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Re: New fast-track definition proposal:_diffrn_radiation_wavelength_nominal

I think this enumerated data item gets us to where we want to be.  We  
want to document the wavelength(s) used in the experiment, as well as  
how it was determined.  Knowing both, one could change/correct the  
wavelength later if desired for some particular purpose.

Jim Kaduk

Quoting James Hester <jamesrhester@gmail.com>:

> 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@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
>>
>> 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
>> MBDP  M002
>>
>> CRICOS Provider Code: 00126G
>>
>> e: Nick.Spadaccini@uwa.edu.au
>>
>>
>>
>>
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>
>
>
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