrc.ac.uk><765CB1E0-804D-4874-A6BD-552CE9EDD0B0@mrc-lmb.cam.ac.uk><4854F2500EA8C4478A508D2D92973E5205F2CA8C@EXCHANGE25.fed.cclrc.ac.uk><3278C1D8-203F-420E-8762-E626361F93EB@mrc-lmb.cam.ac.uk><4854F2500EA8C4478A508D2D92973E52047BE33F@EXCHANGE25.fed.cclrc.ac.uk>
Hi Yes, this would be in the template (a ? i a field in a finished CIF says something unspecfied about the user or the experiment); for example, have a look at the CIFs that SHELX generates - quite a few ? in things that should be edited by the submitter... On 30 Sep 2009, at 10:50, Winter, Graeme (DLSLtd,RAL,DIA) wrote: > Indeed. > > The *isolated* in here is key: if the user has named their > experiment ? > I expect that this says more about them than the sample under > study :o) > > More seriously though, I guess that any title would have some > furniture > like quotes ("?" not ?) around it. > > Finally, this is not in the final CIF file, this is in the template, > which may or may not be a CIF file. > > No worries. > > Graeme > > > > -----Original Message----- > From: imgcif-l-bounces@iucr.org [mailto:imgcif-l-bounces@iucr.org] On > Behalf Of harry powell > Sent: 30 September 2009 10:47 > To: The Crystallographic Binary File and its imgCIF application to > image > data > Subject: Re: [Imgcif-l] CBF file templates > > Hi > > single, isolated "?" is the CIF standard - don't start re-inventing > the > wheel! > > See - http://www.iucr.org/__data/iucr/cif/standard/cifstd11.html - >> "Note that the missing items in this example are flagged with a `?'. >> Programs such as CIFIO can only output the data items present in >> their > >> internal files and the `?' flag represents a simple mechanism for >> identifying missing items. >> >> The use of a `?' as a missing data flag is important for two >> reasons: it signals the inaccessibility of a data item to the >> generating software, and it satisfies the STAR File requirement that >> each data name must be matched with a data value. The use of a `?' >> enables data items from other sources to be added later either >> manually or by software. " >> > > > i.e. if there's only a single "?" there, you know there's something > missing. If there's anything else, you don't know that, and you also > break all the CIF parsers that expect a single "?" to represent > missing > information. > > So "I04?" would not represent a field with a missing item, it would > be a > valid string saying something along the lines that you thought you > were > collecting on I04, but got confused while walking around the ring and > ended up in the wrong hutch (but hopefully, the beamline software > would > put the right value in anyway...). > > You may have a better way, but don't call the result CIF (or CBF). > CIF has its limitations, as we all know. > > On 30 Sep 2009, at 10:16, Ashton, Alun (DLSLtd,RAL,DIA) wrote: > >> >> I don't like a single ? It could be a part of a title for a beamline >> session, would that confuse it? While multiple ? would be unlikely, >> unless they were really unsure what they were doing :). >> >> Alun >> ___________________________________________________________ >> Alun Ashton, alun.ashton@diamond.ac.uk Tel: +44 1235 778404 >> Data Acquisition Group, http://www.diamond.ac.uk/ >> Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K. >> >> >> >>> -----Original Message----- >>> From: imgcif-l-bounces@iucr.org >>> [mailto:imgcif-l-bounces@iucr.org] On Behalf Of harry powell >>> Sent: 30 September 2009 10:09 >>> To: The Crystallographic Binary File and its imgCIF application to >>> image data >>> Subject: Re: [Imgcif-l] CBF file templates >>> >>> Hi >>> >>> a single "?" in an empty field is allowed under CIF rules, as I >>> understand. ISTR it from the days when I deposited CIFs for small >>> molecule structures, and CBF is supposed to be conformant to the >>> normal CIF rules (apart from the binary section, about which people >>> may argue). >>> >>> d*Trek has to be the model of being comprehensive apropos its use of >>> the header. >>> >>> I don't think HKL is an issue, to be honest - I think I'm right in >>> saying that Wladek has said that "CBF is just another image >>> format" - > >>> they will use what they see as useful and/or necessary. >>> >>> On 30 Sep 2009, at 09:45, Winter, Graeme (DLSLtd,RAL,DIA) wrote: >>> >>>> Dear Herbert & list, >>>> >>>> One template per beamline is probably, in reality, the way it would >>>> work. We would just make sure that they are all the same. >>> Adding ???? >>>> For the detector software to fill in sounds like good >>> sense. Is this >>>> kind of thing supported? An alternative is to have some >>> boiler plate >>>> which needs to be copied in, then work on getting the >>> format for the >>>> detector produced