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# Core CIF - revision to accommodate Acta C Notes for Authors

*To*:*COMCIFS@iucr***Subject**:**Core CIF - revision to accommodate Acta C Notes for Authors****From**:**Brian McMahon <bm@iucr.org>***Date*:*Mon Nov 17 11:55:40 1997*

As far back as the beginning of the year, COMCIFS gave implicit approval for the introduction of new data names required by Acta Crystallographica Section C (see circular 54). These were mostly changes of nomenclature to deprecate the use of the terms "thermal displacement", "estimated standard deviation" and "observed". These changes have been worked up into formal definitions which are listed in an appendix to this mailing. There is one additional data name that falls outside of this group, and that is "_reflns_number_Friedel". I would ask you to check through these definitions, and let me know of any errors, ambiguities or lacunae. I shall post the complete dictionary on the web as version 2.1beta1 on 28 November, to permit general public scrutiny, and request formal approval at the beginning of 1998. This is a convenient opportunity to submit additional data items that you feel are lacking from the Core. ############################################################################## APPENDIX Changes to the core CIF Dictionary The core dictionary is a large enough document that it is inconvenient to post, and difficult enough to extract unambiguously the changes between versions. I therefore include here some indications of the changes that have been made, but encourage you to download and look at the full version to resolve any ambiguities that you find. the full version is at ftp://ftp.iucr.org/cifdics/cif_core_2.1beta.dic The following data blocks have been modified. ("<" flags data blocks that have been deleted, ">" ones that have been added. Deletions from the older dictionary file indicate that a composite definition has been broken up into multiple definitions in the newer dictionary - for example to indicate that an "..._obs" data name should be replaced by a "..._gt" one.) > data_atom_site_adp_type > data_diffrn_measured_fraction_theta_full > data_diffrn_measured_fraction_theta_max > data_diffrn_detector_area_resol_mean < data_diffrn_reflns_theta_ > data_diffrn_reflns_theta_full > data_diffrn_reflns_theta_max > data_diffrn_reflns_theta_min < data_refine_ls_goodness_of_fit_ > data_refine_ls_goodness_of_fit_all > data_refine_ls_goodness_of_fit_gt > data_refine_ls_goodness_of_fit_obs > data_refine_ls_goodness_of_fit_ref < data_refine_ls_R_factor_ > data_refine_ls_R_factor_all > data_refine_ls_R_factor_gt > data_refine_ls_R_factor_obs < data_refine_ls_restrained_S_ < data_refine_ls_shift/esd_ > data_refine_ls_restrained_S_all > data_refine_ls_restrained_S_gt > data_refine_ls_restrained_S_obs > data_refine_ls_shift/esd_max > data_refine_ls_shift/esd_mean > data_refine_ls_shift/su_max > data_refine_ls_shift/su_mean < data_refine_ls_wR_factor_ > data_refine_ls_wR_factor_all > data_refine_ls_wR_factor_gt > data_refine_ls_wR_factor_obs > data_refine_ls_wR_factor_ref > data_refln_include_status < data_reflns_number_ > data_reflns_number_Friedel > data_reflns_number_gt > data_reflns_number_observed > data_reflns_number_total > data_reflns_threshold_expression > data_reflns_shell_meanI_over_sigI_gt > data_reflns_shell_number_measured_gt > data_reflns_shell_number_unique_gt > data_reflns_shell_percent_possible_gt > data_reflns_shell_Rmerge_F_gt > data_reflns_shell_Rmerge_I_gt The following definitions are new (the unusual layout here is a feature of the software I have used to extract these items from the full dictionary file): data_atom_site_adp_type _name '_atom_site_adp_type' _category atom_site _type char _list yes _list_reference '_atom_site_label' loop_ _enumeration _enumeration_detail Uani 'anisotropic Uij' Uiso 'isotropic U' Uovl 'overall U' Umpe 'multipole expansion U' Bani 'anisotropic Bij' Biso 'isotropic B' Bovl 'overall B' _definition ; A standard code used to describe the type of atomic displacement parameters used for the site. ; data_diffrn_measured_fraction_theta_full _name '_diffrn_measured_fraction_theta_full' _category diffrn _list yes _type numb _enumeration_range 0:1.0 _definition ; Fraction of unique (symmetry-independent) reflections measured out to _diffrn_reflns_theta_full. ; data_diffrn_measured_fraction_theta_max _name '_diffrn_measured_fraction_theta_max' _category diffrn _list yes _type numb _enumeration_range 0:1.0 _definition ; Fraction of unique (symmetry-independent) reflections measured out to _diffrn_reflns_theta_max. ; data_diffrn_detector_area_resol_mean _name '_diffrn_detector_area_resol_mean' _category diffrn_detector _type numb _enumeration_range 0.0: _units mm^-1^ _units_detail 'pixels per millimetre' _definition ; The resolution of an area detector, in pixels/mm. ; data_diffrn_reflns_theta_full _name '_diffrn_reflns_theta_full' _category diffrn_reflns _type numb _enumeration_range 0.0:90.0 _units deg _units_detail 'degrees' _definition ; The diffractometer theta angle (in degrees) at which the measured reflection count is close to complete. The fraction of unique reflections measured out to this angle is given by _diffrn_measured_fraction_theta_full. ; data_refine_ls_goodness_of_fit_gt _name '_refine_ls_goodness_of_fit_gt' _category refine _type numb _type_conditions esd _enumeration_range 0.0: _definition ; The least-squares goodness-of-fit parameter S for significantly intense reflections, (see _reflns_threshold_expression), after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least squares. See also _refine_ls_restrained_S_ definitions. { sum | w | Y(obs) - Y(calc) |^2^ | }^1/2^ S = { ----------------------------------- } { Nref - Nparam } Y(obs) = the observed coefficients (see _refine_ls_structure_factor_coef) Y(calc) = the calculated coefficients (see _refine_ls_structure_factor_coef) w = the least-squares reflection weight [1/(sigma squared)] sigma = standard uncertainty Nref = the number of reflections used in the refinement Nparam = the number of refined parameters and the sum is taken over the specified reflections ; data_refine_ls_goodness_of_fit_ref _name '_refine_ls_goodness_of_fit_ref' _category refine _type numb _type_conditions esd _enumeration_range 0.0: _definition ; The least-squares goodness-of-fit parameter S for all reflections included in the refinement, after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least squares. See also _refine_ls_restrained_S_ definitions. { sum | w | Y(obs) - Y(calc) |^2^ | }^1/2^ S = { ----------------------------------- } { Nref - Nparam } Y(obs) = the observed coefficients (see _refine_ls_structure_factor_coef) Y(calc) = the calculated coefficients (see _refine_ls_structure_factor_coef) w = the least-squares reflection weight [1/(sigma squared)] sigma = standard uncertainty Nref = the number of reflections used in the refinement Nparam = the number of refined parameters and the sum is taken over the specified reflections ; data_refine_ls_R_factor_gt _name '_refine_ls_R_factor_gt' _category refine _type numb _enumeration_range 0.0: _definition ; Residual factor for the reflections (with number given by _reflns_number_gt) judged significantly intense (i.e. satisfying the threshold specified by _reflns_threshold_expression) and included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_d_res_high and _refine_ls_d_res_low. This is the conventional R factor. See also _refine_ls_wR_factor_ definitions. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the specified reflections ; data_refine_ls_restrained_S_gt _name '_refine_ls_restrained_S_gt' _category refine _type numb _enumeration_range 0.0: _definition ; The least-squares goodness-of-fit parameter S' for significantly intense reflections (satisfying _reflns_threshold_expression) after the final cycle of least squares. This parameter explicitly includes the restraints applied in the least-squares process. See also _refine_ls_goodness_of_fit_ definitions. {sum | w | Y(obs) - Y(calc) |^2^ | )^1/2^ ( + sum~r~ | w~r~ | P(calc) - P(targ) |^2^ | } S' = { -------------------------------------------------- } { N~ref~ + N~restr~ - N~param~ } Y(obs) = the observed coefficients (see _refine_ls_structure_factor_coef) Y(calc) = the observed coefficients (see _refine_ls_structure_factor_coef) w = the least-squares reflection weight [1/square of standard uncertainty (e.s.d.)] P(calc) = the calculated restraint values P(targ) = the target restraint values w~r~ = the restraint weight N~ref~ = the number of reflections used in the refinement (see _refine_ls_number_reflns) N~restr~ = the number of restraints (see _refine_ls_number_restraints) N~param~ = the number of refined parameters (see _refine_ls_number_parameters) sum is taken over the specified reflections sum~r~ is taken over the restraints ; data_refine_ls_shift/su_max _name '_refine_ls_shift/su_max' _category refine _type numb _enumeration_range 0.0: _definition ; The largest ratio of the final least-squares parameter shift divided by the final standard uncertainty. ; data_refine_ls_shift/su_mean _name '_refine_ls_shift/su_mean' _category refine _type numb _related_item '_refine_ls_shift/su_mean' _related_purpose replace _enumeration_range 0.0: _definition ; The average ratio of the final least-squares parameter shift divided by the final standard uncertainty. ; data_refine_ls_wR_factor_gt _name '_refine_ls_wR_factor_gt' _category refine _type numb _enumeration_range 0.0: _definition ; Weighted residual factors for significantly intense reflections (satisfying _reflns_threshold_expression) included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_d_res_high and _refine_ls_d_res_low. See also the _refine_ls_R_factor_ definitions. ( sum | w | Y(obs) - Y(calc) |^2^ | )^1/2^ wR = ( --------------------------------- ) ( sum | w Y(calc)^2^ | ) Y(obs) = the observed amplitude specified by _refine_ls_structure_factor_coef Y(calc) = the calculated amplitude specified by _refine_ls_structure_factor_coef w = the least-squares weight and the