# 「RELIONの定義済みラベル」の版間の差分

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(ページの作成:「* RELION v3.0.5の以下コマンドの出力です。 $ relion_refine --print_metadata_labels * 読みにくいのでそのうち表にします。 * フォーマッ...」) |
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(同じ利用者による、間の1版が非表示) | |||

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− | * RELION v3.0. | + | * RELION v3.0.5の以下コマンドの出力を表にしました。 |

$ relion_refine --print_metadata_labels | $ relion_refine --print_metadata_labels | ||

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− | + | {| class="wikitable" style="width:100%" | |

− | + | |+RELION メタデータラベル一覧表 (v3.0.5) | |

− | + | ! style="width:20%" | パラメータ名 | |

− | rlnAccumMotionEarly | + | ! style="width:5%" | データ型 |

− | + | ! 説明 | |

− | rlnAccumMotionLate | + | |- |

− | + | | rlnAccumMotionEarly | |

− | rlnAccumMotionTotal | + | | double |

− | + | | Accumulated global motion during the first frames of the movie (in A) | |

− | rlnAccuracyRotations | + | |- |

− | + | | rlnAccumMotionLate | |

− | rlnAccuracyTranslations | + | | double |

− | + | | Accumulated global motion during the last frames of the movie (in A) | |

− | rlnAdaptiveOversampleFraction | + | |- |

− | + | | rlnAccumMotionTotal | |

− | rlnAdaptiveOversampleOrder | + | | double |

− | + | | Accumulated global motion during the entire movie (in A) | |

− | rlnAmplitudeContrast | + | |- |

− | + | | rlnAccuracyRotations | |

− | rlnAmplitudeCorrelationMaskedMaps | + | | double |

− | + | | Estimated accuracy (in degrees) with which rotations can be assigned | |

− | rlnAmplitudeCorrelationUnmaskedMaps | + | |- |

− | + | | rlnAccuracyTranslations | |

− | rlnAnglePsi | + | | double |

− | + | | Estimated accuracy (in pixels) with which translations can be assigned | |

− | rlnAnglePsiFlipRatio | + | |- |

− | + | | rlnAdaptiveOversampleFraction | |

− | rlnAnglePsiPrior | + | | double |

− | + | | Fraction of the weights that will be oversampled in a second pass of the adaptive oversampling strategy | |

− | rlnAngleRot | + | |- |

− | + | | rlnAdaptiveOversampleOrder | |

− | rlnAngleRotPrior | + | | int |

− | + | | Order of the adaptive oversampling (0=no oversampling, 1= 2x oversampling; 2= 4x oversampling, etc) | |

− | rlnAngleTilt | + | |- |

− | + | | rlnAmplitudeContrast | |

− | rlnAngleTiltPrior | + | | double |

− | + | | Amplitude contrast (as a fraction, i.e. 10% = 0.1) | |

− | rlnAngstromResolution | + | |- |

− | + | | rlnAmplitudeCorrelationMaskedMaps | |

− | rlnAreaId | + | | double |

− | + | | Correlation coefficient between amplitudes in Fourier shells of masked maps | |

− | rlnAreaName | + | |- |

− | + | | rlnAmplitudeCorrelationUnmaskedMaps | |

− | rlnAutoLocalSearchesHealpixOrder | + | | double |

− | + | | Correlation coefficient between amplitudes in Fourier shells of unmasked maps | |

− | rlnAutopickFigureOfMerit | + | |- |

− | + | | rlnAnglePsi | |

− | rlnAvailableMemory | + | | double |

− | + | | Third Euler, or in-plane angle (psi, in degrees) | |

− | rlnAverageNrOfFrames | + | |- |

− | + | | rlnAnglePsiFlipRatio | |

− | rlnAveragePmax | + | | double |

− | + | | Flip ratio of bimodal psi prior (0~0.5, 0 means an ordinary prior, 0.5 means a perfect bimodal prior) | |

− | rlnAverageValue | + | |- |

− | + | | rlnAnglePsiPrior | |

− | rlnBeamTiltClass | + | | double |

− | + | | Center of the prior (in degrees) on the third Euler angle (psi) | |

− | rlnBeamTiltX | + | |- |

− | + | | rlnAngleRot | |

− | rlnBeamTiltY | + | | double |

− | + | | First Euler angle (rot, in degrees) | |

− | rlnBestResolutionThusFar | + | |- |

− | + | | rlnAngleRotPrior | |

− | rlnBfactorUsedForSharpening | + | | double |

− | + | | Center of the prior (in degrees) on the first Euler angle (rot) | |

− | rlnBodyKeepFixed | + | |- |

− | + | | rlnAngleTilt | |

− | rlnBodyMaskName | + | | double |

− | + | | Second Euler angle (tilt, in degrees) | |

− | rlnBodyReferenceName | + | |- |

− | + | | rlnAngleTiltPrior | |

− | rlnBodyRotateDirectionX | + | | double |

− | + | | Center of the prior (in degrees) on the second Euler angle (tilt) | |

− | rlnBodyRotateDirectionY | + | |- |

− | + | | rlnAngstromResolution | |

− | rlnBodyRotateDirectionZ | + | | double |

− | + | | Resolution (in Angstroms) | |

− | rlnBodyRotateRelativeTo | + | |- |

− | + | | rlnAreaId | |

− | rlnBodySigmaAngles | + | | int |

− | + | | ID (i.e. a unique number) of an area (i.e. field-of-view) | |

− | rlnBodySigmaOffset | + | |- |

− | + | | rlnAreaName | |

− | rlnBodySigmaPsi | + | | string |

− | + | | Name of an area (i.e. field-of-view) | |

− | rlnBodySigmaRot | + | |- |

− | + | | rlnAutoLocalSearchesHealpixOrder | |

− | rlnBodySigmaTilt | + | | int |

− | + | | Healpix order (before oversampling) from which autosampling procedure will use local angular searches | |

− | rlnBodyStarFile | + | |- |

− | + | | rlnAutopickFigureOfMerit | |

− | rlnChangesOptimalClasses | + | | double |

− | + | | Autopicking FOM for a particle | |

− | rlnChangesOptimalOffsets | + | |- |

− | + | | rlnAvailableMemory | |

− | rlnChangesOptimalOrientations | + | | double |

− | + | | Available memory per computing node (i.e. per MPI-process) | |

− | rlnChromaticAberration | + | |- |

− | + | | rlnAverageNrOfFrames | |

− | rlnClassDistribution | + | | int |

− | + | | Number of movie frames that one averages over upon extraction of movie-particles | |

− | rlnClassNumber | + | |- |

− | + | | rlnAveragePmax | |

− | rlnClassPriorOffsetX | + | | double |

− | + | | Average value (over all images) of the maxima of the probability distributions | |

− | rlnClassPriorOffsetY | + | |- |

− | + | | rlnAverageValue | |

− | rlnCoarseImageSize | + | | double |

− | + | | Average value for the pixels in an image | |

− | rlnComment | + | |- |

− | + | | rlnBeamTiltClass | |

− | rlnConvergenceCone | + | | int |

− | + | | Beam-tilt class of a particle | |

− | rlnCoordinateX | + | |- |

− | + | | rlnBeamTiltX | |

− | rlnCoordinateY | + | | double |

− | + | | Beam tilt in the X-direction (in mrad) | |

− | rlnCoordinateZ | + | |- |

− | + | | rlnBeamTiltY | |

− | rlnCorrectedFourierShellCorrelationPhaseRandomizedMaskedMaps | + | | double |

− | + | | Beam tilt in the Y-direction (in mrad) | |

− | rlnCorrelationFitGuinierPlot | + | |- |

− | + | | rlnBestResolutionThusFar | |

− | rlnCtfAstigmatism | + | | double |

− | + | | The highest resolution that has been obtained in this optimization thus far | |

− | rlnCtfBfactor | + | |- |

− | + | | rlnBfactorUsedForSharpening | |

− | rlnCtfDataAreCtfPremultiplied | + | | double |

− | + | | Applied B-factor in the sharpening of the map | |

− | rlnCtfDataArePhaseFlipped | + | |- |

− | + | | rlnBodyKeepFixed | |

− | rlnCtfFigureOfMerit | + | | int |

− | + | | Flag to indicate whether to keep a body fixed (value 1) or keep on refining it (0) | |

− | rlnCtfImage | + | |- |

− | + | | rlnBodyMaskName | |

− | rlnCtfMaxResolution | + | | string |

− | + | | Name of an image that contains a [0,1] body mask for multi-body refinement | |

− | rlnCtfScalefactor | + | |- |

− | + | | rlnBodyReferenceName | |

− | rlnCtfValidationScore | + | | string |

− | + | | Name of an image that contains the initial reference for one body of a multi-body refinement | |

− | rlnCtfValue | + | |- |

− | + | | rlnBodyRotateDirectionX | |

− | rlnCurrentImageSize | + | | double |

− | + | | X-component of axis around which to rotate this body | |

− | rlnCurrentIteration | + | |- |

− | + | | rlnBodyRotateDirectionY | |

− | rlnCurrentResolution | + | | double |

− | + | | Y-component of axis around which to rotate this body | |

− | rlnDataDimensionality | + | |- |

− | + | | rlnBodyRotateDirectionZ | |

− | rlnDataType | + | | double |

− | + | | Z-component of axis around which to rotate this body | |

− | rlnDefocusAngle | + | |- |

− | + | | rlnBodyRotateRelativeTo | |

− | rlnDefocusU | + | | int |

− | + | | Number of the body relative to which this body rotates (if negative, use rlnBodyRotateDirectionXYZ) | |

− | rlnDefocusV | + | |- |

− | + | | rlnBodySigmaAngles | |

− | rlnDetectorPixelSize | + | | double |

− | + | | Width of prior on all three Euler angles of a body in multibody refinement (in degrees) | |

− | rlnDiff2RandomHalves | + | |- |

− | + | | rlnBodySigmaOffset | |

− | rlnDifferentialPhaseResidualMaskedMaps | + | | double |

− | + | | Width of prior on origin offsets of a body in multibody refinement (in pixels) | |

− | rlnDifferentialPhaseResidualUnmaskedMaps | + | |- |

− | + | | rlnBodySigmaPsi | |

− | rlnDoAutoRefine | + | | double |

− | + | | Width of prior on psi angles of a body in multibody refinement (in degrees) | |

− | rlnDoCorrectCtf | + | |- |

− | + | | rlnBodySigmaRot | |

− | rlnDoCorrectMagnification | + | | double |

− | + | | Width of prior on rot angles of a body in multibody refinement (in degrees) | |

− | rlnDoCorrectNorm | + | |- |

− | + | | rlnBodySigmaTilt | |

− | rlnDoCorrectScale | + | | double |

− | + | | Width of prior on tilt angles of a body in multibody refinement (in degrees) | |

− | rlnDoFastSubsetOptimisation | + | |- |

− | + | | rlnBodyStarFile | |

− | rlnDoHelicalRefine | + | | string |

− | + | | Name of STAR file with body masks and metadata | |

− | rlnDoIgnoreCtfUntilFirstPeak | + | |- |

− | + | | rlnChangesOptimalClasses | |

− | rlnDoMapEstimation | + | | double |

− | + | | The number of particles that changed their optimal clsas assignment in the last iteration | |

− | rlnDoOnlyFlipCtfPhases | + | |- |

− | + | | rlnChangesOptimalOffsets | |

− | rlnDoRealignMovies | + | | double |

− | + | | The average change in optimal translation in the last iteration (in pixels) | |

− | rlnDoSkipAlign | + | |- |

− | + | | rlnChangesOptimalOrientations | |

− | rlnDoSkipRotate | + | | double |

− | + | | The average change in optimal orientation in the last iteration (in degrees) | |

− | rlnDoSolventFlattening | + | |- |

− | + | | rlnChromaticAberration | |

− | rlnDoSolventFscCorrection | + | | double |

− | + | | Chromatic aberration (in millimeters) | |

− | rlnDoSplitRandomHalves | + | |- |

− | + | | rlnClassDistribution | |

− | rlnDoStochasticGradientDescent | + | | double |

− | + | | Probability Density Function of the different classes (i.e. fraction of images assigned to each class) | |

