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Re: New fast-track definitionproposal: _diffrn_radiation_wavelength_nominal

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


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

  _name                      '_diffrn_radiation_wavelength_determination'
  _category                    diffrn_radiation_wavelength
  _type                        char
  _list                        both
  _list_reference            '_diffrn_radiation_wavelength_id'
  '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'

;              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@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@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
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