Package org.rcsb.cif.schema.mm

Class RefineAnalyze

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.RefineAnalyze
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class RefineAnalyze
extends DelegatingCategory
Data items in the REFINE_ANALYZE category record details about the refined structure that are often used to analyze the refinement and assess its quality. A given computer program may or may not produce values corresponding to these data names.

  • Constructor Details

  • Method Details

    • createDelegate

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

    • getEntryId

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

    • getPdbxRefineId

      public StrColumn getPdbxRefineId()
      This data item uniquely identifies a refinement within an entry. _refine_analyze.pdbx_refine_id can be used to distinguish the results of joint refinements.
      Returns:
      StrColumn

    • getLuzzatiCoordinateErrorFree

      public FloatColumn getLuzzatiCoordinateErrorFree()
      The estimated coordinate error obtained from the plot of the R value versus sin(theta)/lambda for the reflections treated as a test set during refinement. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810.
      Returns:
      FloatColumn

    • getLuzzatiCoordinateErrorObs

      public FloatColumn getLuzzatiCoordinateErrorObs()
      The estimated coordinate error obtained from the plot of the R value versus sin(theta)/lambda for reflections classified as observed. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810.
      Returns:
      FloatColumn

    • getLuzzatiDResLowFree

      public FloatColumn getLuzzatiDResLowFree()
      The value of the low-resolution cutoff used in constructing the Luzzati plot for reflections treated as a test set during refinement. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810.
      Returns:
      FloatColumn

    • getLuzzatiDResLowObs

      public FloatColumn getLuzzatiDResLowObs()
      The value of the low-resolution cutoff used in constructing the Luzzati plot for reflections classified as observed. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810.
      Returns:
      FloatColumn

    • getLuzzatiSigmaAFree

      public FloatColumn getLuzzatiSigmaAFree()
      The value of sigma~a~ used in constructing the Luzzati plot for the reflections treated as a test set during refinement. Details of the estimation of sigma~a~ can be specified in _refine_analyze.Luzzati_sigma_a_free_details. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810.
      Returns:
      FloatColumn

    • getLuzzatiSigmaAFreeDetails

      public StrColumn getLuzzatiSigmaAFreeDetails()
      Details of the estimation of sigma~a~ for the reflections treated as a test set during refinement. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810.
      Returns:
      StrColumn

    • getLuzzatiSigmaAObs

      public FloatColumn getLuzzatiSigmaAObs()
      The value of sigma~a~ used in constructing the Luzzati plot for reflections classified as observed. Details of the estimation of sigma~a~ can be specified in _refine_analyze.Luzzati_sigma_a_obs_details. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810.
      Returns:
      FloatColumn

    • getLuzzatiSigmaAObsDetails

      public StrColumn getLuzzatiSigmaAObsDetails()
      Special aspects of the estimation of sigma~a~ for the reflections classified as observed. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810.
      Returns:
      StrColumn

    • getNumberDisorderedResidues

      public FloatColumn getNumberDisorderedResidues()
      The number of discretely disordered residues in the refined model.
      Returns:
      FloatColumn

    • getOccupancySumHydrogen

      public FloatColumn getOccupancySumHydrogen()
      The sum of the occupancies of the hydrogen atoms in the refined model.
      Returns:
      FloatColumn

    • getOccupancySumNonHydrogen

      public FloatColumn getOccupancySumNonHydrogen()
      The sum of the occupancies of the non-hydrogen atoms in the refined model.
      Returns:
      FloatColumn

    • getRGDResHigh

      public FloatColumn getRGDResHigh()
      The value of the high-resolution cutoff in angstroms used in the 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.
      Returns:
      FloatColumn

    • getRGDResLow

      public FloatColumn getRGDResLow()
      The value of the low-resolution cutoff in angstroms used in the 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.
      Returns:
      FloatColumn

    • getRGFree

      public FloatColumn getRGFree()
      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 amplitudes 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. 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.
      Returns:
      FloatColumn

    • getRGWork

      public FloatColumn getRGWork()
      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 is 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 amplitudes 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. 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.
      Returns:
      FloatColumn

    • getRGFreeWorkRatio

      public FloatColumn getRGFreeWorkRatio()
      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 the data and the 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 to RGwork with only random uncorrelated errors at convergence depends only on the number of reflections and the number of parameters according to sqrt[(f + m) / (f - m) ] where f = the number of included structure amplitudes and target distances, and m = the 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 the refinement, the RG ratio requires a term for the contribution to the minimized residual at convergence, D~restr~, due to those restraints: D~restr~ = r - sum [w_i . (a_i)^t . (H)^-1 a_i] where r is the number of geometrical, displacement-parameter 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 + D~restr~))/ (f - (m - r + D~restr~)) ] There is no data name for the expected value of RGfree/RGwork yet. Ref: Tickle, I. J., Laskowski, R. A. & Moss, D. S. (1998). Acta Cryst. D54, 547-557.
      Returns:
      FloatColumn

    • getPdbxLuzzatiDResHighObs

      public FloatColumn getPdbxLuzzatiDResHighObs()
      record the high resolution for calculating Luzzati statistics.
      Returns:
      FloatColumn