− | rlnDoZeroMask | + | |- |

− | + | | rlnClassNumber | |

− | rlnEnabled | + | | int |

− | + | | Class number for which a particle has its highest probability | |

− | rlnEnergyLoss | + | |- |

− | + | | rlnClassPriorOffsetX | |

− | rlnEstimatedResolution | + | | double |

− | + | | Prior in the X-offset for a class (in pixels) | |

− | rlnExperimentalDataStarFile | + | |- |

− | + | | rlnClassPriorOffsetY | |

− | rlnFinalResolution | + | | double |

− | + | | Prior in the Y-offset for a class (in pixels) | |

− | rlnFittedInterceptGuinierPlot | + | |- |

− | + | | rlnCoarseImageSize | |

− | rlnFittedSlopeGuinierPlot | + | | int |

− | + | | Current size of the images to be used in the first pass of the adaptive oversampling strategy (may be smaller than the original image size) | |

− | rlnFixSigmaNoiseEstimates | + | |- |

− | + | | rlnComment | |

− | rlnFixSigmaOffsetEstimates | + | | string |

− | + | | A metadata comment (This is treated in a special way) | |

− | rlnFixTauEstimates | + | |- |

− | + | | rlnConvergenceCone | |

− | rlnFourierCompleteness | + | | double |

− | + | | Convergence cone (in mrad) | |

− | rlnFourierShellCorrelation | + | |- |

− | + | | rlnCoordinateX | |

− | rlnFourierShellCorrelationCorrected | + | | double |

− | + | | X-Position of an image in a micrograph (in pixels) | |

− | rlnFourierShellCorrelationMaskedMaps | + | |- |

− | + | | rlnCoordinateY | |

− | rlnFourierShellCorrelationUnmaskedMaps | + | | double |

− | + | | Y-Position of an image in a micrograph (in pixels) | |

− | rlnFourierSpaceInterpolator | + | |- |

− | + | | rlnCoordinateZ | |

− | rlnGoldStandardFsc | + | | double |

− | + | | Z-Position of an image in a 3D micrograph, i.e. tomogram (in pixels) | |

− | rlnGroupName | + | |- |

− | + | | rlnCorrectedFourierShellCorrelationPhaseRandomizedMaskedMaps | |

− | rlnGroupNrParticles | + | | double |

− | + | | FSC value after masking of the randomized-phases maps | |

− | rlnGroupNumber | + | |- |

− | + | | rlnCorrelationFitGuinierPlot | |

− | rlnGroupScaleCorrection | + | | double |

− | + | | The correlation coefficient of the fitted line through the Guinier-plot | |

− | rlnHasConverged | + | |- |

− | + | | rlnCtfAstigmatism | |

− | rlnHasHighFscAtResolLimit | + | | double |

− | + | | Absolute value of the difference between defocus in U- and V-direction (in A) | |

− | rlnHasLargeSizeIncreaseIterationsAgo | + | |- |

− | + | | rlnCtfBfactor | |

− | rlnHealpixOrder | + | | double |

− | + | | B-factor (in A^2) that describes CTF power spectrum fall-off | |

− | rlnHelicalCentralProportion | + | |- |

− | + | | rlnCtfDataAreCtfPremultiplied | |

− | rlnHelicalKeepTiltPriorFixed | + | | bool |

− | + | | Flag to indicate that the input images have been premultiplied with their CTF | |

− | rlnHelicalMaskTubeInnerDiameter | + | |- |

− | + | | rlnCtfDataArePhaseFlipped | |

− | rlnHelicalMaskTubeOuterDiameter | + | | bool |

− | + | | Flag to indicate that the input images have been phase-flipped | |

− | rlnHelicalOffsetStep | + | |- |

− | + | | rlnCtfFigureOfMerit | |

− | rlnHelicalRise | + | | double |

− | + | | Figure of merit for the fit of the CTF (not used inside relion_refine) | |

− | rlnHelicalRiseInitial | + | |- |

− | + | | rlnCtfImage | |

− | rlnHelicalRiseInitialStep | + | | string |

− | + | | Name of an image with all CTF values | |

− | rlnHelicalRiseMax | + | |- |

− | + | | rlnCtfMaxResolution | |

− | rlnHelicalRiseMin | + | | double |

− | + | | Estimated maximum resolution (in A) of significant CTF Thon rings | |

− | rlnHelicalSigmaDistance | + | |- |

− | + | | rlnCtfScalefactor | |

− | rlnHelicalSymmetryLocalRefinement | + | | double |

− | + | | Linear scale-factor on the CTF (values between 0 and 1) | |

− | rlnHelicalTrackLength | + | |- |

− | + | | rlnCtfValidationScore | |

− | rlnHelicalTubeID | + | | double |

− | + | | Gctf-based validation score for the quality of the CTF fit | |

− | rlnHelicalTubePitch | + | |- |

− | + | | rlnCtfValue | |

− | rlnHelicalTwist | + | | double |

− | + | | Value of the Contrast Transfer Function | |

− | rlnHelicalTwistInitial | + | |- |

− | + | | rlnCurrentImageSize | |

− | rlnHelicalTwistInitialStep | + | | int |

− | + | | Current size of the images used in the refinement | |

− | rlnHelicalTwistMax | + | |- |

− | + | | rlnCurrentIteration | |

− | rlnHelicalTwistMin | + | | int |

− | + | | The number of the current iteration | |

− | rlnHighresLimitExpectation | + | |- |

− | + | | rlnCurrentResolution | |

− | rlnHighresLimitSGD | + | | double |

− | + | | Current resolution where SSNR^MAP drops below 1 (in 1/Angstroms) | |

− | rlnIgnoreHelicalSymmetry | + | |- |

− | + | | rlnDataDimensionality | |

− | rlnImageDimensionality | + | | int |

− | + | | Dimensionality of the data (2D/3D) | |

− | rlnImageId | + | |- |

− | + | | rlnDataType | |

− | rlnImageName | + | | int |

− | + | | Type of data stored in an image (e.g. int, RFLOAT etc) | |

− | rlnImageOriginalName | + | |- |

− | + | | rlnDefocusAngle | |

− | rlnImageSize | + | | double |

− | + | | Angle between X and defocus U direction (in degrees) | |

− | rlnImageSizeX | + | |- |

− | + | | rlnDefocusU | |

− | rlnImageSizeY | + | | double |

− | + | | Defocus in U-direction (in Angstroms, positive values for underfocus) | |

− | rlnImageSizeZ | + | |- |

− | + | | rlnDefocusV | |

− | rlnImageWeight | + | | double |

− | + | | Defocus in V-direction (in Angstroms, positive values for underfocus) | |

− | rlnIncrementImageSize | + | |- |

− | + | | rlnDetectorPixelSize | |

− | rlnIs3DSampling | + | | double |

− | + | | Pixel size of the detector (in micrometers) | |

− | rlnIs3DTranslationalSampling | + | |- |

− | + | | rlnDiff2RandomHalves | |

− | rlnIsFlip | + | | double |

− | + | | Power of the differences between two independent reconstructions from random halves of the data | |

− | rlnIsHelix | + | |- |

− | + | | rlnDifferentialPhaseResidualMaskedMaps | |

− | rlnJoinHalvesUntilThisResolution | + | | double |

− | + | | Differential Phase Residual in Fourier shells of masked maps | |

− | rlnKullbackLeiblerDivergence | + | |- |

− | + | | rlnDifferentialPhaseResidualUnmaskedMaps | |

− | rlnKurtosisExcessValue | + | | double |

− | + | | Differential Phase Residual in Fourier shells of unmasked maps | |

− | rlnLensStability | + | |- |

− | + | | rlnDoAutoRefine | |

− | rlnLocalSymmetryFile | + | | bool |

− | + | | Flag to indicate that 3D auto-refine procedure is being used | |

− | rlnLogAmplitudesIntercept | + | |- |

− | + | | rlnDoCorrectCtf | |

− | rlnLogAmplitudesMTFCorrected | + | | bool |

− | + | | Flag to indicate that CTF-correction should be performed | |

− | rlnLogAmplitudesOriginal | + | |- |

− | + | | rlnDoCorrectMagnification | |

− | rlnLogAmplitudesSharpened | + | | bool |

− | + | | Flag to indicate that (per-group) magnification correction should be performed | |

− | rlnLogAmplitudesWeighted | + | |- |

− | + | | rlnDoCorrectNorm | |

− | rlnLogLikeliContribution | + | | bool |

− | + | | Flag to indicate that (per-image) normalisation-error correction should be performed | |

− | rlnLogLikelihood | + | |- |

− | + | | rlnDoCorrectScale | |

− | rlnLongitudinalDisplacement | + | | bool |

− | + | | Flag to indicate that internal (per-group) intensity-scale correction should be performed | |

− | rlnMagnification | + | |- |

− | + | | rlnDoFastSubsetOptimisation | |

− | rlnMagnificationCorrection | + | | bool |

− | + | | Use subsets of the data in the earlier iterations to speed up convergence | |

− | rlnMagnificationSearchRange | + | |- |

− | + | | rlnDoHelicalRefine | |

− | rlnMagnificationSearchStep | + | | bool |

− | + | | Flag to indicate that helical refinement should be performed | |

− | rlnMaskName | + | |- |

− | + | | rlnDoIgnoreCtfUntilFirstPeak | |

− | rlnMatrix_1_1 | + | | bool |

− | + | | Flag to indicate that the CTFs should be ignored until their first peak | |

− | rlnMatrix_1_2 | + | |- |

− | + | | rlnDoMapEstimation | |

− | rlnMatrix_1_3 | + | | bool |

− | + | | Flag to indicate that MAP estimation should be performed (otherwise ML estimation) | |

− | rlnMatrix_2_1 | + | |- |

− | + | | rlnDoOnlyFlipCtfPhases | |

− | rlnMatrix_2_2 | + | | bool |

− | + | | Flag to indicate that CTF-correction should only comprise phase-flipping | |

− | rlnMatrix_2_3 | + | |- |

− | + | | rlnDoRealignMovies | |

− | rlnMatrix_3_1 | + | | bool |

− | + | | Flag to indicate that individual frames of movies are being re-aligned | |

− | rlnMatrix_3_2 | + | |- |

− | + | | rlnDoSkipAlign | |

− | rlnMatrix_3_3 | + | | bool |

− | + | | Flag to indicate that orientational (i.e. rotational and translational) searches will be omitted from the refinement, only marginalisation over classes will take place | |

− | rlnMaxNumberOfPooledParticles | + | |- |

− | + | | rlnDoSkipRotate | |

− | rlnMaxValueProbDistribution | + | | bool |

− | + | | Flag to indicate that rotational searches will be omitted from the refinement, only marginalisation over classes and translations will take place | |

− | rlnMaximumCoarseImageSize | + | |- |

− | + | | rlnDoSolventFlattening | |

− | rlnMaximumValue | + | | bool |

− | + | | Flag to indicate that the references should be masked to set their solvent areas to a constant density | |

− | rlnMicrographBinning | + | |- |

− | + | | rlnDoSolventFscCorrection | |

− | rlnMicrographDefectFile | + | | bool |

− | + | | Flag to indicate that the FSCs should be solvent-corrected during refinement | |

− | rlnMicrographDoseRate | + | |- |

− | + | | rlnDoSplitRandomHalves | |

− | rlnMicrographEndFrame | + | | bool |

− | + | | Flag to indicate that the data should be split into two completely separate, random halves | |

− | rlnMicrographFrameNumber | + | |- |

− | + | | rlnDoStochasticGradientDescent | |

− | rlnMicrographGainName | + | | bool |

− | + | | Flag to indicate that SGD-optimisation should be performed (otherwise expectation maximisation) | |

− | rlnMicrographId | + | |- |

− | + | | rlnDoZeroMask | |

− | rlnMicrographMetadata | + | | bool |

− | + | | Flag to indicate that the surrounding solvent area in the experimental particles will be masked to zeros (by default random noise will be used | |

− | rlnMicrographMovieName | + | |- |

− | + | | rlnEnabled | |

− | rlnMicrographName | + | | bool |

− | + | | Not used in RELION, only included for backward compatibility with XMIPP selfiles | |

