#-------------------------- #mmCIF Extension Dictionary #-------------------------- data_cif_mm.dic-ext-v4 ################# ## PHASING_MIR ## ################# # ############################################################ ## proposed additional data items in an existing category ## ############################################################ # ######################################### ## Submitted by Kim Henrick ## ## Content review by Paula Fitzgerald ## ## Editorial review by HB, JW and PMDF ## ######################################### save__phasing_MIR.d_res_high _item_description.description ; The highest resolution in angstroms for the interplanar spacing in the reflection data used for the native data set. This is the smallest d value. ; _item.name '_phasing_MIR.d_res_high' _item.category_id phasing_MIR _item.mandatory_code yes _item_aliases.alias_name '_phasing_MIR.ebi_d_res_high' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__phasing_MIR.d_res_low _item_description.description ; The lowest resolution in angstroms for the interplanar spacing in the reflection data used for the native data set. This is the largest d value. ; _item.name '_phasing_MIR.d_res_low' _item.category_id phasing_MIR _item.mandatory_code yes _item_aliases.alias_name '_phasing_MIR.ebi_d_res_low' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__phasing_MIR.fom _item_description.description ; The mean value of the figure of merit m for all reflections phased in the native data set. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that phase angle a is correct int is taken over the range alpha = 0 to 2 pi. ; _item.name '_phasing_MIR.fom' _item.category_id phasing_MIR _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR.ebi_fom' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR.fom_acentric _item_description.description ; The mean value of the figure of merit m for the acentric reflections phased in the native data set. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that phase angle a is correct int is taken over the range alpha = 0 to 2 pi. ; _item.name '_phasing_MIR.fom_acentric' _item.category_id phasing_MIR _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR.ebi_fom_acentric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR.fom_centric _item_description.description ; The mean value of the figure of merit m for the centric reflections phased in the native data set. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that phase angle a is correct int is taken over the range alpha = 0 to 2 pi. ; _item.name '_phasing_MIR.fom_centric' _item.category_id phasing_MIR _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR.ebi_fom_centric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR.reflns _item_description.description ; The total number of reflections phased in the native data set. ; _item.name '_phasing_MIR.reflns' _item.category_id phasing_MIR _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR.ebi_reflns' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR.reflns_acentric _item_description.description ; The number of acentric reflections phased in the native data set. ; _item.name '_phasing_MIR.reflns_acentric' _item.category_id phasing_MIR _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR.ebi_reflns_acentric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR.reflns_centric _item_description.description ; The number of centric reflections phased in the native data set. ; _item.name '_phasing_MIR.reflns_centric' _item.category_id phasing_MIR _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR.ebi_reflns_centric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR.reflns_criterion _item_description.description ; Criterion used to limit the reflections used in the phasing calculations. ; _item.name '_phasing_MIR.reflns_criterion' _item.category_id phasing_MIR _item_aliases.alias_name '_phasing_MIR.ebi_reflns_criteria' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item.mandatory_code no _item_type.code text _item_examples.case '> 4 \s(I)' save_ ##################### ## PHASING_MIR_DER ## ##################### # ############################################################ ## proposed additional data items in an existing category ## ############################################################ # ######################################### ## Submitted by Kim Henrick ## ## Content review by Paula Fitzgerald ## ## Editorial review by HB, JW and PMDF ## ######################################### save__phasing_MIR_der.power_acentric _item_description.description ; The mean phasing power P for acentric reflections in this derivative. sum|Fh~calc~^2^| P = (----------------------------)^1/2^ sum|Fph~obs~ - Fph~calc~|^2^ Fph~obs~ = the observed structure factor amplitude of this derivative Fph~calc~ = the calculated structure factor amplitude of this derivative Fh~calc~ = the calculated structure factor amplitude from the heavy atom model sum is taken over the specified reflections ; _item.name '_phasing_MIR_der.power_acentric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_power_acentric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der.power_centric _item_description.description ; The mean phasing power P for centric reflections in this derivative. sum|Fh~calc~^2^| P = (----------------------------)^1/2^ sum|Fph~obs~ - Fph~calc~|^2^ Fph~obs~ = the observed structure factor amplitude of the derivative Fph~calc~ = the calculated structure factor amplitude of the derivative