Package org.rcsb.cif.schema.mm

Class PhasingMIRDerRefln

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.PhasingMIRDerRefln
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class PhasingMIRDerRefln
extends DelegatingCategory
Data items in the PHASING_MIR_DER_REFLN category record details about the calculated structure factors obtained in an MIR phasing experiment. This list may contain information from a number of different derivatives; _phasing_MIR_der_refln.der_id indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a discussion of the meaning of derivative.) It is not necessary for the data items describing the measured value of F to appear in this list, as they will be given in the PHASING_SET_REFLN category. However, these items can also be listed here for completeness.

  • Constructor Details

  • Method Details

    • createDelegate

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

    • getDerId

      public StrColumn getDerId()
      This data item is a pointer to _phasing_MIR_der.id in the PHASING_MIR_DER category.
      Returns:
      StrColumn

    • getFCalc

      public FloatColumn getFCalc()
      The calculated value of the structure factor for this derivative, in electrons.
      Returns:
      FloatColumn

    • getFCalcAu

      public FloatColumn getFCalcAu()
      The calculated value of the structure factor for this derivative, in arbitrary units.
      Returns:
      FloatColumn

    • getFMeas

      public FloatColumn getFMeas()
      The measured value of the structure factor for this derivative, in electrons.
      Returns:
      FloatColumn

    • getFMeasAu

      public FloatColumn getFMeasAu()
      The measured value of the structure factor for this derivative, in arbitrary units.
      Returns:
      FloatColumn

    • getFMeasSigma

      public FloatColumn getFMeasSigma()
      The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_refln.F_meas, in electrons.
      Returns:
      FloatColumn

    • getFMeasSigmaAu

      public FloatColumn getFMeasSigmaAu()
      The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_refln.F_meas_au, in arbitrary units.
      Returns:
      FloatColumn

    • getHLAIso

      public FloatColumn getHLAIso()
      The isomorphous Hendrickson-Lattman coefficient A~iso~ for this reflection for this derivative. -2.0 * (Fp~obs~^2^ + Fh~calc~^2^ - Fph~obs~^2^) * Fp~obs~ * cos(alphah~calc~) A~iso~ = ----------------------------------------------- E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections 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 alphah~calc~ = the calculated phase from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143.
      Returns:
      FloatColumn

    • getHLBIso

      public FloatColumn getHLBIso()
      The isomorphous Hendrickson-Lattman coefficient B~iso~ for this reflection for this derivative. -2.0 * (Fp~obs~^2^ + Fh~calc~^2^ - Fph~obs~^2^) * Fp~obs~ * sin(alphah~calc~) B~iso~ = ----------------------------------------------- E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections 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 alphah~calc~ = the phase calculated from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143.
      Returns:
      FloatColumn

    • getHLCIso

      public FloatColumn getHLCIso()
      The isomorphous Hendrickson-Lattman coefficient C~iso~ for this reflection for this derivative. -Fp~obs~^2^ * [sin(alphah~calc~)^2^ - cos(alphah~calc~)^2^] C~iso~ = ------------------------------------ E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections 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 alphah~calc~ = the phase calculated from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143.
      Returns:
      FloatColumn

    • getHLDIso

      public FloatColumn getHLDIso()
      The isomorphous Hendrickson-Lattman coefficient D~iso~ for this reflection for this derivative. -2.0 * Fp~obs~^2^ * sin(alphah~calc~)^2^ * cos(alphah~calc~)^2^ D~iso~ = ---------------------------------------- E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections 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 alphah~calc~ = the phase calculated from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143.
      Returns:
      FloatColumn

    • getIndexH

      public IntColumn getIndexH()
      Miller index h for this reflection for this derivative.
      Returns:
      IntColumn

    • getIndexK

      public IntColumn getIndexK()
      Miller index k for this reflection for this derivative.
      Returns:
      IntColumn

    • getIndexL

      public IntColumn getIndexL()
      Miller index l for this reflection for this derivative.
      Returns:
      IntColumn

    • getPhaseCalc

      public FloatColumn getPhaseCalc()
      The calculated value of the structure-factor phase based on the heavy-atom model for this derivative in degrees.
      Returns:
      FloatColumn

    • getSetId

      public StrColumn getSetId()
      This data item is a pointer to _phasing_set.id in the PHASING_SET category.
      Returns:
      StrColumn