# 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
> 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
>
> New definition
> ===========
>
>   _type                        char
>   _list                        both
>  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
> >
> >
> > and
> >
> >
> > The latter being free text or preferably an enumerated type that
> indicates
> > the various possibilities. And one could re-use
> >
> >
> > 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
> > 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
> >>
> >>     _type                        numb
> >>     _list                        both
> >>      _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
> >>
> >>
> >>     _type                        numb
> >>     _list                        both
> >>     _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>
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> >
> > CRICOS Provider Code: 00126G
> >
> >
> >
> >
> >
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>
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