Package org.rcsb.cif.schema.mm

Class Reflns

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.Reflns
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class Reflns
extends DelegatingCategory
Data items in the REFLNS category record details about the reflection data used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped.

  • Constructor Details

  • Method Details

    • createDelegate

      protected Column createDelegate​(String columnName, Column column)
      Overrides:
      createDelegate in class DelegatingCategory

    • getBIsoWilsonEstimate

      public FloatColumn getBIsoWilsonEstimate()
      The value of the overall isotropic displacement parameter estimated from the slope of the Wilson plot.
      Returns:
      FloatColumn

    • getEntryId

      public StrColumn getEntryId()
      This data item is a pointer to _entry.id in the ENTRY category.
      Returns:
      StrColumn

    • getDataReductionDetails

      public StrColumn getDataReductionDetails()
      A description of special aspects of the data-reduction procedures.
      Returns:
      StrColumn

    • getDataReductionMethod

      public StrColumn getDataReductionMethod()
      The method used for data reduction. Note that this is not the computer program used, which is described in the SOFTWARE category, but the method itself. This data item should be used to describe significant methodological options used within the data-reduction programs.
      Returns:
      StrColumn

    • getDResolutionHigh

      public FloatColumn getDResolutionHigh()
      The smallest value for the interplanar spacings for the reflection data. This is called the highest resolution.
      Returns:
      FloatColumn

    • getDResolutionLow

      public FloatColumn getDResolutionLow()
      The largest value for the interplanar spacings for the reflection data. This is called the lowest resolution.
      Returns:
      FloatColumn

    • getDetails

      public StrColumn getDetails()
      A description of reflection data not covered by other data names. This should include details of the Friedel pairs.
      Returns:
      StrColumn

    • getLimitHMax

      public IntColumn getLimitHMax()
      Maximum value of the Miller index h for the reflection data. This need not have the same value as _diffrn_reflns.limit_h_max.
      Returns:
      IntColumn

    • getLimitHMin

      public IntColumn getLimitHMin()
      Minimum value of the Miller index h for the reflection data. This need not have the same value as _diffrn_reflns.limit_h_min.
      Returns:
      IntColumn

    • getLimitKMax

      public IntColumn getLimitKMax()
      Maximum value of the Miller index k for the reflection data. This need not have the same value as _diffrn_reflns.limit_k_max.
      Returns:
      IntColumn

    • getLimitKMin

      public IntColumn getLimitKMin()
      Minimum value of the Miller index k for the reflection data. This need not have the same value as _diffrn_reflns.limit_k_min.
      Returns:
      IntColumn

    • getLimitLMax

      public IntColumn getLimitLMax()
      Maximum value of the Miller index l for the reflection data. This need not have the same value as _diffrn_reflns.limit_l_max.
      Returns:
      IntColumn

    • getLimitLMin

      public IntColumn getLimitLMin()
      Minimum value of the Miller index l for the reflection data. This need not have the same value as _diffrn_reflns.limit_l_min.
      Returns:
      IntColumn

    • getNumberAll

      public IntColumn getNumberAll()
      The total number of reflections in the REFLN list (not the DIFFRN_REFLN list). This number may contain Friedel-equivalent reflections according to the nature of the structure and the procedures used. The item _reflns.details describes the reflection data.
      Returns:
      IntColumn

    • getNumberObs

      public IntColumn getNumberObs()
      The number of reflections in the REFLN list (not the DIFFRN_REFLN list) classified as observed (see _reflns.observed_criterion). This number may contain Friedel-equivalent reflections according to the nature of the structure and the procedures used.
      Returns:
      IntColumn

    • getObservedCriterion

      public StrColumn getObservedCriterion()
      The criterion used to classify a reflection as 'observed'. This criterion is usually expressed in terms of a sigma(I) or sigma(F) threshold.
      Returns:
      StrColumn

    • getObservedCriterionFMax

      public FloatColumn getObservedCriterionFMax()
      The criterion used to classify a reflection as 'observed' expressed as an upper limit for the value of F.
      Returns:
      FloatColumn

