java.lang.Object

org.rcsb.cif.schema.mm.RefineLsShell

All Implemented Interfaces:: Category

@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class RefineLsShell
extends DelegatingCategory

Data items in the REFINE_LS_SHELL category record details about the results of the least-squares refinement broken down into shells of resolution.

Nested Class Summary

Nested classes/interfaces inherited from class org.rcsb.cif.schema.DelegatingCategory
DelegatingCategory.DelegatingCifCoreCategory

Nested classes/interfaces inherited from interface org.rcsb.cif.model.Category
Category.EmptyCategory
Field Summary

Fields inherited from class org.rcsb.cif.schema.DelegatingCategory
delegate
Constructor Summary

Constructors

Constructor Description

RefineLsShell(Category delegate)

Method Summary

Modifier and Type	Method	Description
`protected Column`	`createDelegate(String columnName, Column column)`
`FloatColumn`	`getDResHigh()`	The lowest value for the interplanar spacings for the reflection data in this shell.
`FloatColumn`	`getDResLow()`	The highest value for the interplanar spacings for the reflection data in this shell.
`IntColumn`	`getNumberReflnsAll()`	The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low.
`IntColumn`	`getNumberReflnsObs()`	The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion.
`IntColumn`	`getNumberReflnsRFree()`	The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e.
`IntColumn`	`getNumberReflnsRWork()`	The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e.
`FloatColumn`	`getPdbxFscFree()`	Fourier Shell Correlation (FSC) between model and observed structure factors for reflections not included in refinement.
`FloatColumn`	`getPdbxFscWork()`	Fourier Shell Correlation (FSC) between model and observed structure factors for reflections included in refinement.
`FloatColumn`	`getPdbxPhaseError()`	The average phase error for all reflections in the resolution shell.
`FloatColumn`	`getPdbxRComplete()`	The crystallographic reliability index Rcomplete for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion Ref: Luebben, J., Gruene, T., (2015).
`StrColumn`	`getPdbxRefineId()`	This data item uniquely identifies a refinement within an entry.
`IntColumn`	`getPdbxTotalNumberOfBinsUsed()`	Total number of bins used.
`FloatColumn`	`getPercentReflnsObs()`	The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits.
`FloatColumn`	`getPercentReflnsRFree()`	The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e.
`FloatColumn`	`getRedundancyReflnsAll()`	The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low to the number of crystallographically unique reflections that satisfy the same limits.
`FloatColumn`	`getRedundancyReflnsObs()`	The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion to the number of crystallographically unique reflections that satisfy the same limits.
`FloatColumn`	`getRFactorAll()`	Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low.
`FloatColumn`	`getRFactorObs()`	Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion.
`FloatColumn`	`getRFactorRFree()`	Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e.
`FloatColumn`	`getRFactorRFreeError()`	The estimated error in _refine_ls_shell.R_factor_R_free.
`FloatColumn`	`getRFactorRWork()`	Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e.
`FloatColumn`	`getWRFactorAll()`	Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low.
`FloatColumn`	`getWRFactorObs()`	Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion.
`FloatColumn`	`getWRFactorRFree()`	Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e.
`FloatColumn`	`getWRFactorRWork()`	Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e.

Methods inherited from class org.rcsb.cif.schema.DelegatingCategory

getCategoryName, getColumn, getColumns, getRowCount

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.rcsb.cif.model.Category

columns, getColumn, isDefined

Constructor Details
- RefineLsShell
  
  public RefineLsShell(Category delegate)
Method Details
- createDelegate
  
  protected Column createDelegate(String columnName, Column column)
  
  Overrides:
  
  createDelegate in class DelegatingCategory
- getPdbxRefineId
  
  public StrColumn getPdbxRefineId()
  
  This data item uniquely identifies a refinement within an entry. _refine_ls_shell.pdbx_refine_id can be used to distinguish the results of joint refinements.
  
  Returns:
  
  StrColumn
- getDResHigh
  
  public FloatColumn getDResHigh()
  
  The lowest value for the interplanar spacings for the reflection data in this shell. This is called the highest resolution.
  
  Returns:
  
  FloatColumn
- getDResLow
  
  public FloatColumn getDResLow()
  
  The highest value for the interplanar spacings for the reflection data in this shell. This is called the lowest resolution.
  
  Returns:
  
  FloatColumn
- getNumberReflnsAll
  
  public IntColumn getNumberReflnsAll()
  
  The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low.
  
  Returns:
  
  IntColumn
- getNumberReflnsObs
  
  public IntColumn getNumberReflnsObs()
  
  The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion.
  
  Returns:
  
  IntColumn
- getNumberReflnsRFree
  
  public IntColumn getNumberReflnsRFree()
  
  The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details.
  
  Returns:
  
  IntColumn
- getNumberReflnsRWork
  
  public IntColumn getNumberReflnsRWork()
  
  The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details.
  
