Package org.rcsb.cif.model.generated

Class PhasingMIRDer

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

      • PhasingMIRDer

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

      • PhasingMIRDer

        public PhasingMIRDer​(String name)

    • Method Detail

      • 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