New fast-track definition proposal: _diffrn_radiation_wavelength_nominal
David Brown
idbrown at mcmaster.ca
Wed Nov 25 19:35:42 GMT 2009
Dear James,
Thanks for your email copied below. I think it is my responsibility as
chair of the core dictionary maintenance group to circulate this to my
group, so you need not be concerned about it. I agree that Nick's
proposal is a much more elegant one than the original, and I will put it
out to my group for their comment. Six weeks will take us into the New
Year, but since the the COMCIFS list has already had a chance to
comment, I assume that if the core DMG had no objections we could adopt
the new item into the dictionary.
Best wishes
David
James Hester wrote:
> I think Nick makes a fair point here: the same result could be
> achieved by instead defining an additional enumerated dataitem. I
> have fleshed out an example below. If this is acceptable to the rest
> of the committee, I will forward it back to the core CIF DWG for their
> consideration as an alternative to the original proposal.
>
> I think an enumerated dataitem is appropriate, as that will be
> machine-readable.
>
> New definition
> ===========
>
> data_diffrn_radiation_wavelength_determination
> _name '_diffrn_radiation_wavelength_determination'
> _category diffrn_radiation_wavelength
> _type char
> _list both
> _list_reference '_diffrn_radiation_wavelength_id'
> loop_
> _enumeration
> _enumeration_detail
> 'fundamental' 'Wavelength that is a fundamental property
> of matter e.g. MoK\alpha'
> 'estimated' 'Estimated from secondary information
> e.g. monochromator angle or time of flight'
> 'refined' 'Based on refinement of a standard material'
>
> _definition
> ; The method of determination of incident wavelength.
> Further information may be provided in _diffrn_radiation_special_details
> ;
>
> On Mon, Nov 9, 2009 at 8:22 PM, Nick Spadaccini <nick at csse.uwa.edu.au
> <mailto:nick at csse.uwa.edu.au>> wrote:
> > Here is the problem I have with this approach. It seems to me that
> you are
> > suggesting there are two wavelength values, both of which are
> relevant to
> > the data set and both of which have to be recorded.
> >
> > But what I think you have written is that there is only one
> wavelength, but
> > you are trying to record something about its properties. I can
> appreciate
> > the need for a data item that indicates something about the
> properties, but
> > don't appreciate the need for a new wavelength data item.
> >
> > Perhaps something like
> >
> > _diffrn_radiation_wavelength
> >
> > and
> >
> > _diffrn_radiation_wavelength_determination
> >
> > The latter being free text or preferably an enumerated type that
> indicates
> > the various possibilities. And one could re-use
> >
> > _diffrn_radiation_special_details
> >
> > to provide all additional information.
> >
> > I would be very wary of VARIANTS as discussed by Herb in a follow up
> > discussion. Adding variations to existing definitions is going to be
> a great
> > source of error from users. At its basis is a desire to employ CIF
> in a way
> > it was not originally intended to be used. CIF is essentially an
> archival
> > format, for the submission of the final model/data/results etc. Herb is
> > suggesting its use as a lab manual to record every assumption, through
> > process, error etc during the experiment and refinement. Vary
> admirable, but
> > not what CIF is about, and probably such a CIF would not be of great use
> > outside of the home lab.
> >
> > The new DDLm etc supports many powerful features for one to make local
> > changes to dictionaries, and while I have no problem with Herb's
> approach to
> > meet local needs (apart from the fact I would do it differently), I
> would be
> > concerned if it was part of the official archive. The import feature
> of DDLm
> > allows one to make changes at many levels of refinement to the
> dictionary -
> > preferably for local use. The official IUCr submission dictionary (for
> > archive purposes) will have different requirements.