− | rlnMicrographNameNoDW | + | |- |

− | + | | rlnEnergyLoss | |

− | rlnMicrographOriginalPixelSize | + | | double |

− | + | | Energy loss (in eV) | |

− | rlnMicrographPreExposure | + | |- |

− | + | | rlnEstimatedResolution | |

− | rlnMicrographShiftX | + | | double |

− | + | | Estimated resolution (in A) for a reference | |

− | rlnMicrographShiftY | + | |- |

− | + | | rlnExperimentalDataStarFile | |

− | rlnMicrographStartFrame | + | | string |

− | + | | STAR file with metadata for the experimental images | |

− | rlnMicrographTiltAngle | + | |- |

− | + | | rlnFinalResolution | |

− | rlnMicrographTiltAxisDirection | + | | double |

− | + | | Final estimated resolution after postprocessing (in Angstroms) | |

− | rlnMicrographTiltAxisOutOfPlane | + | |- |

− | + | | rlnFittedInterceptGuinierPlot | |

− | rlnMinRadiusNnInterpolation | + | | double |

− | + | | The fitted intercept of the Guinier-plot | |

− | rlnMinimumValue | + | |- |

− | + | | rlnFittedSlopeGuinierPlot | |

− | rlnModelStarFile | + | | double |

− | + | | The fitted slope of the Guinier-plot | |

− | rlnModelStarFile2 | + | |- |

− | + | | rlnFixSigmaNoiseEstimates | |

− | rlnMotionModelCoeff | + | | bool |

− | + | | Flag to indicate that the estimates for the power spectra of the noise should be kept constant | |

− | rlnMotionModelCoeffsIdx | + | |- |

− | + | | rlnFixSigmaOffsetEstimates | |

− | rlnMotionModelVersion | + | | bool |

− | + | | Flag to indicate that the estimates for the stddev in the origin offsets should be kept constant | |

− | rlnMovieFrameNumber | + | |- |

− | + | | rlnFixTauEstimates | |

− | rlnMovieFramesRunningAverage | + | | bool |

− | + | | Flag to indicate that the estimates for the power spectra of the signal (i.e. the references) should be kept constant | |

− | rlnMtfValue | + | |- |

− | + | | rlnFourierCompleteness | |

− | rlnNormCorrection | + | | double |

− | + | | Fraction of Fourier components (per resolution shell) with SNR>1 | |

− | rlnNormCorrectionAverage | + | |- |

− | + | | rlnFourierShellCorrelation | |

− | rlnNrBodies | + | | double |

− | + | | FSC value (of unspecified type, e.g. masked or unmasked) | |

− | rlnNrClasses | + | |- |

− | + | | rlnFourierShellCorrelationCorrected | |

− | rlnNrGroups | + | | double |

− | + | | Final FSC value: i.e. after correction based on masking of randomized-phases maps | |

− | rlnNrHelicalAsymUnits | + | |- |

− | + | | rlnFourierShellCorrelationMaskedMaps | |

− | rlnNrOfFrames | + | | double |

− | + | | FSC value after masking of the original maps | |

− | rlnNrOfSignificantSamples | + | |- |

− | + | | rlnFourierShellCorrelationUnmaskedMaps | |

− | rlnNumberOfIterWithoutChangingAssignments | + | | double |

− | + | | FSC value before masking of the original maps | |

− | rlnNumberOfIterWithoutResolutionGain | + | |- |

− | + | | rlnFourierSpaceInterpolator | |

− | rlnNumberOfIterations | + | | int |

− | + | | The kernel used for Fourier-space interpolation (NN=0, linear=1) | |

− | rlnOffsetRange | + | |- |

− | + | | rlnGoldStandardFsc | |

− | rlnOffsetStep | + | | double |

− | + | | Fourier shell correlation between two independent reconstructions from random halves of the data | |

− | rlnOrientSamplingStarFile | + | |- |

− | + | | rlnGroupName | |

− | rlnOrientationDistribution | + | | string |

− | + | | The name of a group of images (e.g. all images from a micrograph) | |

− | rlnOrientationalPriorMode | + | |- |

− | + | | rlnGroupNrParticles | |

− | rlnOrientationsID | + | | int |

− | + | | Number particles in a group of images | |

− | rlnOriginX | + | |- |

− | + | | rlnGroupNumber | |

− | rlnOriginXPrior | + | | int |

− | + | | The number of a group of images | |

− | rlnOriginY | + | |- |

− | + | | rlnGroupScaleCorrection | |

− | rlnOriginYPrior | + | | double |

− | + | | Intensity-scale correction for a group of images | |

− | rlnOriginZ | + | |- |

− | + | | rlnHasConverged | |

− | rlnOriginZPrior | + | | bool |

− | + | | Flag to indicate that the optimization has converged | |

− | rlnOriginalImageSize | + | |- |

− | + | | rlnHasHighFscAtResolLimit | |

− | rlnOriginalParticleName | + | | bool |

− | + | | Flag to indicate that the FSC at the resolution limit is significant | |

− | rlnOutputRootName | + | |- |

− | + | | rlnHasLargeSizeIncreaseIterationsAgo | |

− | rlnOverallAccuracyRotations | + | | int |

− | + | | How many iterations have passed since the last large increase in image size | |

− | rlnOverallAccuracyTranslations | + | |- |

− | + | | rlnHealpixOrder | |

− | rlnOverallFourierCompleteness | + | | int |

− | + | | Healpix order for the sampling of the first two Euler angles (rot, tilt) on the 3D sphere | |

− | rlnPaddingFactor | + | |- |

− | + | | rlnHelicalCentralProportion | |

− | rlnParticleDiameter | + | | double |

− | + | | Only expand this central fraction of the Z axis when imposing real-space helical symmetry | |

− | rlnParticleFigureOfMerit | + | |- |

− | + | | rlnHelicalKeepTiltPriorFixed | |

− | rlnParticleId | + | | bool |

− | + | | Flag to indicate that helical tilt priors are kept fixed (at 90 degrees) in global angular searches | |

− | rlnParticleName | + | |- |

− | + | | rlnHelicalMaskTubeInnerDiameter | |

− | rlnParticleNumber | + | | double |

− | + | | Inner diameter of helical tubes in Angstroms (for masks of helical references and particles) | |

− | rlnParticleSelectZScore | + | |- |

− | + | | rlnHelicalMaskTubeOuterDiameter | |

− | rlnPerFrameCumulativeWeight | + | | double |

− | + | | Outer diameter of helical tubes in Angstroms (for masks of helical references and particles) | |

− | rlnPerFrameRelativeWeight | + | |- |

− | + | | rlnHelicalOffsetStep | |

− | rlnPhaseShift | + | | double |

− | + | | Step size for the searches of offsets along helical axis (in Angstroms) | |

− | rlnPipeLineEdgeFromNode | + | |- |

− | + | | rlnHelicalRise | |

− | rlnPipeLineEdgeProcess | + | | double |

− | + | | The helical rise (translation per subunit) in Angstroms | |

− | rlnPipeLineEdgeToNode | + | |- |

− | + | | rlnHelicalRiseInitial | |

− | rlnPipeLineJobCounter | + | | double |

− | + | | The initial helical rise (translation per subunit) in Angstroms before refinement | |

− | rlnPipeLineNodeName | + | |- |

− | + | | rlnHelicalRiseInitialStep | |

− | rlnPipeLineNodeType | + | | double |

− | + | | Initial step of helical rise search (in Angstroms) | |

− | rlnPipeLineProcessAlias | + | |- |

− | + | | rlnHelicalRiseMax | |

− | rlnPipeLineProcessName | + | | double |

− | + | | Maximum helical rise (in Angstroms) | |

− | rlnPipeLineProcessStatus | + | |- |

− | + | | rlnHelicalRiseMin | |

− | rlnPipeLineProcessType | + | | double |

− | + | | Minimum helical rise (in Angstroms) | |

− | rlnPixelSize | + | |- |

− | + | | rlnHelicalSigmaDistance | |

− | rlnPsiStep | + | | double |

− | + | | Sigma of distance along the helical tracks | |

− | rlnRadiusMaskExpImages | + | |- |

− | + | | rlnHelicalSymmetryLocalRefinement | |

− | rlnRadiusMaskMap | + | | bool |

− | + | | Flag to indicate that local refinement of helical parameters should be performed | |

− | rlnRandomSeed | + | |- |

− | + | | rlnHelicalTrackLength | |

− | rlnRandomSubset | + | | double |

− | + | | Distance from the position of this helical segment to the starting point of the tube | |

− | rlnRandomiseFrom | + | |- |

− | + | | rlnHelicalTubeID | |

− | rlnReconstructImageName | + | | int |

− | + | | Helical tube ID for a helical segment | |

− | rlnReferenceDimensionality | + | |- |

− | + | | rlnHelicalTubePitch | |

− | rlnReferenceImage | + | | double |

− | + | | Cross-over distance for a helical segment (A) | |

− | rlnReferenceSigma2 | + | |- |

− | + | | rlnHelicalTwist | |

− | rlnReferenceSpectralPower | + | | double |

− | + | | The helical twist (rotation per subunit) in degrees | |

− | rlnReferenceTau2 | + | |- |

− | + | | rlnHelicalTwistInitial | |

− | rlnRefsAreCtfCorrected | + | | double |

− | + | | The intial helical twist (rotation per subunit) in degrees before refinement | |

− | rlnResolution | + | |- |

− | + | | rlnHelicalTwistInitialStep | |

− | rlnResolutionInversePixel | + | | double |

− | + | | Initial step of helical twist search (in degrees) | |

− | rlnResolutionSquared | + | |- |

− | + | | rlnHelicalTwistMax | |

− | rlnSGDGradientImage | + | | double |

− | + | | Maximum helical twist (in degrees, + for right-handedness) | |

− | rlnSamplingPerturbFactor | + | |- |

− | + | | rlnHelicalTwistMin | |

− | rlnSamplingPerturbInstance | + | | double |

− | + | | Minimum helical twist (in degrees, + for right-handedness) | |

− | rlnSamplingRate | + | |- |

− | + | | rlnHighresLimitExpectation | |

− | rlnSamplingRateX | + | | double |

− | + | | High-resolution-limit (in Angstrom) for the expectation step | |

− | rlnSamplingRateY | + | |- |

− | + | | rlnHighresLimitSGD | |

− | rlnSamplingRateZ | + | | double |

− | + | | High-resolution-limit (in Angstrom) for Stochastic Gradient Descent | |

− | rlnSelected | + | |- |

− | + | | rlnIgnoreHelicalSymmetry | |

− | rlnSgdFinalIterations | + | | bool |

− | + | | Flag to indicate that helical symmetry is ignored in 3D reconstruction | |

− | rlnSgdFinalResolution | + | |- |

− | + | | rlnImageDimensionality | |

− | rlnSgdFinalSubsetSize | + | | int |

− | + | | Dimensionality of data stored in an image (i.e. 2 or 3) | |

− | rlnSgdInBetweenIterations | + | |- |

− | + | | rlnImageId | |

− | rlnSgdInitialIterations | + | | int |

− | + | | ID (i.e. a unique number) of an image | |

− | rlnSgdInitialResolution | + | |- |

− | + | | rlnImageName | |

− | rlnSgdInitialSubsetSize | + | | string |

− | + | | Name of an image | |

− | rlnSgdMaxSubsets | + | |- |

− | + | | rlnImageOriginalName | |

− | rlnSgdMuFactor | + | | string |

− | + | | Original name of an image | |

− | rlnSgdSigma2FudgeHalflife | + | |- |

− | + | | rlnImageSize | |

− | rlnSgdSigma2FudgeInitial | + | | int |

− | + | | Size of an image (in pixels) | |

− | rlnSgdSkipAnneal | + | |- |

− | + | | rlnImageSizeX | |

− | rlnSgdStepsize | + | | int |

− | + | | Size of an image in the X-direction (in pixels) | |

− | rlnSgdSubsetSize | + | |- |

− | + | | rlnImageSizeY | |

− | rlnSgdWriteEverySubset | + | | int |

− | + | | Size of an image in the Y-direction (in pixels) | |

− | rlnSigma2Noise | + | |- |

− | + | | rlnImageSizeZ | |

− | rlnSigmaOffsets | + | | int |

− | + | | Size of an image in the Z-direction (in pixels) | |

− | rlnSigmaPriorPsiAngle | + | |- |

− | + | | rlnImageWeight | |

− | rlnSigmaPriorRotAngle | + | | double |

− | + | | Relative weight of an image | |

− | rlnSigmaPriorTiltAngle | + | |- |

− | + | | rlnIncrementImageSize | |

− | rlnSignalToNoiseRatio | + | | int |

− | + | | Number of Fourier shells to be included beyond the resolution where SSNR^MAP drops below 1 | |

