New fast-track definition proposal: _diffrn_radiation_wavelength_nominal
James Hester
jamesrhester at gmail.com
Wed Nov 25 05:10:53 GMT 2009
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>
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> 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
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> CRAWLEY, Perth, WA 6009 AUSTRALIA w3: www.csse.uwa.edu.au/~nick
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>
> e: Nick.Spadaccini at uwa.edu.au
>
>
>
>
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