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(54) Observer; CIF Core 2.0; CIF Core 2.1
- To: COMCIFS@iucr.ac.uk
- Subject: (54) Observer; CIF Core 2.0; CIF Core 2.1
- From: bm
- Date: Wed, 27 Nov 1996 14:17:38 GMT
Dear Colleagues I welcome Professor Andre Authier as the Observer from the Commission on Crystallographic Nomenclature to our discussion list. A54.1 CIF Core version 2.0 -------------------------- I have frozen the working draft of 27 November 1996 as the release version of the CIF Core Dictionary version 2.0. It is available by anonymous ftp at the URL ftp://ftp.iucr.ac.uk/pub/cif_core_2.0.dic A PostScript version of the formatted dictionary will be available from the CIF home page, and will be mailed to you in the near future. The last changes made in fine-tuning the dictionary before release are summarised below. Thank you all for your valuable input into this version of the dictionary. If at times the discussions have seemed unduly protracted, I apologise; but it has seemed important to have the core dictionary which underpins all the extension dictionaries well supported by this Committee as a whole. ---------------------------------------------------------------------------- 1996-11-14 BMcM: Imposed consistency on the nomenclature of diffraction device data names: _diffrn_detector_device_type -> *_detector_type, _diffrn_measurement_device_details -> *_measurement_details, *_measurement_device_type -> *_measurement_type; introduction of _diffrn_source_device and parallel definitions. Existing *_measurement_details example moved to *_special_details (PMDF) 1996-11-21 BMcM: Reintroduced _diffrn_measurement_device_details, further tidying of data names thus: _diffrn_measurement_type -> *_device_type; _diffrn_detector_device and _diffrn_source_device both drop "_device" (PMDF) Added _journal_data_validation_number and _publ_requested_category to enable handling of CIF-access submissions by Acta Cryst. C 1996-11-23 A few typos fixed. BMcM 1996-11-24 BMcM: Added 'gaussian', 'multi-scan' and 'numerical' to enumeration list for _exptl_absorpt_correction_type (SRH) Added 'mixed' to enumeration list for _refine_ls_hydrogen_treatment (SRH) 1996-11-25 A few typos fixed (BMcM) 1996-11-27 BMcM: Removed looped _related_item from _publ_contact_author and reintroduced _diffrn_radiation_detector, *_dtime and _diffrn_radiation_source (see 1996-11-08) with "_related_function replace" as a preparation for using this mechanism further in version 2.1. 1996-11-27 Release version 2.0. IUCr ---------------------------------------------------------------------------- =========================================== D54.1 Proposal for handling future versions ------------------------------------------- It is apparent that the timescale for future updates is likely to be less than 5 years (see below). I am therefore suggesting a modification to our approach for the administration of the dictionaries. As new proposals for additional data names are approved, they shall be entered into a draft version of the dictionary mounted as a public "beta" distribution. Such beta versions will be open to community review (along the lines of the successful mmCIF process). I intend also to open a discussion list (by email server, WWW bulletin board or some combination) for CIF software developers, which will permit advance notice and discussion of changes with software authors. The CIF Home Page will contain links to both the most recent supported dictionary (2.0, as of now), and the most recent beta release. Beta versions will be considered as relatively stable, but with the possibility of changes arising from demonstrable error. It is likely that a number of beta modifications will accumulate before another "full release" is announced. For example, I have some proposals from Syd arising from the evolving needs of Acta C. They include (a) replacement of some data names by new ones better expressing current nomenclature and practice, (b) additional data names to resolve the remaining problems with calculated wR and S, and (c) a description of area detector experiments. If these were to attract increasing amounts of debate, one might envisage versions 2.1beta1, 2.1beta2 and 2.1beta3 incorporating progressively (a), (b) and (c), before the final release of version 2.1. To give you an idea of how this will work, I am going to introduce these points in the next sections. My hope is that they will attract no controversy, and the requested changes can be put in place by 12 December, so that Syd's Notes for Authors which goes to press then can refer to the new data names as listed in version 2.1beta1 of the core. (Note that not every minor change need lead immediately to a new beta release.) D54.2 Replacement data names ---------------------------- Under pressure from the Commission on Journals to eradicate the term 'observed' to describe measurements that fall outside some specified threshold, Syd proposes a number of changes in data name. The way this must work in practice, to maintain compatibility with older files, is to add to the existing definition a set of attributes _related_item '_whatever' _related_function replace that point to the new definition (to see how this works, look at the entry for _diffrn_radiation_source in the new version 2.0 file). The names listed in Notes for Authors (new and old names) are _reflns_number_gt Number of reflections > sigma threshold (new) _reflns_number_observed Number of "observed" reflections _reflns_threshold_sigma_expression Sigma expression for F, F2 or I threshold (new) _reflns_observed_criterion Sigma expression for "observed" F, F2 or I _refine_ls_R_factor_gt R factor of F for reflections > threshold (new) _refine_ls_R_factor_obs R factor of F for "observed" reflections For completeness, the following data names referring to 'obs' should also be replaced: _refln_observed_status _refine_ls_goodness_of_fit_obs _refine_ls_restrained_S_obs _refine_ls_wR_factor_obs _reflns_shell_meanI_over_sigI_obs _reflns_shell_number_measured_obs _reflns_shell_number_unique_obs _reflns_shell_percent_possible_obs _reflns_shell_Rmerge_F_obs _reflns_shell_Rmerge_I_obs There is also pressure from the Nomenclature Commission to drop the use of the term e.s.d. and replace it by standard uncertainty (this has already been implemented in the descriptions within the Dictionary). Hence Syd proposes: _refine_ls_shift/su_max Maximum shift/su ratio after final refinement cycle (new) _refine_ls_shift/esd_max Maximum shift/esd ratio after final refinement cycle For completeness, the following data names referring to 'esd' should also be replaced: _refine_ls_shift/esd_mean Lastly, Syd proposes the following new data name to incorporate the Nomenclature Commission's preference for the phrase "atomic displacement parameter" rather than "thermal motion" or "thermal displacement": _atom_site_adp_type Atom displacement parameter type (new) _atom_site_thermal_displace_type Atom displacement type D54.3 wR and S for refined reflections -------------------------------------- After strong representation from authors of refinement packages, Syd has proposed in his draft NfA the following additional data names, referring to the wR and S values calculated from all the reflections used in the refinement (i.e. _refine_ls_number_reflns), rather than those calculated from "all reflections". _refine_ls_wR_factor_ref R factor of Coeff for refined reflections (new) _refine_ls_goodness_of_fit_ref Goodness of fit S for refined reflections (new) D54.4 Area-detector definitions ------------------------------- A number of participants (including Syd, David and Bill Clegg) are working on definitions for area detector work (with some input from Andy Hammersley, I believe). A complete set of definitions is not imminent, but Syd wishes to include the following items for the purposes of assessing the quality of an area-detector result set reported in Acta C: _diffrn_detector_area_resol_mean Resolution of area detector, in pixels/mm (new) _diffrn_measured_fraction_theta_max Fraction of unique refl'ns measured to q max (new) _diffrn_measured_fraction_theta_full Fraction of unique refl'ns measured to q full (new) _diffrn_reflns_theta_full \q to which available reflections are "complete" (new) Noting Syd's wish to have a reliable set of Notes for Authors (and therefore a reasonably stable documentation of these new data names in the form of a beta dictionary), I would like to hear any objections to these proposals in the near future. Regards Brian
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