Package org.rcsb.cif.model.generated

Class PdbxPhasingMR

  • All Implemented Interfaces:
    Category
    @Generated("org.rcsb.cif.generator.SchemaGenerator")
public class PdbxPhasingMR
extends BaseCategory
    Data items in the PDBX_PHASING_MR category record details about molecular replacement.

    • Constructor Detail

      • PdbxPhasingMR

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

      • PdbxPhasingMR

        public PdbxPhasingMR​(String name)

    • Method Detail

      • getEntryId

        public StrColumn getEntryId()
        The value of _pdbx_phasing_MR.entry_id identifies the data block.
        Returns:
        StrColumn

      • getMethodRotation

        public StrColumn getMethodRotation()
        The value of _pdbx_phasing_MR.method_rotation identifies the method used for rotation search. For example, the rotation method may be realspace, fastdirect, or direct. .
        Returns:
        StrColumn

      • getDResHighRotation

        public FloatColumn getDResHighRotation()
        The value of _pdbx_phasing_MR.d_res_high_rotation identifies the highest resolution used for rotation search.
        Returns:
        FloatColumn

      • getDResLowRotation

        public FloatColumn getDResLowRotation()
        The value of _pdbx_phasing_MR.d_res_low_rotation identifies the lowest resolution used for rotation search.
        Returns:
        FloatColumn

      • getSigmaFRotation

        public FloatColumn getSigmaFRotation()
        The value of _pdbx_phasing_MR.sigma_F_rotation identifies the sigma cut off of structure factor used for rotation search.
        Returns:
        FloatColumn

      • getSigmaIRotation

        public FloatColumn getSigmaIRotation()
        The value of _pdbx_phasing_MR.sigma_I_rotation identifies the sigma cut off of intensity used for rotation search.
        Returns:
        FloatColumn

      • getReflnsPercentRotation

        public FloatColumn getReflnsPercentRotation()
        The value of _pdbx_phasing_MR.reflns_percent_rotation identifies the completness of data used for rotation search.
        Returns:
        FloatColumn

      • getMethodTranslation

        public StrColumn getMethodTranslation()
        The value of _pdbx_phasing_MR.method_translation identifies the method used for translation search. For example in CNS, the translation method may be "general" or "phased" with PC refinement target using "fastf2f2" "e2e2" "e1e1" "f2f2" "f1f1" "residual" "vector". .
        Returns:
        StrColumn

      • getDResHighTranslation

        public FloatColumn getDResHighTranslation()
        The value of _pdbx_phasing_MR.d_res_high_translation identifies the highest resolution used for translation search.
        Returns:
        FloatColumn

      • getDResLowTranslation

        public FloatColumn getDResLowTranslation()
        The value of _pdbx_phasing_MR.d_res_low_translation identifies the lowest resolution used for translation search.
        Returns:
        FloatColumn

      • getSigmaFTranslation

        public FloatColumn getSigmaFTranslation()
        The value of _pdbx_phasing_MR.sigma_F_translation identifies the sigma cut off of structure factor used for translation search.
        Returns:
        FloatColumn

      • getSigmaITranslation

        public FloatColumn getSigmaITranslation()
        The value of _pdbx_phasing_MR.sigma_I_translation identifies the sigma cut off of intensity used for translation search.
        Returns:
        FloatColumn

      • getReflnsPercentTranslation

        public FloatColumn getReflnsPercentTranslation()
        The value of _pdbx_phasing_MR.reflns_percent_translation identifies the completness of data used for translation search.
        Returns:
        FloatColumn

      • getCorrelationCoeffIoToIc

        public FloatColumn getCorrelationCoeffIoToIc()
        The value of _pdbx_phasing_MR.correlation_coeff_Io_to_Ic identifies the correlation between the observed and the calculated intensity (~|F|^2) after rotation and translation.
        Returns:
        FloatColumn

      • getCorrelationCoeffFoToFc

        public FloatColumn getCorrelationCoeffFoToFc()
        The value of _pdbx_phasing_MR.correlation_coeff_Fo_to_Fc identifies the correlation between the observed and the calculated structure factor after rotation and translation.
        Returns:
        FloatColumn

      • getRFactor

        public FloatColumn getRFactor()
        The value of _pdbx_phasing_MR.R_factor identifies the R factor (defined as uasual) after rotation and translation.
        Returns:
        FloatColumn

      • getRRigidBody

        public FloatColumn getRRigidBody()
        The value of _pdbx_phasing_MR.R_rigid_body identifies the R factor for rigid body refinement after rotation and translation.(In general, rigid body refinement has to be carried out after molecular replacement.
        Returns:
        FloatColumn

      • getPacking

        public FloatColumn getPacking()
        The value of _pdbx_phasing_MR.packing identifies the packing of search model in the unit cell. Too many crystallographic contacts may indicate a bad search.
        Returns:
        FloatColumn

      • getModelDetails

        public StrColumn getModelDetails()
        The value of _pdbx_phasing_MR.model_details records the details of model used. For example, the original model can be truncated by deleting side chains, doubtful parts, using the monomer if the original model was an oligomer. The search model may be one domain of a large molecule. What is the pdb IDs.
        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

      • getDResHighFit

        public FloatColumn getDResHighFit()
        The highest resolution limit used for rigid body refinement after molecular replacement (MR) solution.
        Returns:
        FloatColumn

      • getDResLowFit

        public FloatColumn getDResLowFit()
        The lowest resolution limit used for rigid body refinement after molecular replacement (MR) solution.
        Returns:
        FloatColumn

      • getZscoreRotation

        public FloatColumn getZscoreRotation()
        It is computed by comparing the LLG values from the rotation search with LLG values for a set of random rotations. The mean and the RMS deviation from the mean are computed from the random set, then the Z-score for a search peak is defined as its LLG minus the mean, all divided by the RMS deviation. Read, R.J. (2001). "Pushing the boundaries of molecular replacement with maximum likelihood." Acta Cryst. D57, 1373-1382
        Returns:
        FloatColumn

      • getLLGainRotation

        public FloatColumn getLLGainRotation()
        The log-likelihood gain after rotation. Read, R.J. (2001). "Pushing the boundaries of molecular replacement with maximum likelihood." Acta Cryst. D57, 1373-1382
        Returns:
        FloatColumn

      • getZscoreTranslation

        public FloatColumn getZscoreTranslation()
        It is computed by comparing the LLG values from the translation search with LLG values for a set of random translations. The mean and the RMS deviation from the mean are computed from the random set, then the Z-score for a search peak is defined as its LLG minus the mean, all divided by the RMS deviation. Read, R.J. (2001). "Pushing the boundaries of molecular replacement with maximum likelihood." Acta Cryst. D57, 1373-1382
        Returns:
        FloatColumn

      • getLLGainTranslation

        public FloatColumn getLLGainTranslation()
        The log-likelihood gain after translation. Read, R.J. (2001). "Pushing the boundaries of molecular replacement with maximum likelihood." Acta Cryst. D57, 1373-1382
        Returns:
        FloatColumn