Fh~calc~ = the calculated structure factor amplitude from the heavy atom model sum is taken over the specified reflections ; _item.name '_phasing_MIR_der.power_centric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_power_centric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der.R_cullis_acentric _item_description.description ; Residual factor R~cullis,acen~ for acentric reflections in this derivative. The Cullis R factor was originally defined only for centric reflections. It is, however, also a useful statistical measure for acentric reflections, which is how it is used in this data item. sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ | R~cullis,acen~ = ---------------------------------------- sum|Fph~obs~ - Fp~obs~| Fp~obs~ = the observed structure factor amplitude of the native Fph~obs~ = the observed structure factor amplitude of the derivative Fh~calc~ = the calculated structure factor amplitude from the heavy atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. Roy. Soc. A265, 15-38. ; _item.name '_phasing_MIR_der.R_cullis_acentric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_Rcullis_acentric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der.R_cullis_anomalous _item_description.description ; Residual factor R~cullis,ano~ for anomalous reflections in this derivative. The Cullis R factor was originally defined only for centric reflections. It is, however, also a useful statistical measure for anomalous reflections, which is how it is used in this data item. This is tabulated for acentric terms. Any value <1.0 means there is some contribution to the phasing from the anomalous data. sum| |Fph+~obs~Fph-~obs~ - Fh+~calc~ - Fh-~calc~| | R~cullis,ano~ = --------------------------------------------------- sum|Fph+~obs~ - Fph-~obs~| Fph+~obs~ = the observed positive Friedel structure factor amplitude for the derivative Fph-~obs~ = the observed negative Friedel structure factor amplitude for the derivative Fh+~calc~ = the calculated postitive Friedel structure factor amplitude from the heavy atom model Fh-~calc~ = the calculated negative Friedel structure factor amplitude from the heavy atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. Roy. Soc. A265, 15-38. ; _item.name '_phasing_MIR_der.R_cullis_anomalous' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_Rcullis_anomalous' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der.R_cullis_centric _item_description.description ; Residual factor R~cullis~ for centric reflections in this derivative. sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ | R~cullis~ = ---------------------------------------- sum|Fph~obs~ - Fp~obs~| Fp~obs~ = the observed structure factor amplitude of the native Fph~obs~ = the observed structure factor amplitude of the derivative Fh~calc~ = the calculated structure factor amplitude from the heavy atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. Roy. Soc. A265, 15-38. ; _item.name '_phasing_MIR_der.R_cullis_centric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_Rcullis_centric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der.reflns_acentric _item_description.description ; The number of acentric reflections used in phasing for this derivative. ; _item.name '_phasing_MIR_der.reflns_acentric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_reflns_acentric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR_der.reflns_anomalous _item_description.description ; The number of anomalous reflections used in phasing for this derivative. ; _item.name '_phasing_MIR_der.reflns_anomalous' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_reflns_anomalous' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR_der.reflns_centric _item_description.description ; The number of centric reflections used in phasing for this derivative. ; _item.name '_phasing_MIR_der.reflns_centric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_reflns_centric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ ########################## ## PHASING_MIR_DER_SITE ## ########################## # ############################################################ ## proposed additional data items in an existing category ## ############################################################ # ######################################### ## Submitted by Kim Henrick ## ## Content review by Paula Fitzgerald ## ## Editorial review by HB, JW and PMDF ## ######################################### save__phasing_MIR_der_site.occupancy_anom _item_description.description ; The relative anomalous occupancy of the atom type present at this heavy-atom site in a given derivative. This atom occupancy will probably be on an arbitrary scale. ; _item.name '_phasing_MIR_der_site.occupancy_anom' _item.category_id phasing_MIR_der_site _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_anom' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_related.related_name '_phasing_MIR_der_site.occupancy_anom_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd save_ save__phasing_MIR_der_site.occupancy_anom_esd _item_description.description ; The standard uncertainty (e.s.d.) of _phasing_MIR_der_site.occupancy_anom. ; _item.name '_phasing_MIR_der_site.occupancy_anom_esd' _item.category_id phasing_MIR_der_site _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_anom_esd' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_default.value 0.0 _item_related.related_name '_phasing_MIR_der_site.occupancy_anom' _item_related.function_code