− | rlnSkewnessValue | + | |- |

− | + | | rlnIs3DSampling | |

− | rlnSmallestChangesClasses | + | | bool |

− | + | | Flag to indicate this concerns a 3D sampling | |

− | rlnSmallestChangesOffsets | + | |- |

− | + | | rlnIs3DTranslationalSampling | |

− | rlnSmallestChangesOrientations | + | | bool |

− | + | | Flag to indicate this concerns a x,y,z-translational sampling | |

− | rlnSolventMask2Name | + | |- |

− | + | | rlnIsFlip | |

− | rlnSolventMaskName | + | | bool |

− | + | | Flag to indicate that an image should be mirrored | |

− | rlnSortedIndex | + | |- |

− | + | | rlnIsHelix | |

− | rlnSpectralIndex | + | | bool |

− | + | | Flag to indicate that helical refinement should be performed | |

− | rlnSpectralOrientabilityContribution | + | |- |

− | + | | rlnJoinHalvesUntilThisResolution | |

− | rlnSphericalAberration | + | | double |

− | + | | Resolution (in Angstrom) to join the two random half-reconstructions to prevent their diverging orientations (for C-symmetries) | |

− | rlnSsnrMap | + | |- |

− | + | | rlnKullbackLeiblerDivergence | |

− | rlnStandardDeviationValue | + | | double |

− | + | | Kullback-Leibler divergence for a particle | |

− | rlnStarFileMovieParticles | + | |- |

− | + | | rlnKurtosisExcessValue | |

− | rlnSymmetryGroup | + | | double |

− | + | | Kurtosis excess (4th moment - 3) for the pixel values in an image | |

− | rlnTau2FudgeFactor | + | |- |

− | + | | rlnLensStability | |

− | rlnTauSpectrumName | + | | double |

− | + | | Lens stability (in ppm) | |

− | rlnTiltAngleLimit | + | |- |

− | + | | rlnLocalSymmetryFile | |

− | rlnTransversalDisplacement | + | | string |

− | + | | Local symmetry description file containing list of masks and their operators | |

− | rlnUnfilteredMapHalf1 | + | |- |

− | + | | rlnLogAmplitudesIntercept | |

− | rlnUnfilteredMapHalf2 | + | | double |

− | + | | Y-value for Guinier plot: the fitted plateau of the logarithm of the radially averaged amplitudes | |

− | rlnUseTooCoarseSampling | + | |- |

− | + | | rlnLogAmplitudesMTFCorrected | |

− | rlnVoltage | + | | double |

− | + | | Y-value for Guinier plot: the logarithm of the radially averaged amplitudes after MTF correction | |

− | rlnWidthMaskEdge | + | |- |

+ | | rlnLogAmplitudesOriginal | ||

+ | | double | ||

+ | | Y-value for Guinier plot: the logarithm of the radially averaged amplitudes of the input map | ||

+ | |- | ||

+ | | rlnLogAmplitudesSharpened | ||

+ | | double | ||

+ | | Y-value for Guinier plot: the logarithm of the radially averaged amplitudes after sharpening | ||

+ | |- | ||

+ | | rlnLogAmplitudesWeighted | ||

+ | | double | ||

+ | | Y-value for Guinier plot: the logarithm of the radially averaged amplitudes after FSC-weighting | ||

+ | |- | ||

+ | | rlnLogLikeliContribution | ||

+ | | double | ||

+ | | Contribution of a particle to the log-likelihood target function | ||

+ | |- | ||

+ | | rlnLogLikelihood | ||

+ | | double | ||

+ | | Value of the log-likelihood target function | ||

+ | |- | ||

+ | | rlnLongitudinalDisplacement | ||

+ | | double | ||

+ | | Longitudinal displacement (in Angstroms) | ||

+ | |- | ||

+ | | rlnMagnification | ||

+ | | double | ||

+ | | Magnification at the detector (in times) | ||

+ | |- | ||

+ | | rlnMagnificationCorrection | ||

+ | | double | ||

+ | | Magnification correction value for an image | ||

+ | |- | ||

+ | | rlnMagnificationSearchRange | ||

+ | | double | ||

+ | | Search range for magnification correction | ||

+ | |- | ||

+ | | rlnMagnificationSearchStep | ||

+ | | double | ||

+ | | Step size for magnification correction | ||

+ | |- | ||

+ | | rlnMaskName | ||

+ | | string | ||

+ | | Name of an image that contains a [0,1] mask | ||

+ | |- | ||

+ | | rlnMatrix_1_1 | ||

+ | | double | ||

+ | | Matrix element (1,1) of a 3x3 matrix | ||

+ | |- | ||

+ | | rlnMatrix_1_2 | ||

+ | | double | ||

+ | | Matrix element (1,2) of a 3x3 matrix | ||

+ | |- | ||

+ | | rlnMatrix_1_3 | ||

+ | | double | ||

+ | | Matrix element (1,3) of a 3x3 matrix | ||

+ | |- | ||

+ | | rlnMatrix_2_1 | ||

+ | | double | ||

+ | | Matrix element (2,1) of a 3x3 matrix | ||

+ | |- | ||

+ | | rlnMatrix_2_2 | ||

+ | | double | ||

+ | | Matrix element (2,1) of a 3x3 matrix | ||

+ | |- | ||

+ | | rlnMatrix_2_3 | ||

+ | | double | ||

+ | | Matrix element (2,1) of a 3x3 matrix | ||

+ | |- | ||

+ | | rlnMatrix_3_1 | ||

+ | | double | ||

+ | | Matrix element (3,1) of a 3x3 matrix | ||

+ | |- | ||

+ | | rlnMatrix_3_2 | ||

+ | | double | ||

+ | | Matrix element (3,1) of a 3x3 matrix | ||

+ | |- | ||

+ | | rlnMatrix_3_3 | ||

+ | | double | ||

+ | | Matrix element (3,1) of a 3x3 matrix | ||

+ | |- | ||

+ | | rlnMaxNumberOfPooledParticles | ||

+ | | int | ||

+ | | Maximum number particles that are processed together to speed up calculations | ||

+ | |- | ||

+ | | rlnMaxValueProbDistribution | ||

+ | | double | ||

+ | | Maximum value of the (normalised) probability function for a particle | ||

+ | |- | ||

+ | | rlnMaximumCoarseImageSize | ||

+ | | int | ||

+ | | Maximum size of the images to be used in the first pass of the adaptive oversampling strategy (may be smaller than the original image size) | ||

+ | |- | ||

+ | | rlnMaximumValue | ||

+ | | double | ||

+ | | Maximum value for the pixels in an image | ||

+ | |- | ||

+ | | rlnMicrographBinning | ||

+ | | double | ||

+ | | Micrograph binning factor | ||

+ | |- | ||

+ | | rlnMicrographDefectFile | ||

+ | | string | ||

+ | | Name of a defect list file | ||

+ | |- | ||

+ | | rlnMicrographDoseRate | ||

+ | | double | ||

+ | | Dose rate in electrons per square Angstrom per frame | ||

+ | |- | ||

+ | | rlnMicrographEndFrame | ||

+ | | int | ||

+ | | End frame of a motion model | ||

+ | |- | ||

+ | | rlnMicrographFrameNumber | ||

+ | | int | ||

+ | | Micrograph frame number | ||

+ | |- | ||

+ | | rlnMicrographGainName | ||

+ | | string | ||

+ | | Name of a gain reference | ||

+ | |- | ||

+ | | rlnMicrographId | ||

+ | | int | ||

+ | | ID (i.e. a unique number) of a micrograph | ||

+ | |- | ||

+ | | rlnMicrographMetadata | ||

+ | | string | ||

+ | | Name of a micrograph metadata file | ||

+ | |- | ||

+ | | rlnMicrographMovieName | ||

+ | | string | ||

+ | | Name of a micrograph movie stack | ||

+ | |- | ||

+ | | rlnMicrographName | ||

+ | | string | ||

+ | | Name of a micrograph | ||

+ | |- | ||

+ | | rlnMicrographNameNoDW | ||

+ | | string | ||

+ | | Name of a micrograph without dose weighting | ||

+ | |- | ||

+ | | rlnMicrographOriginalPixelSize | ||

+ | | double | ||

+ | | Pixel size of original movie before binning in Angstrom/pixel. | ||

+ | |- | ||

+ | | rlnMicrographPreExposure | ||

+ | | double | ||

+ | | Pre-exposure dose in electrons per square Angstrom | ||

+ | |- | ||

+ | | rlnMicrographShiftX | ||

+ | | double | ||

+ | | X shift of a (patch of) micrograph | ||

+ | |- | ||

+ | | rlnMicrographShiftY | ||

+ | | double | ||

+ | | Y shift of a (patch of) micrograph | ||

+ | |- | ||

+ | | rlnMicrographStartFrame | ||

+ | | int | ||

+ | | Start frame of a motion model | ||

+ | |- | ||

+ | | rlnMicrographTiltAngle | ||

+ | | double | ||

+ | | Tilt angle (in degrees) used to collect a micrograph | ||

+ | |- | ||

+ | | rlnMicrographTiltAxisDirection | ||

+ | | double | ||

+ | | Direction of the tilt-axis (in degrees) used to collect a micrograph | ||

+ | |- | ||

+ | | rlnMicrographTiltAxisOutOfPlane | ||

+ | | double | ||

+ | | Out-of-plane angle (in degrees) of the tilt-axis used to collect a micrograph (90=in-plane) | ||

+ | |- | ||

+ | | rlnMinRadiusNnInterpolation | ||

+ | | int | ||

+ | | Minimum radius for NN-interpolation (in Fourier pixels), for smaller radii linear int. is used | ||

+ | |- | ||

+ | | rlnMinimumValue | ||

+ | | double | ||

+ | | Minimum value for the pixels in an image | ||

+ | |- | ||

+ | | rlnModelStarFile | ||

+ | | string | ||

+ | | STAR file with metadata for the model that is being refined | ||

+ | |- | ||

+ | | rlnModelStarFile2 | ||

+ | | string | ||

+ | | STAR file with metadata for the second model that is being refined (from random halves of the data) | ||

+ | |- | ||

+ | | rlnMotionModelCoeff | ||

+ | | double | ||

+ | | A coefficient of a motion model | ||

+ | |- | ||

+ | | rlnMotionModelCoeffsIdx | ||

+ | | int | ||

+ | | Index of a coefficient of a motion model | ||

+ | |- | ||

+ | | rlnMotionModelVersion | ||

+ | | int | ||

+ | | Version of micrograph motion model | ||

+ | |- | ||

+ | | rlnMovieFrameNumber | ||

+ | | int | ||

+ | | Number of a movie frame | ||

+ | |- | ||

+ | | rlnMovieFramesRunningAverage | ||

+ | | int | ||

+ | | Number of movie frames inside the running average that will be used for movie-refinement | ||

+ | |- | ||

+ | | rlnMtfValue | ||

+ | | double | ||

+ | | Value of the detectors modulation transfer function (between 0 and 1) | ||

+ | |- | ||

+ | | rlnNormCorrection | ||

+ | | double | ||

+ | | Normalisation correction value for an image | ||

+ | |- | ||

+ | | rlnNormCorrectionAverage | ||

+ | | double | ||

+ | | Average value (over all images) of the normalisation correction values | ||

+ | |- | ||

+ | | rlnNrBodies | ||

+ | | int | ||

+ | | The number of independent rigid bodies to be refined in multi-body refinement | ||

+ | |- | ||

+ | | rlnNrClasses | ||

+ | | int | ||

+ | | The number of references (i.e. classes) to be used in refinement | ||

+ | |- | ||

+ | | rlnNrGroups | ||

+ | | int | ||

+ | | The number of different groups of images (each group has its own noise spectrum, and intensity-scale correction) | ||

+ | |- | ||

+ | | rlnNrHelicalAsymUnits | ||

+ | | int | ||

+ | | How many new helical asymmetric units are there in each box | ||

+ | |- | ||

+ | | rlnNrOfFrames | ||

+ | | int | ||

+ | | Number of movie frames that were collected for this particle | ||

+ | |- | ||

+ | | rlnNrOfSignificantSamples | ||

+ | | int | ||

+ | | Number of orientational/class assignments (for a particle) with sign.probabilities in the 1st pass of adaptive oversampling | ||

+ | |- | ||

+ | | rlnNumberOfIterWithoutChangingAssignments | ||

+ | | int | ||

+ | | Number of iterations that have passed without large changes in orientation and class assignments | ||

+ | |- | ||

+ | | rlnNumberOfIterWithoutResolutionGain | ||

+ | | int | ||

+ | | Number of iterations that have passed without a gain in resolution | ||

+ | |- | ||

+ | | rlnNumberOfIterations | ||

+ | | int | ||

+ | | Maximum number of iterations to be performed | ||

+ | |- | ||

+ | | rlnOffsetRange | ||

+ | | double | ||

+ | | Search range for the origin offsets (in Angstroms) | ||

+ | |- | ||

+ | | rlnOffsetStep | ||

+ | | double | ||

+ | | Step size for the searches in the origin offsets (in Angstroms) | ||

+ | |- | ||

+ | | rlnOrientSamplingStarFile | ||

+ | | string | ||

+ | | STAR file with metadata for the orientational sampling | ||

+ | |- | ||

+ | | rlnOrientationDistribution | ||

+ | | double | ||

+ | | Probability Density Function of the orientations (i.e. fraction of images assigned to each orient) | ||

