RELIONの定義済みラベル

提供: Eospedia
2019年5月15日 (水) 13:12時点におけるKttn (トーク | 投稿記録)による版

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  • 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
  • そのうち日本語化、説明充実化を試みます。
RELION メタデータラベル一覧表 (v3.0.5)
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