associated_value _item_type.code float save_ save__phasing_MIR_der_site.occupancy_iso _item_description.description ; The relative real isotropic occupancy of the atom type present at this heavy-atom site in a given derivative. This atom occupancy will probably be on an arbitrary scale. ; _item.name '_phasing_MIR_der_site.occupancy_iso' _item.category_id phasing_MIR_der_site _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_iso' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_related.related_name '_phasing_MIR_der_site.occupancy_iso_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd save_ save__phasing_MIR_der_site.occupancy_iso_esd _item_description.description ; The standard uncertainty (e.s.d.) of _phasing_MIR_der_site.occupancy_iso. ; _item.name '_phasing_MIR_der_site.occupancy_iso_esd' _item.category_id phasing_MIR_der_site _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_iso_esd' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_default.value 0.0 _item_related.related_name '_phasing_MIR_der_site.occupancy_iso' _item_related.function_code associated_value _item_type.code float save_ ####################### ## PHASING_MIR_SHELL ## ####################### # ############################################################ ## proposed additional data items in an existing category ## ############################################################ # ######################################### ## Submitted by Kim Henrick ## ## Content review by Paula Fitzgerald ## ## Editorial review by HB, JW and PMDF ## ######################################### save__phasing_MIR_shell.fom_acentric _item_description.description ; The mean value of the figure of merit m for acentric reflections in this shell. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that phase angle a is correct int is taken over the range alpha = 0 to 2 pi. ; _item.name '_phasing_MIR_shell.fom_acentric' _item.category_id phasing_MIR_shell _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_shell.ebi_fom_acentric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_shell.fom_centric _item_description.description ; The mean value of the figure of merit m for centric reflections in this shell. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that phase angle a is correct int is taken over the range alpha = 0 to 2 pi. ; _item.name '_phasing_MIR_shell.fom_centric' _item.category_id phasing_MIR_shell _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_shell.ebi_fom_centric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_shell.reflns_acentric _item_description.description ; The number of acentric reflections in this shell. ; _item.name '_phasing_MIR_shell.reflns_acentric' _item.category_id phasing_mir_shell _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_shell.ebi_reflns_acentric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR_shell.reflns_anomalous _item_description.description ; The number of anomalous reflections in this shell. ; _item.name '_phasing_MIR_shell.reflns_anomalous' _item.category_id phasing_mir_shell _item.mandatory_code no # _item_aliases.alias_name '_phasing_MIR_shell.ebi_reflns_anomalous' # _item_aliases.dictionary ebi_extensions # _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR_shell.reflns_centric _item_description.description ; The number of centric reflections in this shell. ; _item.name '_phasing_MIR_shell.reflns_centric' _item.category_id phasing_mir_shell _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_shell.ebi_reflns_centric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ ############ ## REFINE ## ############ # ############################################################ ## proposed additional data items in an existing category ## ############################################################ # ################################################### ## Submitted by Kim Henrick ## ## Content review by Dale Tronrud - Mar 19, 1988 ## ## Editorial review by HB, JW and PMDF ## ################################################### save__refine.correlation_coeff_Fo_to_Fc _item_description.description ; The correlation coefficient between the observed and calculated structure factors for reflections included in the refinement. The correlation coefficient is scale independent and gives an idea of the quality of the refined model. sum~i~(Fo~i~ Fc~i~ - ) R~corr~ = ------------------------------------------------------------ SQRT{sum~i~(Fo~i~)^2^-^2^} SQRT{sum~i~(Fc~i~)^2^-^2^} Fo = observed structure factors Fc = calculated structure factors <> = denotes average value of data summation is over reflections included in the refinement ; _item.name '_refine.correlation_coeff_Fo_to_Fc' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_Correlation_coeff_Fo_to_Fc' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.correlation_coeff_Fo_to_Fc_free _item_description.description ; The correlation coefficient between the observed and calculated structure factors for reflections not included in the refinement (free reflections). The correlation coefficient is scale independent and gives an idea of the quality of the refined model. sum~i~(Fo~i~ Fc~i~ - ) R~corr~ = ------------------------------------------------------------ SQRT{sum~i~(Fo~i~)^2^-^2^} SQRT{sum~i~(Fc~i~)^2^-^2^} Fo = observed structure factors Fc = calculated structure factors <> = denotes average value of data summation is over reflections not included (free reflections) in the refinement ; _item.name '_refine.correlation_coeff_Fo_to_Fc_free' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_Correlation_coeff_Fo_to_Fc_free' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.overall_ESU_B _item_description.description ; The overall standard uncertainty (e.s.d.) of the thermal parameters based on a maximum likelihood residual. The overall ESU (sigma~B~)^2 gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N_a (sigma~B~)^2 = 8 ---------------------------------------------- sum~i~ {(1/Sigma - (E_o)^2 (1-m^2)(SUM_AS)s^4} SUM_AS = (sigma_A)^2/Sigma^2) N_a = number of atoms Sigma = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2) E_o = normalized structure factors sigma_{E;exp} = experimental uncertainties of normalized structure factors sigma_A = SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f^2 Sigma_N = sum_{atoms in crystal} f^2 f = is form factor of atoms delta_x = expected error m = is figure of merit of phases of reflection included in summation delta_x expected error s = reciprocal space vector epsilon = multiplicity of diffracting plane summation is over all reflections included in refinement Ref: (sigma_A estimation) "Refinement of Macromolecular Structures by the Maximum-Likelihood Method", Murshudov, G. N., Vagin A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. (ESU ML estimation) "Simplified error estimation a la Cruickshank in macromolecular crystallography", Murshudov G. N. & Dodson E. J. (1997). CCP4 Newsletter, no. 33. http://www.dl.ac.uk/CCP/CCP4/newsletter33/ ; _item.name '_refine.overall_ESU_B' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_Overall_ESU_B' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.overall_ESU_ML _item_description.description ; The overall standard uncertainty (e.s.d.) of the positional parameters based on a maximum likelihood residual. The overall ESU (sigma~X~)^2 gives an idea of the uncertainty in the position of averagely defined atoms (atoms with B values equal to average B value) 3 N_a (sigma~X~)^2 = ----------------------------------------------------- 8 pi^2 sum~i~ {(1/Sigma - (E_o)^2 (1-m^2)(SUM_AS)s^2} SUM_AS = (sigma_A)^2/Sigma^2) N_a = number of atoms Sigma = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2) E_o = normalized structure factors sigma_{E;exp} = experimental uncertainties of normalized structure factors sigma_A = SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f^2 Sigma_N = sum_{atoms in crystal} f^2 f = is formfactor of atoms delta_x = expected error m = is figure of merit of phases of reflection included in summation delta_x expected error s = reciprocal space vector epsilon = multiplicity of diffracting plane summation is over all reflections included in refinement Ref: (sigma_A estimation) "Refinement of Macromolecular Structures by the Maximum-Likelihood Method", Murshudov, G. N., Vagin A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. (ESU ML estimation) "Simplified error estimation a la Cruickshank in macromolecular crystallography", Murshudov G. N. & Dodson E. J. (1997). CCP4 Newsletter, no. 33. http://www.dl.ac.uk/CCP/CCP4/newsletter33/ ; _item.name '_refine.overall_ESU_ML' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_Overall_ESU_ML' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.overall_ESU_R_Cruickshank_DPI _item_description.description ; The overall standard uncertainty (e.s.d.) of the thermal parameters based on the crystallographic R value, expressed in a formalism known as the dispersion precisions indicator (DPI). The overall ESU (sigma~B~) gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N_a (sigma_B)^2 = 0.65 --------- (R_value)^2 (D_min)^2 C^(-2/3) (N_o-N_p) N_a = number of atoms N_o = number of reflections included in refinement N_p = number of refined parameters R_value = conventional crystallographic R-value D_min = maximum resolution C = completeness of data Ref: Cruickshank, D. W. (1997). "Refinement of macromolecular structures". Proc. CCP4 study weekend. "Simplified error estimation a la Cruickshank in macromolecular crystallography", Murshudov G. N. & Dodson E. J. (1997). CCP4 Newsletter, no. 33. http://www.dl.ac.uk/CCP/CCP4/newsletter33/ ; _item.name '_refine.overall_ESU_R_Cruickshank_DPI' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_Overall_ESU_R_Cruickshanks_DPI' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.overall_ESU_R_free _item_description.description ; The overall standard uncertainty (e.s.d.) of the thermal parameters based on the free R value. The overall ESU gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N_a (sigma_B)^2 = 0.65 ----- (R_free)^2 (D_min)^2 C^(-2/3) N_o N_a = number of atoms N_o = number of reflections included in refinement N_p = number of refined parameters R_free = conventional free crystallographic R-value calculated using reflections not included in refinement D_min = maximum resolution C = completeness of data Ref: Cruickshank, D. W. (1997). "Refinement of macromolecular structures". Proc. CCP4 study weekend. "Simplified error estimation a la Cruickshank in macromolecular crystallography", Murshudov G. N. & Dodson E. J. (1997). CCP4 Newsletter, no. 33. http://www.dl.ac.uk/CCP/CCP4/newsletter33/ ; _item.name '_refine.overall_ESU_R_free' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_Overall_ESU_Rfree' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.overall_FOM_free_R_set _item_description.description ; Average figure of merit of phases of reflections not included in the refinement. This value is derived from the likelihood