> >
> >
> > On 3/11/09 10:52 AM, "James Hester" <jamesrhester at gmail.com
> <mailto:jamesrhester at gmail.com>> wrote:
> >
> >> Dear COMCIFS members: the following fast track proposal for a minor
> >> change to the coreCIF dictionary has been approved by the core
> >> Dictionary Maintenance Group after a 6-week comment period. As per
> >> the recently approved fast track process, it is now open for comments
> >> from COMCIFS for a further 6 week period.
> >>
> >> James.
> >>
> ------------------------------------------------------------------------------
> >> ----------------
> >>
> >> 2009-08-23 proposed by James Hester.
> >> 2009-10-16 approved by the core Dictionary Maintenance Group under
> a fast
> >> track approval process.
> >>
> >> Explanation
> >> ===========
> >> The wavelength used for a measurement defines the
> >> length scales used in the crystallographic unit cell, so it is
> >> important that the quality of the number used for wavelength is
> >> understood. When the bulk of experiments came from lab X-ray sources,
> >> the wavelength value was an accurate and precise quantity that could
> >> be relied on. In contrast, synchrotron and neutron sources have
> >> comparatively poorly-defined wavelengths, subject to systematic errors
> >> (for example, changes in the monochromator d-spacing due to
> >> temperature effects, and angular offset errors). Many facilities do
> >> not attempt to characterise the accuracy of such derived wavelength
> >> values. Instead users may (or may not) refine against a standard
> >> compound in order to recover an accurate wavelength value. I therefore
> >> propose a separate tag for those wavelength values that are nominal,
> >> that is, derived from positioning of optical elements rather than
> >> proper standards. This removes ambiguity in determining whether or
> >> not a wavelength has been obtained from refinement against a standard,
> >> or is simply a nominal value based on beamline optics.
> >>
> >>
> >> A new DDL1 item
> >>
> >> data_diffrn_radiation_wavelength_nominal
> >> _name '_diffrn_radiation_wavelength_nominal'
> >> _category diffrn_radiation_wavelength
> >> _type numb
> >> _list both
> >> _list_reference '_diffrn_radiation_wavelength_id'
> >> _enumeration_range 0.0:
> >> _units A
> >> _units_detail 'angstroms'
> >> _definition
> >> ; The incident radiation wavelength in Angstroms
> >> calculated from secondary information,
> >> for example monochromator angle or time of flight.
> >> If the wavelength has been determined
> >> using some type of standard,
> >> _diffrn_radiation_wavelength should be used
> >> ;
> >>
> >> A change in definition of an existing item. The current
> >> definition reads 'The radiation wavelength in angstroms'.
> >>
> >>
> >> data_diffrn_radiation_wavelength
> >> _name '_diffrn_radiation_wavelength'
> >> _category diffrn_radiation_wavelength
> >> _type numb
> >> _list both
> >> _list_reference '_diffrn_radiation_wavelength_id'
> >> _enumeration_range 0.0:
> >> _units A
> >> _units_detail 'angstroms'
> >> _definition
> >> ; The radiation wavelength in angstroms as
> >> determined from measurements using standards,
> >> for example an X-ray emission line,
> >> or when a refinement based on a standard
> >> material has been carried out.
> >> The details of such a refinement should be
> >> recorded in the _diffrn_radiation_special_details
> >> item.
> >> ;
> >
> > cheers
> >
> > Nick
> >
> > --------------------------------
> > Associate Professor N. Spadaccini, PhD
> > School of Computer Science & Software Engineering
> >
> > The University of Western Australia t: +61 (0)8 6488 3452
> > 35 Stirling Highway f: +61 (0)8 6488 1089
> > CRAWLEY, Perth, WA 6009 AUSTRALIA w3: www.csse.uwa.edu.au/~nick
> <http://www.csse.uwa.edu.au/%7Enick>
> > MBDP M002
> >
> > CRICOS Provider Code: 00126G
> >
> > e: Nick.Spadaccini at uwa.edu.au <mailto:Nick.Spadaccini at uwa.edu.au>
> >
> >
> >
> >
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> >
>
>
>
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