+ | |- | ||

+ | | rlnOrientationalPriorMode | ||

+ | | int | ||

+ | | Mode for prior distributions on the orientations (0=no prior; 1=(rot,tilt,psi); 2=(rot,tilt); 3=rot; 4=tilt; 5=psi) | ||

+ | |- | ||

+ | | rlnOrientationsID | ||

+ | | int | ||

+ | | ID (i.e. a unique number) for an orientation | ||

+ | |- | ||

+ | | rlnOriginX | ||

+ | | double | ||

+ | | X-coordinate (in pixels) for the origin of rotation | ||

+ | |- | ||

+ | | rlnOriginXPrior | ||

+ | | double | ||

+ | | Center of the prior on the X-coordinate (in pixels) for the origin of rotation | ||

+ | |- | ||

+ | | rlnOriginY | ||

+ | | double | ||

+ | | Y-coordinate (in pixels) for the origin of rotation | ||

+ | |- | ||

+ | | rlnOriginYPrior | ||

+ | | double | ||

+ | | Center of the prior on the X-coordinate (in pixels) for the origin of rotation | ||

+ | |- | ||

+ | | rlnOriginZ | ||

+ | | double | ||

+ | | Z-coordinate (in pixels) for the origin of rotation | ||

+ | |- | ||

+ | | rlnOriginZPrior | ||

+ | | double | ||

+ | | Center of the prior on the X-coordinate (in pixels) for the origin of rotation | ||

+ | |- | ||

+ | | rlnOriginalImageSize | ||

+ | | int | ||

+ | | Original size of the images (in pixels) | ||

+ | |- | ||

+ | | rlnOriginalParticleName | ||

+ | | string | ||

+ | | Original name for a particles | ||

+ | |- | ||

+ | | rlnOutputRootName | ||

+ | | string | ||

+ | | Rootname for all output files (this may include a directory structure, which should then exist) | ||

+ | |- | ||

+ | | rlnOverallAccuracyRotations | ||

+ | | double | ||

+ | | Overall accuracy of the rotational assignments (in degrees) | ||

+ | |- | ||

+ | | rlnOverallAccuracyTranslations | ||

+ | | double | ||

+ | | Overall accuracy of the translational assignments (in pixels) | ||

+ | |- | ||

+ | | rlnOverallFourierCompleteness | ||

+ | | double | ||

+ | | Fraction of all Fourier components up to the current resolution with SNR>1 | ||

+ | |- | ||

+ | | rlnPaddingFactor | ||

+ | | double | ||

+ | | Oversampling factor for Fourier transforms of the references | ||

+ | |- | ||

+ | | rlnParticleDiameter | ||

+ | | double | ||

+ | | Diameter of the circular mask to be applied to all experimental images (in Angstroms) | ||

+ | |- | ||

+ | | rlnParticleFigureOfMerit | ||

+ | | double | ||

+ | | Developmental FOM for a particle | ||

+ | |- | ||

+ | | rlnParticleId | ||

+ | | int | ||

+ | | ID (i.e. a unique number) for a particle | ||

+ | |- | ||

+ | | rlnParticleName | ||

+ | | string | ||

+ | | Name for a particle | ||

+ | |- | ||

+ | | rlnParticleNumber | ||

+ | | int | ||

+ | | Number of particles | ||

+ | |- | ||

+ | | rlnParticleSelectZScore | ||

+ | | double | ||

+ | | Sum of Z-scores from particle_select. High Z-scores are likely to be outliers. | ||

+ | |- | ||

+ | | rlnPerFrameCumulativeWeight | ||

+ | | double | ||

+ | | Sum of the resolution-dependent relative weights from the first frame until the given frame | ||

+ | |- | ||

+ | | rlnPerFrameRelativeWeight | ||

+ | | double | ||

+ | | The resolution-dependent relative weights for a given frame | ||

+ | |- | ||

+ | | rlnPhaseShift | ||

+ | | double | ||

+ | | Phase-shift from a phase-plate (in degrees) | ||

+ | |- | ||

+ | | rlnPipeLineEdgeFromNode | ||

+ | | string | ||

+ | | Name of the origin of an edge | ||

+ | |- | ||

+ | | rlnPipeLineEdgeProcess | ||

+ | | string | ||

+ | | Name of the destination of an edge | ||

+ | |- | ||

+ | | rlnPipeLineEdgeToNode | ||

+ | | string | ||

+ | | Name of the to-Node in an edge | ||

+ | |- | ||

+ | | rlnPipeLineJobCounter | ||

+ | | int | ||

+ | | Number of the last job in the pipeline | ||

+ | |- | ||

+ | | rlnPipeLineNodeName | ||

+ | | string | ||

+ | | Name of a Node in the pipeline | ||

+ | |- | ||

+ | | rlnPipeLineNodeType | ||

+ | | int | ||

+ | | Type of a Node in the pipeline | ||

+ | |- | ||

+ | | rlnPipeLineProcessAlias | ||

+ | | string | ||

+ | | Alias of a Process in the pipeline | ||

+ | |- | ||

+ | | rlnPipeLineProcessName | ||

+ | | string | ||

+ | | Name of a Process in the pipeline | ||

+ | |- | ||

+ | | rlnPipeLineProcessStatus | ||

+ | | int | ||

+ | | Status of a Process in the pipeline (running, scheduled, finished or cancelled) | ||

+ | |- | ||

+ | | rlnPipeLineProcessType | ||

+ | | int | ||

+ | | Type of a Process in the pipeline | ||

+ | |- | ||

+ | | rlnPixelSize | ||

+ | | double | ||

+ | | Size of the pixels in the references and images (in Angstroms) | ||

+ | |- | ||

+ | | rlnPsiStep | ||

+ | | double | ||

+ | | Step size (in degrees) for the sampling of the in-plane rotation angle (psi) | ||

+ | |- | ||

+ | | rlnRadiusMaskExpImages | ||

+ | | int | ||

+ | | Radius of the circular mask to be applied to all experimental images (in Angstroms) | ||

+ | |- | ||

+ | | rlnRadiusMaskMap | ||

+ | | int | ||

+ | | Radius of the spherical mask to be applied to all references (in Angstroms) | ||

+ | |- | ||

+ | | rlnRandomSeed | ||

+ | | int | ||

+ | | Seed (i.e. a number) for the random number generator | ||

+ | |- | ||

+ | | rlnRandomSubset | ||

+ | | int | ||

+ | | Random subset to which this particle belongs | ||

+ | |- | ||

+ | | rlnRandomiseFrom | ||

+ | | double | ||

+ | | Resolution (in A) from which the phases are randomised in the postprocessing step | ||

+ | |- | ||

+ | | rlnReconstructImageName | ||

+ | | string | ||

+ | | Name of an image to be used for reconstruction only | ||

+ | |- | ||

+ | | rlnReferenceDimensionality | ||

+ | | int | ||

+ | | Dimensionality of the references (2D/3D) | ||

+ | |- | ||

+ | | rlnReferenceImage | ||

+ | | string | ||

+ | | Name of a reference image | ||

+ | |- | ||

+ | | rlnReferenceSigma2 | ||

+ | | double | ||

+ | | Spherical average of the estimated power in the noise of a reference | ||

+ | |- | ||

+ | | rlnReferenceSpectralPower | ||

+ | | double | ||

+ | | Spherical average of the power of the reference | ||

+ | |- | ||

+ | | rlnReferenceTau2 | ||

+ | | double | ||

+ | | Spherical average of the estimated power in the signal of a reference | ||

+ | |- | ||

+ | | rlnRefsAreCtfCorrected | ||

+ | | bool | ||

+ | | Flag to indicate that the input references have been CTF-amplitude corrected | ||

+ | |- | ||

+ | | rlnResolution | ||

+ | | double | ||

+ | | Resolution (in 1/Angstroms) | ||

+ | |- | ||

+ | | rlnResolutionInversePixel | ||

+ | | double | ||

+ | | Resolution (in 1/pixel, Nyquist = 0.5) | ||

+ | |- | ||

+ | | rlnResolutionSquared | ||

+ | | double | ||

+ | | X-value for Guinier plot: squared resolution in 1/Angstrom^2 | ||

+ | |- | ||

+ | | rlnSGDGradientImage | ||

+ | | string | ||

+ | | Name of image containing the SGD gradient | ||

+ | |- | ||

+ | | rlnSamplingPerturbFactor | ||

+ | | double | ||

+ | | Factor for random perturbation on the orientational sampling (between 0 no perturbation and 1 very strong perturbation) | ||

+ | |- | ||

+ | | rlnSamplingPerturbInstance | ||

+ | | double | ||

+ | | Random instance of the random perturbation on the orientational sampling | ||

+ | |- | ||

+ | | rlnSamplingRate | ||

+ | | double | ||

+ | | Sampling rate of an image (in Angstrom/pixel) | ||

+ | |- | ||

+ | | rlnSamplingRateX | ||

+ | | double | ||

+ | | Sampling rate in X-direction of an image (in Angstrom/pixel) | ||

+ | |- | ||

+ | | rlnSamplingRateY | ||

+ | | double | ||

+ | | Sampling rate in Y-direction of an image (in Angstrom/pixel) | ||

+ | |- | ||

+ | | rlnSamplingRateZ | ||

+ | | double | ||

+ | | Sampling rate in Z-direction of an image (in Angstrom/pixel) | ||

+ | |- | ||

+ | | rlnSelected | ||

+ | | int | ||

+ | | Flag whether an entry in a metadatatable is selected (1) in the viewer or not (0) | ||

+ | |- | ||

+ | | rlnSgdFinalIterations | ||

+ | | int | ||

+ | | Number of final SGD iterations (at rlnSgdFinalResolution and with rlnSgdFinalSubsetSize) | ||

+ | |- | ||

+ | | rlnSgdFinalResolution | ||

+ | | double | ||

+ | | Resolution (in A) to use during the final SGD iterations | ||

+ | |- | ||

+ | | rlnSgdFinalSubsetSize | ||

+ | | int | ||

+ | | Number of particles in a mini-batch (subset) during the final SGD iteration | ||

+ | |- | ||

+ | | rlnSgdInBetweenIterations | ||

+ | | int | ||

+ | | Number of SGD iteration in between the initial ones to the final ones (with linear interpolation of resolution and subset size) | ||

+ | |- | ||

+ | | rlnSgdInitialIterations | ||

+ | | int | ||

+ | | Number of initial SGD iterations (at rlnSgdInitialResolution and with rlnSgdInitialSubsetSize) | ||

+ | |- | ||

+ | | rlnSgdInitialResolution | ||

+ | | double | ||

+ | | Resolution (in A) to use during the initial SGD iterations | ||

+ | |- | ||

+ | | rlnSgdInitialSubsetSize | ||

+ | | int | ||

+ | | Number of particles in a mini-batch (subset) during the initial SGD iterations | ||

+ | |- | ||

+ | | rlnSgdMaxSubsets | ||

+ | | int | ||

+ | | Stop SGD after doing this many subsets (possibly spanning more than 1 iteration) | ||

+ | |- | ||

+ | | rlnSgdMuFactor | ||

+ | | double | ||

+ | | The mu-parameter that controls the momentum of the SGD gradients | ||

+ | |- | ||

+ | | rlnSgdSigma2FudgeHalflife | ||

+ | | int | ||

+ | | After processing this many particles the multiplicative factor for the noise variance will have halved | ||

+ | |- | ||

+ | | rlnSgdSigma2FudgeInitial | ||

+ | | double | ||

+ | | The variance of the noise will initially be multiplied with this value (larger than 1) | ||