    • getObservedCriterionFMin

      public FloatColumn getObservedCriterionFMin()
      The criterion used to classify a reflection as 'observed' expressed as a lower limit for the value of F.
      Returns:
      FloatColumn

    • getObservedCriterionIMax

      public FloatColumn getObservedCriterionIMax()
      The criterion used to classify a reflection as 'observed' expressed as an upper limit for the value of I.
      Returns:
      FloatColumn

    • getObservedCriterionIMin

      public FloatColumn getObservedCriterionIMin()
      The criterion used to classify a reflection as 'observed' expressed as a lower limit for the value of I.
      Returns:
      FloatColumn

    • getObservedCriterionSigmaF

      public FloatColumn getObservedCriterionSigmaF()
      The criterion used to classify a reflection as 'observed' expressed as a multiple of the value of sigma(F).
      Returns:
      FloatColumn

    • getObservedCriterionSigmaI

      public FloatColumn getObservedCriterionSigmaI()
      The criterion used to classify a reflection as 'observed' expressed as a multiple of the value of sigma(I).
      Returns:
      FloatColumn

    • getPercentPossibleObs

      public FloatColumn getPercentPossibleObs()
      The percentage of geometrically possible reflections represented by reflections that satisfy the resolution limits established by _reflns.d_resolution_high and _reflns.d_resolution_low and the observation limit established by _reflns.observed_criterion.
      Returns:
      FloatColumn

    • getRFreeDetails

      public StrColumn getRFreeDetails()
      A description of the method by which a subset of reflections was selected for exclusion from refinement so as to be used in the calculation of a 'free' R factor.
      Returns:
      StrColumn

    • getRmergeFAll

      public FloatColumn getRmergeFAll()
      Residual factor Rmerge for all reflections that satisfy the resolution limits established by _reflns.d_resolution_high and _reflns.d_resolution_low. 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
      Returns:
      FloatColumn

    • getRmergeFObs

      public FloatColumn getRmergeFObs()
      Residual factor Rmerge for reflections that satisfy the resolution limits established by _reflns.d_resolution_high and _reflns.d_resolution_low and the observation limit established by _reflns.observed_criterion. 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
      Returns:
      FloatColumn

    • getFriedelCoverage

      public FloatColumn getFriedelCoverage()
      The proportion of Friedel-related reflections present in the number of 'independent' reflections specified by the item _reflns.number_all. This proportion is calculated as the ratio: [N(Crystal class) - N(Laue symmetry)] / N(Laue symmetry) where, working from the DIFFRN_REFLN list, N(Crystal class) is the number of reflections obtained on averaging under the symmetry of the crystal class N(Laue symmetry) is the number of reflections obtained on averaging under the Laue symmetry. Examples: (a) For centrosymmetric structures, the value of _reflns.Friedel_coverage is necessarily equal to 0.0, as the crystal class is identical to the Laue symmetry. (b) For whole-sphere data for a crystal in the space group P1, _reflns.Friedel_coverage is equal to 1.0, as no reflection h k l is equivalent to -h -k -l in the crystal class and all Friedel pairs {h k l; -h -k -l} have been measured. (c) For whole-sphere data in space group Pmm2, _reflns.Friedel_coverage will be < 1.0 because although reflections h k l and -h -k -l are not equivalent when h k l indices are nonzero, they are when l=0. (d) For a crystal in space group Pmm2, measurements of the two inequivalent octants h >= 0, k >=0, l lead to the same value as in (c), whereas measurements of the two equivalent octants h >= 0, k, l >= 0 will lead to a zero value for _reflns.Friedel_coverage.
      Returns:
      FloatColumn

    • getNumberGt

      public IntColumn getNumberGt()
      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. This may include Friedel-equivalent reflections (i.e. those which are symmetry-equivalent under the Laue symmetry but inequivalent under the crystal class) according to the nature of the structure and the procedures used. Any special characteristics of the reflections included in the REFLN list should be described using the item _reflns.details.
      Returns:
      IntColumn

