Package org.rcsb.cif.model.generated

Class PhasingMIRDerRefln

  • All Implemented Interfaces:
    Category
    @Generated("org.rcsb.cif.generator.SchemaGenerator")
public class PhasingMIRDerRefln
extends BaseCategory
    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 Detail

      • PhasingMIRDerRefln

        public PhasingMIRDerRefln​(String name,
                          int rowCount,
                          Object[] encodedColumns)

      • PhasingMIRDerRefln

        public PhasingMIRDerRefln​(String name)

    • Method Detail

      • 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