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Re: [Fwd: Re: New fast-track definition proposal:_diffrn_radiation_wavelength_nominal]
- To: Distribution list of the IUCr COMCIFS Core Dictionary Maintenance Group <coredmg@iucr.org>
- Subject: Re: [Fwd: Re: New fast-track definition proposal:_diffrn_radiation_wavelength_nominal]
- From: "Herbert J. Bernstein" <yaya@bernstein-plus-sons.com>
- Date: Wed, 25 Nov 2009 16:44:13 -0500 (EST)
- In-Reply-To: <4B0D90EC.1090102@mcmaster.ca>
- References: <4B0D90EC.1090102@mcmaster.ca>
Dear Colleagues, While you are revisiting this item, I would suggest you consider the more complete (and, I believe, more elegant and general) solution of defining "variants", that we have introduced into the imgCIF dictionary to handled quantities that may be determined in different ways. Instead of adding _diffrn_radiation_wavelength_determination you would add _diffrn_radiation_wavelength_variant and a new variant category _variant_variant _variant_role _variant_timestamp _variant_variant_of _variant_details which would allow you with complete generality to manage any number a refined or redefined quantities, such as wavelengths. This would then allow you to us the same variant identifier, for, say cell dimensions, which could be expected to change in a coupled manner with the changes in wavelength. If you are interested in this more complete approach, I can provide you with the full item definitions, but the short form is: _variant_variant The value of _variant_variant must uniquely identify each variant for the given diffraction experiment and/or entry _variant_role The value of _variant_role specifies a role for this variant. Possible roles are null, "preferred", "raw data", and "unsuccessful trial". _variant_timestamp The date and time identifying a variant. This is not necessarily the precise time of the measurement or calculation of the individual related data items, but a timestamp that reflects the order in which the variants were defined. _variant_variant_of The value of _variant.variant_of gives the variant from which this variant was derived. If this value is not given, the variant is assumed to be derived from the default null variant. _variant_details A description of special aspects of the variant > An example of how this might be used is: > > loop_ > _diffrn_radiation_wavelength_id > _diffrn_radiation_wavelength > _diffrn_radiation_wavelength_determinaton > 1 1.23456 fundamental > 2 1.25 estimated would become loop_ _diffrn_radiation_wavelength_variant _diffrn_radiation_wavelength final 1.23456 pelim 1.25 loop_ _variant_variant _variant_role _variant_timestamp _variant_variant_of _variant_details final preferred 2007-08-04T01:17:28 prelim refined prelim . 2007-08-03T23:20:00 . . loop_ _cell_variant _cell_length_a _cell_length_b _cell_length_c _cell_angle_alpha _cell_angle_beta _cell_angle_gamma final 22.5 22.5 22.5 90. 90. 90. prelim 22.3 22.3 22.3 90. 90. 90. Regards, Herbert ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Wed, 25 Nov 2009, David Brown wrote: > Dear Colleagues, > > Last September I circulated for fast track approvel a recommendation for adding a > new item: > > _diffrn_radiation_wavelength_nominal, > > to the core dictionary (see below for details). The intent was that this could be > used for giving a nominal wavelength calculated e.g., from the paparmeters of a > diffractometer. It was proposed tht this might be needed for completeness even > though it was not accurate enough for calculating lattice parameters, etc. This > proposal was passed by the core CIR dictionary maintenance group by default (no > one raised any objection). When this proposal was subsequently presented for > final approval to COMCIFS, Nick Spadaccini suggested a more elegant alternative, > namely that by adding instead the item > > _diffrn_radiation_wavelength_determination > > we could loop the nomiinal wavelength with the refined (and any other > interesting) wavelengths. This would be more informative and allow for future > expansion. > > An example of how this might be used is: > > loop_ > _diffrn_radiation_wavelength_id > _diffrn_radiation_wavelength > _diffrn_radiation_wavelength_determinaton > 1 1.23456 fundamental > 2 1.25 estimated > > According to our rules, this proposal is being posted for comment to the coreCIF > dictionary maintenance group for the next six weeks. At the end of this time, if > there are no unresolved issues, the core dictionary maintenance group will be > deemed to have accepted the proposal. > > David Brown > > ============================================================== > > The proposal is to add the following item to the coreCIF dictionary: > ============================================= > > 2009-09-25 Proposal from the Nick Spadaccini on the COMCIFS dicsussion list to > replace a withdrawn proposal. > > 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 using a standard material with known cell parameters' > > _definition > ; The method of determination of incident wavelength. Further > information may be provided in _diffrn_radiation_special_details > ; > > > The original proposal was as follows: > ========================= > >> > >> 2009-08-23 proposed by James Hester. > >> 2009-10-16 approved by the core Dictionary Maintenance Group under a fast > >> track approval process. > > > 2009-11-25 proposal withdrawn in favour of an alternative > >> > >> 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. > >> ; > > > > > >
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