sum is taken over the specified reflections ; data_refine_ls_wR_factor_ref _name '_refine_ls_wR_factor_ref' _category refine _type numb _enumeration_range 0.0: _definition ; Weighted residual factors for all reflections included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_d_res_high and _refine_ls_d_res_low. See also the _refine_ls_R_factor_ definitions. ( sum | w | Y(obs) - Y(calc) |^2^ | )^1/2^ wR = ( --------------------------------- ) ( sum | w Y(calc)^2^ | ) Y(obs) = the observed amplitude specified by _refine_ls_structure_factor_coef Y(calc) = the calculated amplitude specified by _refine_ls_structure_factor_coef w = the least-squares weight and the sum is taken over the specified reflections ; data_refln_include_status _name '_refln_include_status' _category refln _type char _list yes _list_reference '_refln_index_' loop_ _enumeration _enumeration_detail o ; satisfies _refine_ls_d_res_high satisfies _refine_ls_d_res_low exceeds _reflns_threshold_expression ; < ; satisfies _refine_ls_d_res_high satisfies _refine_ls_d_res_low does not exceed _reflns_threshold_expression ; - 'systematically absent reflection' x 'unreliable measurement -- not used' h 'does not satisfy _refine_ls_d_res_high' l 'does not satisfy _refine_ls_d_res_low' _enumeration_default o _definition ; Classification of a reflection so as to indicate its status with respect to inclusion in refinement and calculation of R factors. ; data_reflns_number_Friedel _name '_reflns_number_Friedel' _category reflns _type numb _enumeration_range 0: _definition ; The number of Friedel equivalent reflections in the _refln_ list. Friedel equivalent reflections may be treated as independent reflections in the least-squares refinement because, although related by symmetry, they may differ in intensity owing to inelastic scattering. ; data_reflns_number_gt _name '_reflns_number_gt' _category reflns _type numb _enumeration_range 0: _definition ; The number of reflections in the _refln_ list (not the _diffrn_refln_ list) that are significantly intense, satisfying the criterion specified by _reflns_threshold_expression. They may include Friedel equivalent reflections according to the nature of the structure and the procedures used. The item _reflns_special_details describes the reflection data. ; data_reflns_threshold_expression _name '_reflns_threshold_expression' _category reflns _type char _example 'I>2\s(I)' _definition ; The threshold, based on multiples of \s(I), \s(F^2^) or \s(F), that serves to identify significantly intense reflections, the number of which is given by _reflns_number_gt. These reflections are used in the calculation of _refine_ls_R_factor_gt. ; data_reflns_shell_meanI_over_sigI_gt _name '_reflns_shell_meanI_over_sigI_gt' _category reflns_shell _type numb _list yes _definition ; The ratio of the mean of the intensities of the significantly intense reflections (see _reflns_threshold_expression) in this shell to the mean of the standard uncertainties of the intensities of the significantly intense reflections in the resolution shell. ; data_reflns_shell_number_measured_gt _name '_reflns_shell_number_measured_gt' _category reflns_shell _type numb _list yes _definition ; The number of significantly intense reflections (see _reflns_threshold_expression) measured for this resolution shell. ; data_reflns_shell_number_unique_gt _name '_reflns_shell_number_unique_gt' _category reflns_shell _type numb _list yes _enumeration_range 0: _definition ; The total number of significantly intense reflections (see _reflns_threshold_expression) which are symmetrically unique after merging for this resolution shell. ; data_reflns_shell_percent_possible_gt _name '_reflns_shell_percent_possible_gt' _category reflns_shell _type numb _list yes _enumeration_range 0.0: _definition ; The percentage of geometrically possible reflections represented by significantly intense reflections (see _reflns_threshold_expression) measured for this resolution shell. ; data_reflns_shell_Rmerge_F_gt _name '_reflns_shell_Rmerge_F_gt' _category reflns_shell _type numb _list yes _enumeration_range 0.0: _definition ; The value of Rmerge(F) for significantly intense reflections (see _reflns_threshold_expression) in a given shell. sum~i~ ( sum~j~ | F~j~ - <F> | ) Rmerge(F) = -------------------------------- sum~i~ ( sum~j~ <F> ) F~j~ = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. ; data_reflns_shell_Rmerge_I_gt _name '_reflns_shell_Rmerge_I_gt' _category reflns_shell _type numb _list yes _enumeration_range 0.0: _definition ; The value of Rmerge(I) for significantly intense reflections (see _reflns_threshold_expression) in a given shell. sum~i~ ( sum~j~ | I~j~ - <I> | ) Rmerge(I) = -------------------------------- sum~i~ ( sum~j~ <I> ) I~j~ = the intensity of the jth observation of reflection i <I> = the mean of the intensities of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. ; ##############################################################################

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