function. fom = I_1(X)/I_0(X) I_0, I_1 = zero- and first-order modified Bessel function of the first kind X = sigma_A |E_o| |E_c|/SIGMA E_o, E_c = normalized observed and calculated structure factors sigma_A = SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f^2 Sigma_N = sum_{atoms in crystal} f^2 f = formfactor of atoms delta_x = expected error SIGMA = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2) sigma_{E;exp} = uncertainties of normalized observed structure factors epsilon = multiplicity of diffracting plane Ref: (sigma_A estimation) "Refinement of Macromolecular Structures by the Maximum-Likelihood Method", Murshudov, G. N., Vagin A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. ; _item.name '_refine.overall_FOM_free_R_set' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_overall_FOM_free_Rset' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.overall_FOM_work_R_set _item_description.description ; Average figure of merit of phases of reflections included in the refinement. This value is derived from the likelihood function. fom = I_1(X)/I_0(X) I_0, I_1 = zero- and first-order modified Bessel function of the first kind X = sigma_A |E_o| |E_c|/SIGMA E_o, E_c = normalized observed and calculated structure factors sigma_A = SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f^2 Sigma_N = sum_{atoms in crystal} f^2 f = is formfactor of atoms delta_x = expected error SIGMA = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2) sigma_{E;exp} = uncertainties of normalized observed structure factors epsilon = multiplicity of diffracting plane Ref: (sigma_A estimation) "Refinement of Macromolecular Structures by the Maximum-Likelihood Method", Murshudov, G. N., Vagin A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. ; _item.name '_refine.overall_FOM_work_R_set' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_overall_FOM_work_Rset' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ #################### ## REFINE_ANALYZE ## #################### # ############################################################ ## proposed additional data items in an existing category ## ############################################################ # ################################################### ## Submitted by Kim Henrick ## ## Content review by Dale Tronrud - Jan 13, 1998 ## ## Editorial review by HB, JW and PMDF ## ################################################### save__refine_analyze.RG_d_res_high _item_description.description ; The value of the high-resolution cutoff in angstroms used in calculation of the Hamilton generalized R factor (RG) stored in refine_analyze.RG_work and _refine_analyze.RG_free. Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. ; _item.name '_refine_analyze.RG_d_res_high' _item.category_id refine_analyze _item.mandatory_code no _item_aliases.alias_name '_refine_analyze.ebi_RG_d_res_high' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine_analyze.RG_d_res_low _item_description.description ; The value of the low-resolution cutoff in angstroms used in calculation of the Hamilton generalized R factor (RG) stored in refine_analyze.RG_work and _refine_analyze.RG_free. Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. ; _item.name '_refine_analyze.RG_d_res_low' _item.category_id refine_analyze _item.mandatory_code no _item_aliases.alias_name '_refine_analyze.ebi_RG_d_res_low' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine_analyze.RG_free _item_description.description ; The Hamilton generalized R factor for all reflections that satisfy the resolution limits established by _refine_analyze.RG_d_res_high and _refine_analyze.RG_d_res_low for the free R set of reflections that were excluded from the refinement. sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j) Rg = Sqrt( ----------------------------------------------------------------- ) sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j where |Fobs| = the observed structure factor amplitudes |Fcalc| = the calculated structure factor amplitudes G = the scale factor which puts |Fcalc| on the same scale as |Fobs| w_{i,j} = the weight for the combination of the reflections i and j. sum_i and sum_j are taken over the specified reflections When the covariance of the amplitude of reflection i and reflection j is zero (i.e. the reflections are independent) w{i,i} can be redefined as w_i and the nested sums collapsed into one. sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2 Rg = Sqrt( ----------------------------------- ) sum_i w_i |Fobs|_i^2 Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. ; _item.name '_refine_analyze.RG_free' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_analyze.ebi_RG_free' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine_analyze.RG_work _item_description.description ; The Hamilton generalized R factor for all reflections that satisfy the resolution limits established by _refine_analyze.RG_d_res_high and _refine_analyze.RG_d_res_low and for those reflections included in the working set when a free R set of reflections are omitted from the refinement. sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j) Rg = Sqrt( ----------------------------------------------------------------- ) sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j where |Fobs| = the observed structure factor amplitudes |Fcalc| = the calculated structure factor amplitudes G = the scale factor which puts |Fcalc| on the same scale as |Fobs| w_{i,j} = the weight for the combination