+ | |- | ||

+ | | rlnSgdSkipAnneal | ||

+ | | bool | ||

+ | | Option to switch off annealing of multiple references in SGD | ||

+ | |- | ||

+ | | rlnSgdStepsize | ||

+ | | double | ||

+ | | Stepsize in SGD updates) | ||

+ | |- | ||

+ | | rlnSgdSubsetSize | ||

+ | | int | ||

+ | | The number of particles in the random subsets for SGD | ||

+ | |- | ||

+ | | rlnSgdWriteEverySubset | ||

+ | | int | ||

+ | | Every this many iterations the model is written to disk in SGD | ||

+ | |- | ||

+ | | rlnSigma2Noise | ||

+ | | double | ||

+ | | Spherical average of the standard deviation in the noise (sigma) | ||

+ | |- | ||

+ | | rlnSigmaOffsets | ||

+ | | double | ||

+ | | Standard deviation in the origin offsets (in Angstroms) | ||

+ | |- | ||

+ | | rlnSigmaPriorPsiAngle | ||

+ | | double | ||

+ | | Standard deviation of the prior on the psi (i.e. third Euler) angle | ||

+ | |- | ||

+ | | rlnSigmaPriorRotAngle | ||

+ | | double | ||

+ | | Standard deviation of the prior on the rot (i.e. first Euler) angle | ||

+ | |- | ||

+ | | rlnSigmaPriorTiltAngle | ||

+ | | double | ||

+ | | Standard deviation of the prior on the tilt (i.e. second Euler) angle | ||

+ | |- | ||

+ | | rlnSignalToNoiseRatio | ||

+ | | double | ||

+ | | Spectral signal-to-noise ratio for a reference | ||

+ | |- | ||

+ | | rlnSkewnessValue | ||

+ | | double | ||

+ | | Skewness (3rd moment) for the pixel values in an image | ||

+ | |- | ||

+ | | rlnSmallestChangesClasses | ||

+ | | int | ||

+ | | Smallest changes thus far in the optimal class assignments (in numer of particles). | ||

+ | |- | ||

+ | | rlnSmallestChangesOffsets | ||

+ | | double | ||

+ | | Smallest changes thus far in the optimal offset assignments (in pixels). | ||

+ | |- | ||

+ | | rlnSmallestChangesOrientations | ||

+ | | double | ||

+ | | Smallest changes thus far in the optimal orientation assignments (in degrees). | ||

+ | |- | ||

+ | | rlnSolventMask2Name | ||

+ | | string | ||

+ | | Name of a secondary solvent mask (e.g. to flatten density inside an icosahedral virus) | ||

+ | |- | ||

+ | | rlnSolventMaskName | ||

+ | | string | ||

+ | | Name of an image that contains a (possibly soft) mask for the solvent area (values=0 for solvent, values =1 for protein) | ||

+ | |- | ||

+ | | rlnSortedIndex | ||

+ | | int | ||

+ | | Index of a metadata entry after sorting (first sorted index is 0). | ||

+ | |- | ||

+ | | rlnSpectralIndex | ||

+ | | int | ||

+ | | Spectral index (i.e. distance in pixels to the origin in Fourier space) | ||

+ | |- | ||

+ | | rlnSpectralOrientabilityContribution | ||

+ | | double | ||

+ | | Spectral SNR contribution to the orientability of individual particles | ||

+ | |- | ||

+ | | rlnSphericalAberration | ||

+ | | double | ||

+ | | Spherical aberration (in millimeters) | ||

+ | |- | ||

+ | | rlnSsnrMap | ||

+ | | double | ||

+ | | Spectral signal-to-noise ratio as defined for MAP estimation (SSNR^MAP) | ||

+ | |- | ||

+ | | rlnStandardDeviationValue | ||

+ | | double | ||

+ | | Standard deviation for the pixel values in an image | ||

+ | |- | ||

+ | | rlnStarFileMovieParticles | ||

+ | | string | ||

+ | | Filename of a STAR file with movie-particles in it | ||

+ | |- | ||

+ | | rlnSymmetryGroup | ||

+ | | string | ||

+ | | Symmetry group (e.g., C1, D7, I2, I5, etc.) | ||

+ | |- | ||

+ | | rlnTau2FudgeFactor | ||

+ | | double | ||

+ | | Regularisation parameter with which estimates for the power in the references will be multiplied (T in original paper) | ||

+ | |- | ||

+ | | rlnTauSpectrumName | ||

+ | | string | ||

+ | | Name of a STAR file that holds a tau2-spectrum | ||

+ | |- | ||

+ | | rlnTiltAngleLimit | ||

+ | | double | ||

+ | | Values to which to limit the tilt angles (positive for keeping side views, negative for keeping top views) | ||

+ | |- | ||

+ | | rlnTransversalDisplacement | ||

+ | | double | ||

+ | | Transversal displacement (in Angstroms) | ||

+ | |- | ||

+ | | rlnUnfilteredMapHalf1 | ||

+ | | string | ||

+ | | Name of the unfiltered map from halfset 1 | ||

+ | |- | ||

+ | | rlnUnfilteredMapHalf2 | ||

+ | | string | ||

+ | | Name of the unfiltered map from halfset 2 | ||

+ | |- | ||

+ | | rlnUseTooCoarseSampling | ||

+ | | bool | ||

+ | | Flag to indicate that the angular sampling on the sphere will be one step coarser than needed to speed up calculations | ||

+ | |- | ||

+ | | rlnVoltage | ||

+ | | double | ||

+ | | Voltage of the microscope (in kV) | ||

+ | |- | ||

+ | | rlnWidthMaskEdge | ||

+ | | int | ||

+ | | Width (in pixels) of the soft edge for spherical/circular masks to be used for solvent flattening | ||

+ | |} |

## 2019年5月16日 (木) 11:13時点における最新版

- RELION v3.0.5の以下コマンドの出力を表にしました。

$ relion_refine --print_metadata_labels

パラメータ名 | データ型 | 説明 |
---|---|---|

rlnAccumMotionEarly | double | Accumulated global motion during the first frames of the movie (in A) |

rlnAccumMotionLate | double | Accumulated global motion during the last frames of the movie (in A) |

rlnAccumMotionTotal | double | Accumulated global motion during the entire movie (in A) |

rlnAccuracyRotations | double | Estimated accuracy (in degrees) with which rotations can be assigned |

rlnAccuracyTranslations | double | Estimated accuracy (in pixels) with which translations can be assigned |

rlnAdaptiveOversampleFraction | double | Fraction of the weights that will be oversampled in a second pass of the adaptive oversampling strategy |

rlnAdaptiveOversampleOrder | int | Order of the adaptive oversampling (0=no oversampling, 1= 2x oversampling; 2= 4x oversampling, etc) |

rlnAmplitudeContrast | double | Amplitude contrast (as a fraction, i.e. 10% = 0.1) |

rlnAmplitudeCorrelationMaskedMaps | double | Correlation coefficient between amplitudes in Fourier shells of masked maps |

rlnAmplitudeCorrelationUnmaskedMaps | double | Correlation coefficient between amplitudes in Fourier shells of unmasked maps |

rlnAnglePsi | double | Third Euler, or in-plane angle (psi, in degrees) |

rlnAnglePsiFlipRatio | double | Flip ratio of bimodal psi prior (0~0.5, 0 means an ordinary prior, 0.5 means a perfect bimodal prior) |

rlnAnglePsiPrior | double | Center of the prior (in degrees) on the third Euler angle (psi) |

rlnAngleRot | double | First Euler angle (rot, in degrees) |

rlnAngleRotPrior | double | Center of the prior (in degrees) on the first Euler angle (rot) |

rlnAngleTilt | double | Second Euler angle (tilt, in degrees) |

rlnAngleTiltPrior | double | Center of the prior (in degrees) on the second Euler angle (tilt) |

rlnAngstromResolution | double | Resolution (in Angstroms) |

rlnAreaId | int | ID (i.e. a unique number) of an area (i.e. field-of-view) |

rlnAreaName | string | Name of an area (i.e. field-of-view) |

rlnAutoLocalSearchesHealpixOrder | int | Healpix order (before oversampling) from which autosampling procedure will use local angular searches |

rlnAutopickFigureOfMerit | double | Autopicking FOM for a particle |

rlnAvailableMemory | double | Available memory per computing node (i.e. per MPI-process) |

rlnAverageNrOfFrames | int | Number of movie frames that one averages over upon extraction of movie-particles |

rlnAveragePmax | double | Average value (over all images) of the maxima of the probability distributions |

rlnAverageValue | double | Average value for the pixels in an image |

rlnBeamTiltClass | int | Beam-tilt class of a particle |

rlnBeamTiltX | double | Beam tilt in the X-direction (in mrad) |

rlnBeamTiltY | double | Beam tilt in the Y-direction (in mrad) |

rlnBestResolutionThusFar | double | The highest resolution that has been obtained in this optimization thus far |

rlnBfactorUsedForSharpening | double | Applied B-factor in the sharpening of the map |

rlnBodyKeepFixed | int | Flag to indicate whether to keep a body fixed (value 1) or keep on refining it (0) |

rlnBodyMaskName | string | Name of an image that contains a [0,1] body mask for multi-body refinement |

rlnBodyReferenceName | string | Name of an image that contains the initial reference for one body of a multi-body refinement |

rlnBodyRotateDirectionX | double | X-component of axis around which to rotate this body |

rlnBodyRotateDirectionY | double | Y-component of axis around which to rotate this body |

rlnBodyRotateDirectionZ | double | Z-component of axis around which to rotate this body |

rlnBodyRotateRelativeTo | int | Number of the body relative to which this body rotates (if negative, use rlnBodyRotateDirectionXYZ) |

rlnBodySigmaAngles | double | Width of prior on all three Euler angles of a body in multibody refinement (in degrees) |

rlnBodySigmaOffset | double | Width of prior on origin offsets of a body in multibody refinement (in pixels) |

rlnBodySigmaPsi | double | Width of prior on psi angles of a body in multibody refinement (in degrees) |

rlnBodySigmaRot | double | Width of prior on rot angles of a body in multibody refinement (in degrees) |

rlnBodySigmaTilt | double | Width of prior on tilt angles of a body in multibody refinement (in degrees) |

rlnBodyStarFile | string | Name of STAR file with body masks and metadata |

rlnChangesOptimalClasses | double | The number of particles that changed their optimal clsas assignment in the last iteration |

rlnChangesOptimalOffsets | double | The average change in optimal translation in the last iteration (in pixels) |

rlnChangesOptimalOrientations | double | The average change in optimal orientation in the last iteration (in degrees) |

rlnChromaticAberration | double | Chromatic aberration (in millimeters) |

rlnClassDistribution | double | Probability Density Function of the different classes (i.e. fraction of images assigned to each class) |

rlnClassNumber | int | Class number for which a particle has its highest probability |

rlnClassPriorOffsetX | double | Prior in the X-offset for a class (in pixels) |

rlnClassPriorOffsetY | double | Prior in the Y-offset for a class (in pixels) |

rlnCoarseImageSize | int | Current size of the images to be used in the first pass of the adaptive oversampling strategy (may be smaller than the original image size) |

rlnComment | string | A metadata comment (This is treated in a special way) |

rlnConvergenceCone | double | Convergence cone (in mrad) |

rlnCoordinateX | double | X-Position of an image in a micrograph (in pixels) |

rlnCoordinateY | double | Y-Position of an image in a micrograph (in pixels) |

rlnCoordinateZ | double | Z-Position of an image in a 3D micrograph, i.e. tomogram (in pixels) |

rlnCorrectedFourierShellCorrelationPhaseRandomizedMaskedMaps | double | FSC value after masking of the randomized-phases maps |

rlnCorrelationFitGuinierPlot | double | The correlation coefficient of the fitted line through the Guinier-plot |

rlnCtfAstigmatism | double | Absolute value of the difference between defocus in U- and V-direction (in A) |

rlnCtfBfactor | double | B-factor (in A^2) that describes CTF power spectrum fall-off |

rlnCtfDataAreCtfPremultiplied | bool | Flag to indicate that the input images have been premultiplied with their CTF |

rlnCtfDataArePhaseFlipped | bool | Flag to indicate that the input images have been phase-flipped |

rlnCtfFigureOfMerit | double | Figure of merit for the fit of the CTF (not used inside relion_refine) |

rlnCtfImage | string | Name of an image with all CTF values |

rlnCtfMaxResolution | double | Estimated maximum resolution (in A) of significant CTF Thon rings |

rlnCtfScalefactor | double | Linear scale-factor on the CTF (values between 0 and 1) |

rlnCtfValidationScore | double | Gctf-based validation score for the quality of the CTF fit |

rlnCtfValue | double | Value of the Contrast Transfer Function |

rlnCurrentImageSize | int | Current size of the images used in the refinement |

rlnCurrentIteration | int | The number of the current iteration |

rlnCurrentResolution | double | Current resolution where SSNR^MAP drops below 1 (in 1/Angstroms) |

rlnDataDimensionality | int | Dimensionality of the data (2D/3D) |

rlnDataType | int | Type of data stored in an image (e.g. int, RFLOAT etc) |

rlnDefocusAngle | double | Angle between X and defocus U direction (in degrees) |

