Package org.rcsb.cif.schema.mm

Class PhasingMIRDer

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.PhasingMIRDer
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class PhasingMIRDer
extends DelegatingCategory
Data items in the PHASING_MIR_DER category record details about individual derivatives used in the phasing of the structure when methods involving isomorphous replacement are involved. A derivative in this context does not necessarily equate with a data set; for instance, the same data set could be used to one resolution limit as an isomorphous scatterer and to a different resolution (and with a different sigma cutoff) as an anomalous scatterer. These would be treated as two distinct derivatives, although both derivatives would point to the same data sets via _phasing_MIR_der.der_set_id and _phasing_MIR_der.native_set_id.

  • Constructor Details

  • Method Details

    • createDelegate

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

    • getDResHigh

      public FloatColumn getDResHigh()
      The lowest value for the interplanar spacings for the reflection data used for this derivative. This is called the highest resolution.
      Returns:
      FloatColumn

    • getDResLow

      public FloatColumn getDResLow()
      The highest value for the interplanar spacings for the reflection data used for this derivative. This is called the lowest resolution.
      Returns:
      FloatColumn

    • getDerSetId

      public StrColumn getDerSetId()
      The data set that was treated as the derivative in this experiment. This data item is a pointer to _phasing_set.id in the PHASING_SET category.
      Returns:
      StrColumn

    • getDetails

      public StrColumn getDetails()
      A description of special aspects of this derivative, its data, its solution or its use in phasing.
      Returns:
      StrColumn

    • getId

      public StrColumn getId()
      The value of _phasing_MIR_der.id must uniquely identify a record in the PHASING_MIR_DER list. Note that this item need not be a number; it can be any unique identifier.
      Returns:
      StrColumn

    • getNativeSetId

      public StrColumn getNativeSetId()
      The data set that was treated as the native in this experiment. This data item is a pointer to _phasing_set.id in the PHASING_SET category.
      Returns:
      StrColumn

    • getNumberOfSites

      public IntColumn getNumberOfSites()
      The number of heavy-atom sites in this derivative.
      Returns:
      IntColumn

    • getPowerAcentric

      public FloatColumn getPowerAcentric()
      The mean phasing power P for acentric reflections for 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
      Returns:
      FloatColumn

    • getPowerCentric

      public FloatColumn getPowerCentric()
      The mean phasing power P for centric reflections for 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
      Returns:
      FloatColumn

    • getRCullisAcentric

      public FloatColumn getRCullisAcentric()
      Residual factor R~cullis,acen~ for acentric reflections for 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. R. Soc. London Ser. A, 265, 15-38.
      Returns:
      FloatColumn

    • getRCullisAnomalous

      public FloatColumn getRCullisAnomalous()
      Residual factor R~cullis,ano~ for anomalous reflections for 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. A value less than 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 positive 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. R. Soc. London Ser. A, 265, 15-38.
      Returns:
      FloatColumn

    • getRCullisCentric

      public FloatColumn getRCullisCentric()
      Residual factor R~cullis~ for centric reflections for 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. R. Soc. London Ser. A, 265, 15-38.
      Returns:
      FloatColumn

    • getReflnsAcentric

      public IntColumn getReflnsAcentric()
      The number of acentric reflections used in phasing for this derivative.
      Returns:
      IntColumn

    • getReflnsAnomalous

      public IntColumn getReflnsAnomalous()
      The number of anomalous reflections used in phasing for this derivative.
      Returns:
      IntColumn

    • getReflnsCentric

      public IntColumn getReflnsCentric()
      The number of centric reflections used in phasing for this derivative.
      Returns:
      IntColumn

    • getReflnsCriteria

      public StrColumn getReflnsCriteria()
      Criteria used to limit the reflections used in the phasing calculations.
      Returns:
      StrColumn

    • getPdbxRKrautCentric

      public FloatColumn getPdbxRKrautCentric()
      record R_kraut obtained from centric data for each derivative.
      Returns:
      FloatColumn

    • getPdbxRKrautAcentric

      public FloatColumn getPdbxRKrautAcentric()
      record R_kraut obtained from acentric data for each derivative.
      Returns:
      FloatColumn

    • getPdbxRKraut

      public FloatColumn getPdbxRKraut()
      record R_kraut obtained from all data data for each derivative.
      Returns:
      FloatColumn

    • getPdbxLocCentric

      public FloatColumn getPdbxLocCentric()
      record lack of closure obtained from centric data for each derivative.
      Returns:
      FloatColumn

    • getPdbxLocAcentric

      public FloatColumn getPdbxLocAcentric()
      record lack of closure obtained from acentric data for each derivative.
      Returns:
      FloatColumn

    • getPdbxLoc

      public FloatColumn getPdbxLoc()
      record lack of closure obtained from all data for each derivative.
      Returns:
      FloatColumn

    • getPdbxFomCentric

      public FloatColumn getPdbxFomCentric()
      record figure of merit obtained from centric data for each derivative.
      Returns:
      FloatColumn

    • getPdbxFomAcentric

      public FloatColumn getPdbxFomAcentric()
      record figure of merit obtained from acentric data for each derivative.
      Returns:
      FloatColumn

    • getPdbxFom

      public FloatColumn getPdbxFom()
      record figure of merit obtained from all data for each derivative.
      Returns:
      FloatColumn

    • getPdbxPower

      public FloatColumn getPdbxPower()
      record phasing power for each derivative.
      Returns:
      FloatColumn

    • getPdbxRCullis

      public FloatColumn getPdbxRCullis()
      record R_cullis for each derivative.
      Returns:
      FloatColumn

    • getPdbxReflns

      public IntColumn getPdbxReflns()
      record number of reflections used for each derivative.
      Returns:
      IntColumn