bit the same. These are essentially the same >>>> problem. >>>> >>>> What's the consensus on the best approach? Does everyone >>> support the >>>> use of templates? >>>> >>>> At the other end, I assume that the contents of the current >>> ADSC CBF >>>> header represent the minimum which should be in place for e.g. >>>> Mosflm to >>>> make sense of the image, and anything we add will be ignored. XDS >>>> ignores the header anyway. D*TREK, HKL - any comments? >>>> >>>> Thanks, >>>> >>>> Graeme >>>> >>>> -----Original Message----- >>>> From: imgcif-l-bounces@iucr.org >>> [mailto:imgcif-l-bounces@iucr.org] On >>>> Behalf Of Herbert J. Bernstein >>>> Sent: 29 September 2009 11:34 >>>> To: The Crystallographic Binary File and its imgCIF application to >>>> image data >>>> Subject: Re: [Imgcif-l] CBF file templates >>>> >>>> Dear Colleagues, >>>> >>>> Right now the utilities in the library use templates that are >>>> intended to be for just one beamline per template, so they >>> are set up >>>> with tags with zero values for the items that they know will be >>>> populated from the detector and known specific values for >>> the beamline >>>> for items that come from the beamline geometry. If we are going to >>>> have master templates, there would seem to be more cases: >>>> >>>> 1. Items that will be supplied by every detector. >>>> 2. Items that will be supplied by some detectors but not >>>> others >>>> 3. Items that will be supplied by every beamline >>>> 4. Items that will be supplied by some beamlines but not >>>> others >>>> >>>> I would suggest using "?", rather than "0" values for all >>> items that >>>> are know known for sure in writing the master template. Then in >>>> specializing for a given beamline (e.g. in setting up the >>> axes), all >>>> of the "?" for 3, hopefully a lot for 4 could be removed >>> and replaced >>>> with known values. >>>> When the detector data is merged with the beam-line >>> specific tempate, >>>> hopefully all "?" for 1 and a lot for 2 would be replaced with data >>>> from the detector. The "?" that are left would then be >>> clear markers >>>> of what was supplied neither by the beamline nor by the >>> detector. I >>>> am working on the code to allow comments to be preserved and copied >>>> along with data, so we could carry remarks such as: >>>> >>>> # This item should be supplied by every beamline >>>> # This item should be supplied on beamlines ..., ... ... >>>> # This item should be supplied by every detector >>>> # This item should be supplied by detectors ..., ... ... >>>> >>>> or is people, prefer, we can add CIF tags with the same info >>>> >>>> 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 Tue, 29 Sep 2009, Winter, Graeme (DLSLtd,RAL,DIA) wrote: >>>> >>>>> Dear CBF'ers, >>>>> >>>>> I'm working on trying to establish a "Diamond standard" >>> template for >>>>> our CBF files across a number of detectors, and I was >>> wondering how >>>>> this is best specified. What would be ideal would be to set up a >>>>> template which contains those things that the beamline "knows" but >>>>> the >>>> >>>>> detector does not, then have the detector software >>> populate the other >>>> fields (e.g. >>>>> exposure time, integration time, maximum trusted pixel, >>> oscillation >>>>> start / end) to give a full description. >>>>> >>>>> Now, has anyone done something like this? If so, how do >>> you specify >>>>> the fields which are to be replaced? If not, does anyone have an >>>>> opinion on how this should be done? >>>>> >>>>> Thanks, >>>>> >>>>> Graeme >>>>> >>>>> Graeme Winter >>>>> Software and MX Support Scientist >>>>> Diamond Light Source >>>>> >>>>> +44 1235 778091 (work) >>>>> +44 7786 662784 (work mobile) >>>>> >>>>> >>>>> >>>>> This e-mail and any attachments may contain confidential, >>> copyright >>>>> and or privileged material, and are for the use of the intended >>>>> addressee only. If you are not the intended addressee or an >>>>> authorised >>>> >>>>> recipient of the addressee please notify us of receipt by >>> returning >>>>> the e-mail and do not use, copy, retain, distribute or >>> disclose the >>>>> information in or attached to the e-mail. >>>>> >>>>> Any opinions expressed within this e-mail are those of the >>> individual >>>>> and not necessarily of Diamond Light Source Ltd. >>>>> >>>>> Diamond Light Source Ltd. cannot guarantee that this e-mail or any >>>>> attachments are free from viruses and we cannot accept >>> liability for >>>>> any damage which you may sustain as a result of software viruses >>>>> which >>>> >>>>> may be transmitted in or with the message. >>>>> >>>>> Diamond Light Source Limited (company no. 4375679). Registered in >>>>> England and Wales with its registered office at