of the reflections i and j. sum_i and sum_j are taken over the specified reflections When the covariance of the amplitude of reflection i and reflection j is zero (i.e. the reflections are independent) w{i,i} can be redefined as w_i and the nested sums collapsed into one. sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2 Rg = Sqrt( ----------------------------------- ) sum_i w_i |Fobs|_i^2 Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. ; _item.name '_refine_analyze.RG_work' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_analyze.ebi_RG_work' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine_analyze.RG_free_work_ratio _item_description.description : The observed ratio of RGfree to RGwork. The expected RG ratio is the value that should be achievable at the end of a structure refinement when only random uncorrelated errors exist in data and model provided that the observations are properly weighted. When compared with the observed RG ratio it may indicate that a structure has not reached convergence or a model has been over-refined with no corresponding improvement in the model. In an unrestrained refinement the ratio of RGfree/RGwork with only random uncorrelated errors at convergence depends only on the number of reflections and the number of parameters as: sqrt[(f + m) / (f - m) ] where f = number of included structure amplitudes and target distances, and m = number of parameters being refined. In the restrained case, RGfree is calculated from a random selection of residuals including both structure amplitudes and restraints. When restraints are included in refinement the RG ratio requires a term for the contribution to the minimized residual at convergence, Drest, due to those restraints: Drest = r - sum (w_i . (a_i)^t . (H)^-1 a_i where r is the number of geometrical, temperature factor and other restraints H is the (m,m) normal matrix given by A^t.W.A W is the (n,n) symmetric weight matrix of the included observations A is the least-squares design matrix of derivatives of order (n,m) a_i is the ith row of A Then the expected RGratio becomes sqrt [ (f + (m - r + Drest))/ (f - (m - r + Drest)) ] The expected RGfree/RGwork is not yet included in the mmCIF dictionary. Ref: "Rfree and the Rfree ratio. Part I: derivation of expected values of cross-validation residuals used in macromolecular least-squares refinement". Tickle, I. J., Laskowski, R. A. & Moss, D.S. (1998). Acta Cryst. D, in the press. ; _item.name '_refine_analyze.RG_free_work_ratio' _item.category_id refine_analyze _item.mandatory_code no _item_aliases.alias_name '_refine_analyze.ebi_RG_work_free_ratio' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ ############################### ## REFINE_FUNCT_MINIMIZED ## ############################### # ########################### ## proposed new category ## ########################### # ################################################### ## Submitted by Kim Henrick ## ## Content review by Dale Tronrud - Jan 13, 1998 ## ## Editorial review by HB, JW and PMDF ## ################################################### save_REFINE_FUNCT_MINIMIZED _category.description ; Data items in the REFINE_FUNCT_MINIMIZED category record details about the individual terms of the function minimized during refinement. ; _category.id refine_funct_minimized _category.mandatory_code no _category_key.name '_refine_funct_minimized.type' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on RESTRAIN refinement for the CCP4 text data set toxd. ; ; loop_ _refine_funct_minimized.type _refine_funct_minimized.number_terms _refine_funct_minimized.residual 'sum(W*Delta(Amplitude)^2' 3009 1621.3 'sum(W*Delta(Plane+Rigid)^2' 85 56.68 'sum(W*Delta(Distance)^2' 1219 163.59 'sum(W*Delta(U-tempfactors)^2' 1192 69.338 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine_funct_minimized.number_terms _item_description.description ; The number of observations in this term. For example, if the term is a residual of the X-ray data this item would contain the number of reflections used in the refinement. ; _item.name '_refine_funct_minimized.number_terms' _item.category_id refine_funct_minimized _item.mandatory_code no _item_aliases.alias_name '_ebi_refine_funct_minimized.NumTerms' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_funct_minimized.residual _item_description.description ; The residual for this term of the function which was minimized in refinement. ; _item.name '_refine_funct_minimized.residual' _item.category_id refine_funct_minimized _item.mandatory_code no _item_aliases.alias_name '_ebi_refine_funct_minimized.Residual' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine_funct_minimized.type _item_description.description ; The type of the function being minimized. ; _item.name '_refine_funct_minimized.type' _item.category_id refine_funct_minimized _item.mandatory_code yes _item_aliases.alias_name '_ebi_refine_funct_minimized.type' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code line save_ save__refine_funct_minimized.weight _item_description.description ; The weight applied to this term of the function which was minimized in the refinement. ; _item.name '_refine_funct_minimized.weight' _item.category_id refine_funct_minimized _item.mandatory_code no _item_aliases.alias_name '_ebi_refine_funct_minimized.weight' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ ##################### ## REFINE_LS_RESTR ## ##################### # ################################################### ## proposed