RELIONの定義済みラベル
提供: Eospedia
- 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 |