Diamond House, >>>>> Harwell >>>> >>>>> Science and Innovation Campus, Didcot, Oxfordshire, OX11 >>> 0DE, United >>>>> Kingdom >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> imgcif-l mailing list >>>>> imgcif-l@iucr.org >>>>> http://scripts.iucr.org/mailman/listinfo/imgcif-l >>>>> >>>> _______________________________________________ >>>> imgcif-l mailing list >>>> imgcif-l@iucr.org >>>> http://scripts.iucr.org/mailman/listinfo/imgcif-l >>>> This e-mail and any attachments may contain confidential, copyright >>>> and or privileged material, and are for the use of the intended >>>> addressee only. If you are not the intended addressee or an >>> authorised >>>> recipient of the addressee please notify us of receipt by returning >>>> the e-mail and do not use, copy, retain, distribute or disclose the >>>> information in or attached to the e-mail. >>>> Any opinions expressed within this e-mail are those of the >>> individual >>>> and not necessarily of Diamond Light Source Ltd. >>>> Diamond Light Source Ltd. cannot guarantee that this e-mail or any >>>> attachments are free from viruses and we cannot accept >>> liability for >>>> any damage which you may sustain as a result of software >>> viruses which >>>> may be transmitted in or with the message. >>>> Diamond Light Source Limited (company no. 4375679). Registered in >>>> England and Wales with its registered office at Diamond >>> House, Harwell >>>> Science and Innovation Campus, Didcot, Oxfordshire, OX11 >>> 0DE, United >>>> Kingdom >>>> >>>> _______________________________________________ >>>> imgcif-l mailing list >>>> imgcif-l@iucr.org >>>> http://scripts.iucr.org/mailman/listinfo/imgcif-l >>> >>> Harry >>> -- >>> Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, >>> Hills Road, Cambridge, CB2 0QH >>> >>> >>> >>> >>> _______________________________________________ >>> imgcif-l mailing list >>> imgcif-l@iucr.org >>> http://scripts.iucr.org/mailman/listinfo/imgcif-l >>> >> This e-mail and any attachments may contain confidential, copyright >> and or privileged material, and are for the use of the intended >> addressee only. If you are not the intended addressee or an >> authorised > >> recipient of the addressee please notify us of receipt by returning >> the e-mail and do not use, copy, retain, distribute or disclose the >> information in or attached to the e-mail. >> Any opinions expressed within this e-mail are those of the individual >> and not necessarily of Diamond Light Source Ltd. >> Diamond Light Source Ltd. cannot guarantee that this e-mail or any >> attachments are free from viruses and we cannot accept liability for >> any damage which you may sustain as a result of software viruses >> which > >> may be transmitted in or with the message. >> Diamond Light Source Limited (company no. 4375679). Registered in >> England and Wales with its registered office at Diamond House, >> Harwell > >> Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United >> Kingdom >> >> _______________________________________________ >> imgcif-l mailing list >> imgcif-l@iucr.org >> http://scripts.iucr.org/mailman/listinfo/imgcif-l > > Harry > -- > Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, > Hills > Road, Cambridge, CB2 0QH > > > > > _______________________________________________ > imgcif-l mailing list > imgcif-l@iucr.org > http://scripts.iucr.org/mailman/listinfo/imgcif-l > This e-mail and any attachments may contain confidential, copyright > and or privileged material, and are for the use of the intended > addressee only. If you are not the intended addressee or an > authorised recipient of the addressee please notify us of receipt > by returning the e-mail and do not use, copy, retain, distribute or > disclose the information in or attached to the e-mail. > Any opinions expressed within this e-mail are those of the > individual and not necessarily of Diamond Light Source Ltd. > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from viruses and we cannot accept liability > for any damage which you may sustain as a result of software > viruses which may be transmitted in or with the message. > Diamond Light Source Limited (company no. 4375679). Registered in > England and Wales with its registered office at Diamond House, > Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 > 0DE, United Kingdom > > _______________________________________________ > imgcif-l mailing list > imgcif-l@iucr.org > http://scripts.iucr.org/mailman/listinfo/imgcif-l Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH _______________________________________________ imgcif-l mailing list imgcif-l@iucr.org http://scripts.iucr.org/mailman/listinfo/imgcif-l
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