  Returns:
  
  IntColumn
- getPercentReflnsObs
  
  public FloatColumn getPercentReflnsObs()
  
  The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits.
  
  Returns:
  
  FloatColumn
- getPercentReflnsRFree
  
  public FloatColumn getPercentReflnsRFree()
  
  The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor, expressed as a percentage of the number of geometrically observable reflections that satisfy the reflection limits.
  
  Returns:
  
  FloatColumn
- getRFactorAll
  
  public FloatColumn getRFactorAll()
  
  Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections
  
  Returns:
  
  FloatColumn
- getRFactorObs
  
  public FloatColumn getRFactorObs()
  
  Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections
  
  Returns:
  
  FloatColumn
- getRFactorRFree
  
  public FloatColumn getRFactorRFree()
  
  Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections
  
  Returns:
  
  FloatColumn
- getRFactorRFreeError
  
  public FloatColumn getRFactorRFreeError()
  
  The estimated error in _refine_ls_shell.R_factor_R_free. The method used to estimate the error is described in the item _refine.ls_R_factor_R_free_error_details.
  
  Returns:
  
  FloatColumn
- getRFactorRWork
  
  public FloatColumn getRFactorRWork()
  
  Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections
  
  Returns:
  
  FloatColumn
- getRedundancyReflnsAll
  
  public FloatColumn getRedundancyReflnsAll()
  
  The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low to the number of crystallographically unique reflections that satisfy the same limits.
  
  Returns:
  
  FloatColumn
- getRedundancyReflnsObs
  
  public FloatColumn getRedundancyReflnsObs()
  
  The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion to the number of crystallographically unique reflections that satisfy the same limits.
  
  Returns:
  
  FloatColumn
- getWRFactorAll
  
  public FloatColumn getWRFactorAll()
  
  Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections
  
  Returns:
  
  FloatColumn
- getWRFactorObs
  
  public FloatColumn getWRFactorObs()
  
  Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections
  
  Returns:
  
  FloatColumn
- getWRFactorRFree
  
  public FloatColumn getWRFactorRFree()
  
  Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections
  
  Returns:
  
  FloatColumn
- getWRFactorRWork
  
  public FloatColumn getWRFactorRWork()
  
  Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections
  
  Returns:
  
  FloatColumn
- getPdbxRComplete
  
  public FloatColumn getPdbxRComplete()
  
  The crystallographic reliability index Rcomplete for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion Ref: Luebben, J., Gruene, T., (2015). Proc.Nat.Acad.Sci. 112(29) 8999-9003
  
  Returns:
  
  FloatColumn
- getPdbxTotalNumberOfBinsUsed
  
  public IntColumn getPdbxTotalNumberOfBinsUsed()
  
  Total number of bins used.
  
  Returns:
  
  IntColumn
- getPdbxPhaseError
  
  public FloatColumn getPdbxPhaseError()
  
  The average phase error for all reflections in the resolution shell.
  
  Returns:
  
  FloatColumn
- getPdbxFscWork
  
  public FloatColumn getPdbxFscWork()
  
  Fourier Shell Correlation (FSC) between model and observed structure factors for reflections included in refinement. FSC is a measure of the agreement between observed and calculated structure factors as complex numbers. (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~))) FSC~work~ = -------------------------------------- (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^ |F~o~| = amplitude of observed structure factor |F~c~| = amplitude of calculated structure factor phi~o~ = phase of observed structure factor phi~c~ = phase of calculated structure factor fom = figure of merit of the experimental phases. Summation is carried over all working reflections in the resolution shell. Ref: Rosenthal P.B., Henderson R. "Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology. 2003;333(4):721-745, equation (A6).
  
  Returns:
  
  FloatColumn
- getPdbxFscFree
  
  public FloatColumn getPdbxFscFree()
  
  Fourier Shell Correlation (FSC) between model and observed structure factors for reflections not included in refinement. FSC is a measure of the agreement between observed and calculated structure factors as complex numbers. (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~))) FSC~free~ = -------------------------------------- (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^ |F~o~| = amplitude of observed structure factor |F~c~| = amplitude of calculated structure factor phi~o~ = phase of observed structure factor phi~c~ = phase of calculated structure factor fom = figure of merit of the experimental phases. Summation is carried over all free reflections in the resolution shell. Ref: Rosenthal P.B., Henderson R. "Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology. 2003;333(4):721-745, equation (A6).
  
  Returns:
  
  FloatColumn

Class RefineLsShell

Nested Class Summary

Nested classes/interfaces inherited from class org.rcsb.cif.schema.DelegatingCategory

Nested classes/interfaces inherited from interface org.rcsb.cif.model.Category

Field Summary

Fields inherited from class org.rcsb.cif.schema.DelegatingCategory

Constructor Summary

Method Summary

Methods inherited from class org.rcsb.cif.schema.DelegatingCategory

Methods inherited from class java.lang.Object

Methods inherited from interface org.rcsb.cif.model.Category

Constructor Details

Method Details