elaboration of an existing data item ## ################################################### # #################################################### ## Submitted by Kim Henrick ## ## Content review by John Westbrook ## ## Kim Henrick approval of changes - Jan 22, 1998 ## ## Editorial review by HB, JW and PMDF ## #################################################### save__refine_ls_restr.type _item_description.description ; The type of the parameter being restrained. An explicit set of data values is provided for the programs Protin/ Prolsq (beginning with p_) and X-plor (beginning with x_). As computer programs will evolve, these data values are given as examples, and not as an enumeration list. Computer programs converting a data block to a refinement table will expect the exact form of the data values given here to be used. ; loop_ _item.name _item.category_id _item.mandatory_code '_refine_ls_restr.type' refine_ls_restr yes '_refine_ls_restr_type.type' refine_ls_restr_type yes loop_ _item_linked.child_name _item_linked.parent_name '_refine_ls_restr_type.type' '_refine_ls_restr.type' _item_type.code line loop_ _item_examples.case _item_examples.detail 'p_bond_d' 'bond distance' 'p_angle_d' 'bond angle expressed as a distance' 'p_planar_d' 'planar 1,4 distance' 'p_xhbond_d' 'x-h bond distance' 'p_xhangle_d' 'x-h bond angle expressed as a distance' 'p_hydrog_d' 'hydrogen distance' 'p_special_d' 'special distance' 'p_planar' 'planes' 'p_chiral' 'chiral centers' 'p_singtor_nbd' 'single-torsion non-bonded contact' 'p_multtor_nbd' 'multiple-torsion non-bonded contact' 'p_xyhbond_nbd' 'possible (x...y) hydrogen-bond' 'p_xhyhbond_nbd' 'possible (x-h...y) hydrogen-bond' 'p_special_tor' 'special torsion angle' 'p_planar_tor' 'planar torsion angle' 'p_staggered_tor' 'staggered torsion angle' 'p_orthonormal_tor' 'orthonormal torsion angle' 'p_mcbond_it' 'main-chain bond isotropic thermal factor' 'p_mcangle_it' 'main-chain angle isotropic thermal factor' 'p_scbond_it' 'side-chain bond isotropic thermal factor' 'p_scangle_it' 'side-chain angle isotropic thermal factor' 'p_xhbond_it' 'x-h bond isotropic thermal factor' 'p_xhangle_it' 'x-h angle isotropic thermal factor' 'p_special_it' 'special isotropic thermal factor' 'RESTRAIN_Distances < 2.12' ; For the program RESTRAIN, the root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves in the distance range less than 2.12 Angtroms. ; 'RESTRAIN_Distances 2.12 < D < 2.625' ; For the program RESTRAIN, the root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves in the distance range 2.12 - 2.625 Angtroms. ; 'RESTRAIN_Distances > 2.625' ; For the program RESTRAIN, the root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves in the distance range greater than 2.625 Angtroms. ; 'RESTRAIN_Peptide Planes' ; For the program RESTRAIN, the root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves for peptide planes. ; 'RESTRAIN_Ring and other planes' ; For the program RESTRAIN, the root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves for rings and planes other than peptide planes. ; 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.2-1.4' . 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.4-1.6' . 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.8-2.0' . 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.0-2.2' . 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.2-2.4' . 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist >2.4' . save_ ########################### ## REFINE_LS_RESTR_TYPE ## ########################### # ########################### ## proposed new category ## ########################### # #################################################### ## Submitted by Kim Henrick ## ## Content review by John Westbrook ## ## Kim Henrick approval of changes - Jan 22, 1998 ## ## Editorial review by HB, JW and PMDF ## #################################################### save_REFINE_LS_RESTR_TYPE _category.description ; Data items in the REFINE_LS_RESTR_TYPE category record details about the restraints types used in the least-squares refinement. ; _category.id refine_ls_restr_type _category.mandatory_code no _category_key.name '_refine_ls_restr_type.type' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on RESTRAIN refinement for the CCP4 text data set toxd. ; ; loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target 'RESTRAIN_Distances < 2.12' 509 0.005 0.022 'RESTRAIN_Distances 2.12 < D < 2.625' 671 0.016 0.037 'RESTRAIN_Distances > 2.625' 39 0.034 0.043 'RESTRAIN_Peptide Planes' 59 0.002 0.010 'RESTRAIN_Ring and other planes' 26 0.014 0.010 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.2-1.4' 212 0.106 . 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.4-1.6' 288 0.101 . 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.8-2.0' 6 0.077 . 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.0-2.2' 10 0.114 . 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.2-2.4' 215 0.119 . 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist >2.4' 461 0.106 . loop_ _refine_ls_restr_type.type _refine_ls_restr_type.distance_cutoff_low _refine_ls_restr_type.distance_cutoff_high _refine_ls_restr_type.U_sigma_weights 'RESTRAIN_Distances < 2.12' . 2.12 . 'RESTRAIN_Distances 2.12 < D < 2.625' 2.12 2.625 . 'RESTRAIN_Distances > 2.625' 2.625 . . 'RESTRAIN_Peptide Planes' . . . 'RESTRAIN_Ring and other planes' . . . 