rlnDefocusU | double | Defocus in U-direction (in Angstroms, positive values for underfocus) |

rlnDefocusV | double | Defocus in V-direction (in Angstroms, positive values for underfocus) |

rlnDetectorPixelSize | double | Pixel size of the detector (in micrometers) |

rlnDiff2RandomHalves | double | Power of the differences between two independent reconstructions from random halves of the data |

rlnDifferentialPhaseResidualMaskedMaps | double | Differential Phase Residual in Fourier shells of masked maps |

rlnDifferentialPhaseResidualUnmaskedMaps | double | Differential Phase Residual in Fourier shells of unmasked maps |

rlnDoAutoRefine | bool | Flag to indicate that 3D auto-refine procedure is being used |

rlnDoCorrectCtf | bool | Flag to indicate that CTF-correction should be performed |

rlnDoCorrectMagnification | bool | Flag to indicate that (per-group) magnification correction should be performed |

rlnDoCorrectNorm | bool | Flag to indicate that (per-image) normalisation-error correction should be performed |

rlnDoCorrectScale | bool | Flag to indicate that internal (per-group) intensity-scale correction should be performed |

rlnDoFastSubsetOptimisation | bool | Use subsets of the data in the earlier iterations to speed up convergence |

rlnDoHelicalRefine | bool | Flag to indicate that helical refinement should be performed |

rlnDoIgnoreCtfUntilFirstPeak | bool | Flag to indicate that the CTFs should be ignored until their first peak |

rlnDoMapEstimation | bool | Flag to indicate that MAP estimation should be performed (otherwise ML estimation) |

rlnDoOnlyFlipCtfPhases | bool | Flag to indicate that CTF-correction should only comprise phase-flipping |

rlnDoRealignMovies | bool | Flag to indicate that individual frames of movies are being re-aligned |

rlnDoSkipAlign | bool | Flag to indicate that orientational (i.e. rotational and translational) searches will be omitted from the refinement, only marginalisation over classes will take place |

rlnDoSkipRotate | bool | Flag to indicate that rotational searches will be omitted from the refinement, only marginalisation over classes and translations will take place |

rlnDoSolventFlattening | bool | Flag to indicate that the references should be masked to set their solvent areas to a constant density |

rlnDoSolventFscCorrection | bool | Flag to indicate that the FSCs should be solvent-corrected during refinement |

rlnDoSplitRandomHalves | bool | Flag to indicate that the data should be split into two completely separate, random halves |

rlnDoStochasticGradientDescent | bool | Flag to indicate that SGD-optimisation should be performed (otherwise expectation maximisation) |

rlnDoZeroMask | bool | Flag to indicate that the surrounding solvent area in the experimental particles will be masked to zeros (by default random noise will be used |

rlnEnabled | bool | Not used in RELION, only included for backward compatibility with XMIPP selfiles |

rlnEnergyLoss | double | Energy loss (in eV) |

rlnEstimatedResolution | double | Estimated resolution (in A) for a reference |

rlnExperimentalDataStarFile | string | STAR file with metadata for the experimental images |

rlnFinalResolution | double | Final estimated resolution after postprocessing (in Angstroms) |

rlnFittedInterceptGuinierPlot | double | The fitted intercept of the Guinier-plot |

rlnFittedSlopeGuinierPlot | double | The fitted slope of the Guinier-plot |

rlnFixSigmaNoiseEstimates | bool | Flag to indicate that the estimates for the power spectra of the noise should be kept constant |

rlnFixSigmaOffsetEstimates | bool | Flag to indicate that the estimates for the stddev in the origin offsets should be kept constant |

rlnFixTauEstimates | bool | Flag to indicate that the estimates for the power spectra of the signal (i.e. the references) should be kept constant |

rlnFourierCompleteness | double | Fraction of Fourier components (per resolution shell) with SNR>1 |

rlnFourierShellCorrelation | double | FSC value (of unspecified type, e.g. masked or unmasked) |

rlnFourierShellCorrelationCorrected | double | Final FSC value: i.e. after correction based on masking of randomized-phases maps |

rlnFourierShellCorrelationMaskedMaps | double | FSC value after masking of the original maps |

rlnFourierShellCorrelationUnmaskedMaps | double | FSC value before masking of the original maps |

rlnFourierSpaceInterpolator | int | The kernel used for Fourier-space interpolation (NN=0, linear=1) |

rlnGoldStandardFsc | double | Fourier shell correlation between two independent reconstructions from random halves of the data |

rlnGroupName | string | The name of a group of images (e.g. all images from a micrograph) |

rlnGroupNrParticles | int | Number particles in a group of images |

rlnGroupNumber | int | The number of a group of images |

rlnGroupScaleCorrection | double | Intensity-scale correction for a group of images |

rlnHasConverged | bool | Flag to indicate that the optimization has converged |

rlnHasHighFscAtResolLimit | bool | Flag to indicate that the FSC at the resolution limit is significant |

rlnHasLargeSizeIncreaseIterationsAgo | int | How many iterations have passed since the last large increase in image size |

rlnHealpixOrder | int | Healpix order for the sampling of the first two Euler angles (rot, tilt) on the 3D sphere |

rlnHelicalCentralProportion | double | Only expand this central fraction of the Z axis when imposing real-space helical symmetry |

rlnHelicalKeepTiltPriorFixed | bool | Flag to indicate that helical tilt priors are kept fixed (at 90 degrees) in global angular searches |

rlnHelicalMaskTubeInnerDiameter | double | Inner diameter of helical tubes in Angstroms (for masks of helical references and particles) |

rlnHelicalMaskTubeOuterDiameter | double | Outer diameter of helical tubes in Angstroms (for masks of helical references and particles) |

rlnHelicalOffsetStep | double | Step size for the searches of offsets along helical axis (in Angstroms) |

rlnHelicalRise | double | The helical rise (translation per subunit) in Angstroms |

rlnHelicalRiseInitial | double | The initial helical rise (translation per subunit) in Angstroms before refinement |

rlnHelicalRiseInitialStep | double | Initial step of helical rise search (in Angstroms) |

rlnHelicalRiseMax | double | Maximum helical rise (in Angstroms) |

rlnHelicalRiseMin | double | Minimum helical rise (in Angstroms) |

rlnHelicalSigmaDistance | double | Sigma of distance along the helical tracks |

rlnHelicalSymmetryLocalRefinement | bool | Flag to indicate that local refinement of helical parameters should be performed |

rlnHelicalTrackLength | double | Distance from the position of this helical segment to the starting point of the tube |

rlnHelicalTubeID | int | Helical tube ID for a helical segment |

rlnHelicalTubePitch | double | Cross-over distance for a helical segment (A) |

rlnHelicalTwist | double | The helical twist (rotation per subunit) in degrees |

rlnHelicalTwistInitial | double | The intial helical twist (rotation per subunit) in degrees before refinement |

rlnHelicalTwistInitialStep | double | Initial step of helical twist search (in degrees) |

rlnHelicalTwistMax | double | Maximum helical twist (in degrees, + for right-handedness) |

rlnHelicalTwistMin | double | Minimum helical twist (in degrees, + for right-handedness) |

rlnHighresLimitExpectation | double | High-resolution-limit (in Angstrom) for the expectation step |

rlnHighresLimitSGD | double | High-resolution-limit (in Angstrom) for Stochastic Gradient Descent |

rlnIgnoreHelicalSymmetry | bool | Flag to indicate that helical symmetry is ignored in 3D reconstruction |

rlnImageDimensionality | int | Dimensionality of data stored in an image (i.e. 2 or 3) |

rlnImageId | int | ID (i.e. a unique number) of an image |

rlnImageName | string | Name of an image |

rlnImageOriginalName | string | Original name of an image |

rlnImageSize | int | Size of an image (in pixels) |

rlnImageSizeX | int | Size of an image in the X-direction (in pixels) |

rlnImageSizeY | int | Size of an image in the Y-direction (in pixels) |

rlnImageSizeZ | int | Size of an image in the Z-direction (in pixels) |

rlnImageWeight | double | Relative weight of an image |

rlnIncrementImageSize | int | Number of Fourier shells to be included beyond the resolution where SSNR^MAP drops below 1 |

rlnIs3DSampling | bool | Flag to indicate this concerns a 3D sampling |

rlnIs3DTranslationalSampling | bool | Flag to indicate this concerns a x,y,z-translational sampling |

rlnIsFlip | bool | Flag to indicate that an image should be mirrored |

rlnIsHelix | bool | Flag to indicate that helical refinement should be performed |

rlnJoinHalvesUntilThisResolution | double | Resolution (in Angstrom) to join the two random half-reconstructions to prevent their diverging orientations (for C-symmetries) |

rlnKullbackLeiblerDivergence | double | Kullback-Leibler divergence for a particle |

rlnKurtosisExcessValue | double | Kurtosis excess (4th moment - 3) for the pixel values in an image |

rlnLensStability | double | Lens stability (in ppm) |

rlnLocalSymmetryFile | string | Local symmetry description file containing list of masks and their operators |

rlnLogAmplitudesIntercept | double | Y-value for Guinier plot: the fitted plateau of the logarithm of the radially averaged amplitudes |

rlnLogAmplitudesMTFCorrected | double | Y-value for Guinier plot: the logarithm of the radially averaged amplitudes after MTF correction |

rlnLogAmplitudesOriginal | double | Y-value for Guinier plot: the logarithm of the radially averaged amplitudes of the input map |

rlnLogAmplitudesSharpened | double | Y-value for Guinier plot: the logarithm of the radially averaged amplitudes after sharpening |

rlnLogAmplitudesWeighted | double | Y-value for Guinier plot: the logarithm of the radially averaged amplitudes after FSC-weighting |

rlnLogLikeliContribution | double | Contribution of a particle to the log-likelihood target function |

rlnLogLikelihood | double | Value of the log-likelihood target function |

rlnLongitudinalDisplacement | double | Longitudinal displacement (in Angstroms) |

rlnMagnification | double | Magnification at the detector (in times) |

rlnMagnificationCorrection | double | Magnification correction value for an image |

rlnMagnificationSearchRange | double | Search range for magnification correction |

rlnMagnificationSearchStep | double | Step size for magnification correction |

rlnMaskName | string | Name of an image that contains a [0,1] mask |

rlnMatrix_1_1 | double | Matrix element (1,1) of a 3x3 matrix |

rlnMatrix_1_2 | double | Matrix element (1,2) of a 3x3 matrix |

rlnMatrix_1_3 | double | Matrix element (1,3) of a 3x3 matrix |

rlnMatrix_2_1 | double | Matrix element (2,1) of a 3x3 matrix |

rlnMatrix_2_2 | double | Matrix element (2,1) of a 3x3 matrix |

rlnMatrix_2_3 | double | Matrix element (2,1) of a 3x3 matrix |

rlnMatrix_3_1 | double | Matrix element (3,1) of a 3x3 matrix |

rlnMatrix_3_2 | double | Matrix element (3,1) of a 3x3 matrix |

rlnMatrix_3_3 | double | Matrix element (3,1) of a 3x3 matrix |

rlnMaxNumberOfPooledParticles | int | Maximum number particles that are processed together to speed up calculations |

rlnMaxValueProbDistribution | double | Maximum value of the (normalised) probability function for a particle |

rlnMaximumCoarseImageSize | int | Maximum size of the images to be used in the first pass of the adaptive oversampling strategy (may be smaller than the original image size) |

rlnMaximumValue | double | Maximum value for the pixels in an image |

rlnMicrographBinning | double | Micrograph binning factor |

rlnMicrographDefectFile | string | Name of a defect list file |

rlnMicrographDoseRate | double | Dose rate in electrons per square Angstrom per frame |

rlnMicrographEndFrame | int | End frame of a motion model |

rlnMicrographFrameNumber | int | Micrograph frame number |

rlnMicrographGainName | string | Name of a gain reference |

rlnMicrographId | int | ID (i.e. a unique number) of a micrograph |

rlnMicrographMetadata | string | Name of a micrograph metadata file |

rlnMicrographMovieName | string | Name of a micrograph movie stack |

rlnMicrographName | string | Name of a micrograph |

rlnMicrographNameNoDW | string | Name of a micrograph without dose weighting |

rlnMicrographOriginalPixelSize | double | Pixel size of original movie before binning in Angstrom/pixel. |

rlnMicrographPreExposure | double | Pre-exposure dose in electrons per square Angstrom |