    • getThresholdExpression

      public StrColumn getThresholdExpression()
      The threshold, usually based on multiples of u(I), u(F^2^) or u(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.
      Returns:
      StrColumn

    • getPdbxRedundancy

      public FloatColumn getPdbxRedundancy()
      Overall redundancy for this data set (%).
      Returns:
      FloatColumn

    • getPdbxRmergeIObs

      public FloatColumn getPdbxRmergeIObs()
      The R value for merging intensities satisfying the observed criteria in this data set.
      Returns:
      FloatColumn

    • getPdbxRmergeIAll

      public FloatColumn getPdbxRmergeIAll()
      The R value for merging all intensities in this data set.
      Returns:
      FloatColumn

    • getPdbxRsymValue

      public FloatColumn getPdbxRsymValue()
      The R sym value as a decimal number.
      Returns:
      FloatColumn

    • getPdbxNetIOverAvSigmaI

      public FloatColumn getPdbxNetIOverAvSigmaI()
      The ratio of the average intensity to the average uncertainty, <I>/<sigma(I)>.
      Returns:
      FloatColumn

    • getPdbxNetIOverSigmaI

      public FloatColumn getPdbxNetIOverSigmaI()
      The mean of the ratio of the intensities to their standard uncertainties, <I/sigma(I)>.
      Returns:
      FloatColumn

    • getPdbxResNetIOverAvSigmaI2

      public FloatColumn getPdbxResNetIOverAvSigmaI2()
      Resolution (angstrom) for reflections with <I>/<sigma(I)> = 2.
      Returns:
      FloatColumn

    • getPdbxResNetIOverSigmaI2

      public FloatColumn getPdbxResNetIOverSigmaI2()
      Resolution (angstroms) for reflections with <I/sigma(I)> = 2.
      Returns:
      FloatColumn

    • getPdbxChiSquared

      public FloatColumn getPdbxChiSquared()
      Overall Chi-squared statistic.
      Returns:
      FloatColumn

    • getPdbxScalingRejects

      public IntColumn getPdbxScalingRejects()
      Number of reflections rejected in scaling operations.
      Returns:
      IntColumn

    • getPdbxDResHighOpt

      public FloatColumn getPdbxDResHighOpt()
      The highest optical resolution for this reflection data set as determined by computational method _reflns.pdbx_d_res_opt_method.
      Returns:
      FloatColumn

    • getPdbxDResLowOpt

      public FloatColumn getPdbxDResLowOpt()
      The lowest optical resolution for this reflection data set as determined by computational method _reflns.pdbx_d_res_opt_method.
      Returns:
      FloatColumn

    • getPdbxDResOptMethod

      public StrColumn getPdbxDResOptMethod()
      The computational method used to determine the optical resolution limits _reflns.pdbx_d_res_high_opt and _reflns.pdbx_d_res_low_opt.
      Returns:
      StrColumn

    • getPhaseCalculationDetails

      public StrColumn getPhaseCalculationDetails()
      The value of _reflns.phase_calculation_details describes a special details about calculation of phases in _refln.phase_calc.
      Returns:
      StrColumn

    • getPdbxRrimIAll

      public FloatColumn getPdbxRrimIAll()
      The redundancy-independent merging R factor value Rrim, also denoted Rmeas, for merging all intensities in this data set. sum~i~ [N~i~/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> | Rrim = ---------------------------------------------------- sum~i~ ( sum~j~ I~j~ ) I~j~ = the intensity of the jth observation of reflection i <I~i~> = the mean of the intensities of all observations of reflection i N~i~ = the redundancy (the number of times reflection i has been measured). sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct. Biol. 4, 269-275. Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst. 30, 203-205. Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
      Returns:
      FloatColumn