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.2-1.4' 1.2 1.4 1.800 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.4-1.6' 1.4 1.6 1.800 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.8-2.0' 1.8 2.0 1.800 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.0-2.2' 2.0 2.2 1.800 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.2-2.4' 2.2 2.4 1.800 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist >2.4' 2.4 . 1.800 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine_ls_restr_type.distance_cutoff_high _item_description.description ; The upper limit in angstroms of the distance range applied to the current restraint type. ; _item.name '_refine_ls_restr_type.distance_cutoff_high' _item.category_id refine_ls_restr_type _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine_ls_restr_type.distance_cutoff_low _item_description.description ; The lower limit in angstroms of the distance range applied to the current restraint type. ; _item.name '_refine_ls_restr_type.distance_cutoff_low' _item.category_id refine_ls_restr_type _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine_ls_restr_type.type _item_description.description ; This data item is a pointer to _refine_ls_restr.type in the REFINE_LS_RESTR category. ; _item.name '_refine_ls_restr_type.type' _item.category_id refine_ls_restr_type _item.mandatory_code yes _item_type.code line save_ ################### ## REFLN_SYS_ABS ## ################### # ########################### ## proposed new category ## ########################### # ######################################### ## Submitted by Kim Henrick ## ## Content review by Paula Fitzgerald ## ## Editorial review by HB, JW and PMDF ## ######################################### save_REFLN_SYS_ABS _category.description ; Data items in the REFLN_SYS_ABS category record details about the reflection data that should be systematically absent, given the designated space group. ; _category.id refln_sys_abs _category.mandatory_code no loop_ _category_key.name '_refln_sys_abs.index_h' '_refln_sys_abs.index_k' '_refln_sys_abs.index_l' loop_ _category_group.id 'inclusive_group' 'refln_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - completely arbitrary ; ; loop_ _refln_sys_abs.index_h _refln_sys_abs.index_k _refln_sys_abs.index_l _refln_sys_abs.I _refln_sys_abs.sigmaI _refln_sys_abs.I_over_sigmaI 0 3 0 28.32 22.95 1.23 0 5 0 14.11 16.38 0.86 0 7 0 114.81 20.22 5.67 0 9 0 32.99 24.51 1.35 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refln_sys_abs.I _item_description.description ; The measured value of the intensity in arbitrary units. ; _item.name '_refln_sys_abs.I' _item.category_id refln_sys_abs _item.mandatory_code no _item_aliases.alias_name '_ebi_refln_sys_abs.I' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_related.related_name _item_related.function_code '_refln_sys_abs.sigmaI' associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code arbitrary save_ save__refln_sys_abs.I_over_sigmaI _item_description.description ; The ratio of _refln_sys_abs.I to _refln_sys_abs.sigmaI. Used to evaluate whether a reflection that should be systematically absent according to the designated space group is in fact absent. ; _item.name '_refln_sys_abs.I_over_sigmaI' _item.category_id refln_sys_abs _item_aliases.alias_name '_ebi_refln_sys_abs.I_over_sigma' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item.mandatory_code no _item_type.code float save_ save__refln_sys_abs.index_h _item_description.description ; Miller index h of the reflection. The values of the Miller indices in the REFLN_SYS_ABS category must correspond to the cell defined by cell lengths and cell angles in the CELL category. ; _item.name '_refln_sys_abs.index_h' _item.category_id refln_sys_abs _item.mandatory_code yes _item_aliases.alias_name '_ebi_refln_sys_abs.h' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_dependent.dependent_name '_refln_sys_abs.index_k' '_refln_sys_abs.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__refln_sys_abs.index_k _item_description.description ; Miller index k of the reflection. The values of the Miller indices in the REFLN_SYS_ABS category must correspond to the cell defined by cell lengths and cell angles in the CELL category. ; _item.name '_refln_sys_abs.index_k' _item.category_id refln_sys_abs _item.mandatory_code yes _item_aliases.alias_name '_ebi_refln_sys_abs.k' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_dependent.dependent_name '_refln_sys_abs.index_h' '_refln_sys_abs.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__refln_sys_abs.index_l _item_description.description ; Miller index l of the reflection. The values of the Miller indices in the REFLN_SYS_ABS category must correspond to the cell defined by cell lengths and cell angles in the CELL category. ; _item.name '_refln_sys_abs.index_l' _item.category_id refln_sys_abs _item.mandatory_code yes _item_aliases.alias_name '_ebi_refln_sys_abs.l' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_dependent.dependent_name '_refln_sys_abs.index_h' '_refln_sys_abs.index_k' _item_sub_category.id miller_index _item_type.code int save_ save__refln_sys_abs.sigmaI _item_description.description ; The standard uncertainty (e.s.d.) of _refln_sys_abs.I, in arbitrary units. ; _item.name '_refln_sys_abs.sigmaI' _item.category_id refln_sys_abs _item.mandatory_code no _item_aliases.alias_name '_ebi_refln_sys_abs.sigmaI' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_related.related_name _item_related.function_code '_ebi_refln_sys_abs.I' associated_value _item_type.code float _item_units.code arbitrary save_ ####