Package org.rcsb.cif.schema.mm

Class PdbxPhasingMR

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.PdbxPhasingMR
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class PdbxPhasingMR
extends DelegatingCategory
Data items in the PDBX_PHASING_MR category record details about molecular replacement.

  • Constructor Details

  • Method Details

    • createDelegate

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

    • 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