rlnMicrographShiftX | double | X shift of a (patch of) micrograph |

rlnMicrographShiftY | double | Y shift of a (patch of) micrograph |

rlnMicrographStartFrame | int | Start frame of a motion model |

rlnMicrographTiltAngle | double | Tilt angle (in degrees) used to collect a micrograph |

rlnMicrographTiltAxisDirection | double | Direction of the tilt-axis (in degrees) used to collect a micrograph |

rlnMicrographTiltAxisOutOfPlane | double | Out-of-plane angle (in degrees) of the tilt-axis used to collect a micrograph (90=in-plane) |

rlnMinRadiusNnInterpolation | int | Minimum radius for NN-interpolation (in Fourier pixels), for smaller radii linear int. is used |

rlnMinimumValue | double | Minimum value for the pixels in an image |

rlnModelStarFile | string | STAR file with metadata for the model that is being refined |

rlnModelStarFile2 | string | STAR file with metadata for the second model that is being refined (from random halves of the data) |

rlnMotionModelCoeff | double | A coefficient of a motion model |

rlnMotionModelCoeffsIdx | int | Index of a coefficient of a motion model |

rlnMotionModelVersion | int | Version of micrograph motion model |

rlnMovieFrameNumber | int | Number of a movie frame |

rlnMovieFramesRunningAverage | int | Number of movie frames inside the running average that will be used for movie-refinement |

rlnMtfValue | double | Value of the detectors modulation transfer function (between 0 and 1) |

rlnNormCorrection | double | Normalisation correction value for an image |

rlnNormCorrectionAverage | double | Average value (over all images) of the normalisation correction values |

rlnNrBodies | int | The number of independent rigid bodies to be refined in multi-body refinement |

rlnNrClasses | int | The number of references (i.e. classes) to be used in refinement |

rlnNrGroups | int | The number of different groups of images (each group has its own noise spectrum, and intensity-scale correction) |

rlnNrHelicalAsymUnits | int | How many new helical asymmetric units are there in each box |

rlnNrOfFrames | int | Number of movie frames that were collected for this particle |

rlnNrOfSignificantSamples | int | Number of orientational/class assignments (for a particle) with sign.probabilities in the 1st pass of adaptive oversampling |

rlnNumberOfIterWithoutChangingAssignments | int | Number of iterations that have passed without large changes in orientation and class assignments |

rlnNumberOfIterWithoutResolutionGain | int | Number of iterations that have passed without a gain in resolution |

rlnNumberOfIterations | int | Maximum number of iterations to be performed |

rlnOffsetRange | double | Search range for the origin offsets (in Angstroms) |

rlnOffsetStep | double | Step size for the searches in the origin offsets (in Angstroms) |

rlnOrientSamplingStarFile | string | STAR file with metadata for the orientational sampling |

rlnOrientationDistribution | double | Probability Density Function of the orientations (i.e. fraction of images assigned to each orient) |

rlnOrientationalPriorMode | int | Mode for prior distributions on the orientations (0=no prior; 1=(rot,tilt,psi); 2=(rot,tilt); 3=rot; 4=tilt; 5=psi) |

rlnOrientationsID | int | ID (i.e. a unique number) for an orientation |

rlnOriginX | double | X-coordinate (in pixels) for the origin of rotation |

rlnOriginXPrior | double | Center of the prior on the X-coordinate (in pixels) for the origin of rotation |

rlnOriginY | double | Y-coordinate (in pixels) for the origin of rotation |

rlnOriginYPrior | double | Center of the prior on the X-coordinate (in pixels) for the origin of rotation |

rlnOriginZ | double | Z-coordinate (in pixels) for the origin of rotation |

rlnOriginZPrior | double | Center of the prior on the X-coordinate (in pixels) for the origin of rotation |

rlnOriginalImageSize | int | Original size of the images (in pixels) |

rlnOriginalParticleName | string | Original name for a particles |

rlnOutputRootName | string | Rootname for all output files (this may include a directory structure, which should then exist) |

rlnOverallAccuracyRotations | double | Overall accuracy of the rotational assignments (in degrees) |

rlnOverallAccuracyTranslations | double | Overall accuracy of the translational assignments (in pixels) |

rlnOverallFourierCompleteness | double | Fraction of all Fourier components up to the current resolution with SNR>1 |

rlnPaddingFactor | double | Oversampling factor for Fourier transforms of the references |

rlnParticleDiameter | double | Diameter of the circular mask to be applied to all experimental images (in Angstroms) |

rlnParticleFigureOfMerit | double | Developmental FOM for a particle |

rlnParticleId | int | ID (i.e. a unique number) for a particle |

rlnParticleName | string | Name for a particle |

rlnParticleNumber | int | Number of particles |

rlnParticleSelectZScore | double | Sum of Z-scores from particle_select. High Z-scores are likely to be outliers. |

rlnPerFrameCumulativeWeight | double | Sum of the resolution-dependent relative weights from the first frame until the given frame |

rlnPerFrameRelativeWeight | double | The resolution-dependent relative weights for a given frame |

rlnPhaseShift | double | Phase-shift from a phase-plate (in degrees) |

rlnPipeLineEdgeFromNode | string | Name of the origin of an edge |

rlnPipeLineEdgeProcess | string | Name of the destination of an edge |

rlnPipeLineEdgeToNode | string | Name of the to-Node in an edge |

rlnPipeLineJobCounter | int | Number of the last job in the pipeline |

rlnPipeLineNodeName | string | Name of a Node in the pipeline |

rlnPipeLineNodeType | int | Type of a Node in the pipeline |

rlnPipeLineProcessAlias | string | Alias of a Process in the pipeline |

rlnPipeLineProcessName | string | Name of a Process in the pipeline |

rlnPipeLineProcessStatus | int | Status of a Process in the pipeline (running, scheduled, finished or cancelled) |

rlnPipeLineProcessType | int | Type of a Process in the pipeline |

rlnPixelSize | double | Size of the pixels in the references and images (in Angstroms) |

rlnPsiStep | double | Step size (in degrees) for the sampling of the in-plane rotation angle (psi) |

rlnRadiusMaskExpImages | int | Radius of the circular mask to be applied to all experimental images (in Angstroms) |

rlnRadiusMaskMap | int | Radius of the spherical mask to be applied to all references (in Angstroms) |

rlnRandomSeed | int | Seed (i.e. a number) for the random number generator |

rlnRandomSubset | int | Random subset to which this particle belongs |

rlnRandomiseFrom | double | Resolution (in A) from which the phases are randomised in the postprocessing step |

rlnReconstructImageName | string | Name of an image to be used for reconstruction only |

rlnReferenceDimensionality | int | Dimensionality of the references (2D/3D) |

rlnReferenceImage | string | Name of a reference image |

rlnReferenceSigma2 | double | Spherical average of the estimated power in the noise of a reference |

rlnReferenceSpectralPower | double | Spherical average of the power of the reference |

rlnReferenceTau2 | double | Spherical average of the estimated power in the signal of a reference |

rlnRefsAreCtfCorrected | bool | Flag to indicate that the input references have been CTF-amplitude corrected |

rlnResolution | double | Resolution (in 1/Angstroms) |

rlnResolutionInversePixel | double | Resolution (in 1/pixel, Nyquist = 0.5) |

rlnResolutionSquared | double | X-value for Guinier plot: squared resolution in 1/Angstrom^2 |

rlnSGDGradientImage | string | Name of image containing the SGD gradient |

rlnSamplingPerturbFactor | double | Factor for random perturbation on the orientational sampling (between 0 no perturbation and 1 very strong perturbation) |

rlnSamplingPerturbInstance | double | Random instance of the random perturbation on the orientational sampling |

rlnSamplingRate | double | Sampling rate of an image (in Angstrom/pixel) |

rlnSamplingRateX | double | Sampling rate in X-direction of an image (in Angstrom/pixel) |

rlnSamplingRateY | double | Sampling rate in Y-direction of an image (in Angstrom/pixel) |

rlnSamplingRateZ | double | Sampling rate in Z-direction of an image (in Angstrom/pixel) |

rlnSelected | int | Flag whether an entry in a metadatatable is selected (1) in the viewer or not (0) |

rlnSgdFinalIterations | int | Number of final SGD iterations (at rlnSgdFinalResolution and with rlnSgdFinalSubsetSize) |

rlnSgdFinalResolution | double | Resolution (in A) to use during the final SGD iterations |

rlnSgdFinalSubsetSize | int | Number of particles in a mini-batch (subset) during the final SGD iteration |

rlnSgdInBetweenIterations | int | Number of SGD iteration in between the initial ones to the final ones (with linear interpolation of resolution and subset size) |

rlnSgdInitialIterations | int | Number of initial SGD iterations (at rlnSgdInitialResolution and with rlnSgdInitialSubsetSize) |

rlnSgdInitialResolution | double | Resolution (in A) to use during the initial SGD iterations |

rlnSgdInitialSubsetSize | int | Number of particles in a mini-batch (subset) during the initial SGD iterations |

rlnSgdMaxSubsets | int | Stop SGD after doing this many subsets (possibly spanning more than 1 iteration) |

rlnSgdMuFactor | double | The mu-parameter that controls the momentum of the SGD gradients |

rlnSgdSigma2FudgeHalflife | int | After processing this many particles the multiplicative factor for the noise variance will have halved |

rlnSgdSigma2FudgeInitial | double | The variance of the noise will initially be multiplied with this value (larger than 1) |

rlnSgdSkipAnneal | bool | Option to switch off annealing of multiple references in SGD |

rlnSgdStepsize | double | Stepsize in SGD updates) |

rlnSgdSubsetSize | int | The number of particles in the random subsets for SGD |

rlnSgdWriteEverySubset | int | Every this many iterations the model is written to disk in SGD |

rlnSigma2Noise | double | Spherical average of the standard deviation in the noise (sigma) |

rlnSigmaOffsets | double | Standard deviation in the origin offsets (in Angstroms) |

rlnSigmaPriorPsiAngle | double | Standard deviation of the prior on the psi (i.e. third Euler) angle |

rlnSigmaPriorRotAngle | double | Standard deviation of the prior on the rot (i.e. first Euler) angle |

rlnSigmaPriorTiltAngle | double | Standard deviation of the prior on the tilt (i.e. second Euler) angle |

rlnSignalToNoiseRatio | double | Spectral signal-to-noise ratio for a reference |

rlnSkewnessValue | double | Skewness (3rd moment) for the pixel values in an image |

rlnSmallestChangesClasses | int | Smallest changes thus far in the optimal class assignments (in numer of particles). |

rlnSmallestChangesOffsets | double | Smallest changes thus far in the optimal offset assignments (in pixels). |

rlnSmallestChangesOrientations | double | Smallest changes thus far in the optimal orientation assignments (in degrees). |

rlnSolventMask2Name | string | Name of a secondary solvent mask (e.g. to flatten density inside an icosahedral virus) |

rlnSolventMaskName | string | Name of an image that contains a (possibly soft) mask for the solvent area (values=0 for solvent, values =1 for protein) |

rlnSortedIndex | int | Index of a metadata entry after sorting (first sorted index is 0). |

rlnSpectralIndex | int | Spectral index (i.e. distance in pixels to the origin in Fourier space) |

rlnSpectralOrientabilityContribution | double | Spectral SNR contribution to the orientability of individual particles |

rlnSphericalAberration | double | Spherical aberration (in millimeters) |

rlnSsnrMap | double | Spectral signal-to-noise ratio as defined for MAP estimation (SSNR^MAP) |

rlnStandardDeviationValue | double | Standard deviation for the pixel values in an image |

rlnStarFileMovieParticles | string | Filename of a STAR file with movie-particles in it |

rlnSymmetryGroup | string | Symmetry group (e.g., C1, D7, I2, I5, etc.) |

rlnTau2FudgeFactor | double | Regularisation parameter with which estimates for the power in the references will be multiplied (T in original paper) |

rlnTauSpectrumName | string | Name of a STAR file that holds a tau2-spectrum |

rlnTiltAngleLimit | double | Values to which to limit the tilt angles (positive for keeping side views, negative for keeping top views) |

rlnTransversalDisplacement | double | Transversal displacement (in Angstroms) |

rlnUnfilteredMapHalf1 | string | Name of the unfiltered map from halfset 1 |

rlnUnfilteredMapHalf2 | string | Name of the unfiltered map from halfset 2 |

rlnUseTooCoarseSampling | bool | Flag to indicate that the angular sampling on the sphere will be one step coarser than needed to speed up calculations |

rlnVoltage | double | Voltage of the microscope (in kV) |

rlnWidthMaskEdge | int | Width (in pixels) of the soft edge for spherical/circular masks to be used for solvent flattening |