    • getPdbxRpimIAll

      public FloatColumn getPdbxRpimIAll()
      The precision-indicating merging R factor value Rpim, for merging all intensities in this data set. sum~i~ [1/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> | Rpim = -------------------------------------------------- sum~i~ ( sum~j~ I~j~ ) I~j~ = the intensity of the jth observation of reflection i <I~i~> = the mean of the intensities of all observations of reflection i N~i~ = the redundancy (the number of times reflection i has been measured). sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct. Biol. 4, 269-275. Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst. 30, 203-205. Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
      Returns:
      FloatColumn

    • getPdbxDOpt

      public FloatColumn getPdbxDOpt()
      The optical resolution of the data set, d(opt), is the expected minimum distance between two resolved peaks in an electron-density map. d(opt) = {2[sigma(Patt)2^ + sigma(sph)2^]}1/2^ sigma(Patt) = standard deviation of the Gaussian function fitted to the Patterson origin peak sigma(sph) = standard deviation of the Gaussian function fitted to the origin peak of the spherical interference function, representing the Fourier transform of a sphere with radius 1/dmin dmin = nominal resolution (_reflns.d_resolution_high) Ref: Vaguine, A. A., Richelle, J. & Wodak, S. J. (1999). Acta Cryst. D55, 191-205. (see also http://www.ysbl.york.ac.uk/~alexei/sfcheck.html) Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
      Returns:
      FloatColumn

    • getPdbxNumberMeasuredAll

      public IntColumn getPdbxNumberMeasuredAll()
      Total number of measured reflections.
      Returns:
      IntColumn

    • getPdbxDiffrnId

      public StrColumn getPdbxDiffrnId()
      An identifier for the diffraction data set for this set of summary statistics. Multiple diffraction data sets entered as a comma separated list.
      Returns:
      StrColumn

    • getPdbxOrdinal

      public IntColumn getPdbxOrdinal()
      An ordinal identifier for this set of reflection statistics.
      Returns:
      IntColumn

    • getPdbxCCHalf

      public FloatColumn getPdbxCCHalf()
      The Pearson's correlation coefficient expressed as a decimal value between the average intensities from randomly selected half-datasets. Ref: Karplus & Diederichs (2012), Science 336, 1030-33
      Returns:
      FloatColumn

    • getPdbxCCStar

      public FloatColumn getPdbxCCStar()
      Estimates the value of CC_true, the true correlation coefficient between the average intensities from randomly selected half-datasets. CC_star = sqrt(2*CC_half/(1+CC_half)), where both CC_star and CC_half (CC1/2) Ref: Karplus & Diederichs (2012), Science 336, 1030-33
      Returns:
      FloatColumn

    • getPdbxRSplit

      public FloatColumn getPdbxRSplit()
      R split measures the agreement between the sets of intensities created by merging odd- and even-numbered images from the overall data. Ref: T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty and H. N. Chapman (2012), J. Appl. Cryst. 45, 335-341
      Returns:
      FloatColumn

    • getPdbxRedundancyReflnsObs

      public FloatColumn getPdbxRedundancyReflnsObs()
      The redundancy in set of observed reflections.
      Returns:
      FloatColumn

    • getPdbxNumberAnomalous

      public IntColumn getPdbxNumberAnomalous()
      This item is the same as _reflns.number_obs, but applies to observed Friedel pairs only.
      Returns:
      IntColumn

    • getPdbxRrimIAllAnomalous

      public FloatColumn getPdbxRrimIAllAnomalous()
      This item is the same as _reflns.pdbx_Rrim_I_all, but applies to the observed Friedel pairs only.
      Returns:
      FloatColumn

    • getPdbxRpimIAllAnomalous

      public FloatColumn getPdbxRpimIAllAnomalous()
      This item is the same as _reflns.pdbx_Rpim_I_all, but applies only to observed Friedel pairs.
      Returns:
      FloatColumn

    • getPdbxRmergeIAnomalous

      public FloatColumn getPdbxRmergeIAnomalous()
      This item is the same as _reflns.pdbx_Rmerge_I, but applies only to observed Friedel pairs.
      Returns:
      FloatColumn