「RELIONの定義済みラベル」の版間の差分

提供: Eospedia
移動: 案内検索
(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...」)
 
行1: 行1:
* RELION v3.0.5の以下コマンドの出力です。
+
* 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
  
* 読みにくいのでそのうち表にします。
+
* そのうち日本語化、説明充実化を試みます。
* フォーマットは "ラベル名 (C++型名) : 説明"です。
+
  
 
+
{| class="wikitable" style="width:100%"
+++ RELION MetaDataLabel (EMDL) definitions: +++
+
|+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 (double) : Accumulated global motion during the first frames of the movie (in A)
+
! style="width:5%" | データ型
 
+
! 説明
rlnAccumMotionLate (double) : Accumulated global motion during the last frames of the movie (in A)
+
|-
 
+
| rlnAccumMotionEarly
rlnAccumMotionTotal (double) : Accumulated global motion during the entire movie (in A)
+
| double
 
+
| Accumulated global motion during the first frames of the movie (in A)
rlnAccuracyRotations (double) : Estimated accuracy (in degrees) with which rotations can be assigned
+
|-
 
+
| rlnAccumMotionLate
rlnAccuracyTranslations (double) : Estimated accuracy (in pixels) with which translations can be assigned
+
| double
 
+
| Accumulated global motion during the last frames of the movie (in A)
rlnAdaptiveOversampleFraction (double) : Fraction of the weights that will be oversampled in a second pass of the adaptive oversampling strategy
+
|-
 
+
| rlnAccumMotionTotal
rlnAdaptiveOversampleOrder (int)    : Order of the adaptive oversampling (0=no oversampling, 1= 2x oversampling; 2= 4x oversampling, etc)
+
| double
 
+
| Accumulated global motion during the entire movie (in A)
rlnAmplitudeContrast (double) : Amplitude contrast (as a fraction, i.e. 10% = 0.1)
+
|-
 
+
| rlnAccuracyRotations
rlnAmplitudeCorrelationMaskedMaps (double) : Correlation coefficient between amplitudes in Fourier shells of masked maps
+
| double
 
+
| Estimated accuracy (in degrees) with which rotations can be assigned
rlnAmplitudeCorrelationUnmaskedMaps (double) : Correlation coefficient between amplitudes in Fourier shells of unmasked maps
+
|-
 
+
| rlnAccuracyTranslations
rlnAnglePsi (double) : Third Euler, or in-plane angle (psi, in degrees)
+
| double
 
+
| Estimated accuracy (in pixels) with which translations can be assigned
rlnAnglePsiFlipRatio (double) : Flip ratio of bimodal psi prior (0~0.5, 0 means an ordinary prior, 0.5 means a perfect bimodal prior)
+
|-
 
+
| rlnAdaptiveOversampleFraction
rlnAnglePsiPrior (double) : Center of the prior (in degrees) on the third Euler angle (psi)
+
| double
 
+
| Fraction of the weights that will be oversampled in a second pass of the adaptive oversampling strategy
rlnAngleRot (double) : First Euler angle (rot, in degrees)
+
|-
 
+
| rlnAdaptiveOversampleOrder
rlnAngleRotPrior (double) : Center of the prior (in degrees) on the first Euler angle (rot)
+
| int
 
+
| Order of the adaptive oversampling (0=no oversampling, 1= 2x oversampling; 2= 4x oversampling, etc)
rlnAngleTilt (double) : Second Euler angle (tilt, in degrees)
+
|-
 
+
| rlnAmplitudeContrast
rlnAngleTiltPrior (double) : Center of the prior (in degrees) on the second Euler angle (tilt)
+
| double
 
+
| Amplitude contrast (as a fraction, i.e. 10% = 0.1)
rlnAngstromResolution (double) : Resolution (in Angstroms)
+
|-
 
+
| rlnAmplitudeCorrelationMaskedMaps
rlnAreaId (int)    : ID (i.e. a unique number) of an area (i.e. field-of-view)
+
| double
 
+
| Correlation coefficient between amplitudes in Fourier shells of masked maps
rlnAreaName (string) : Name of an area (i.e. field-of-view)
+
|-
 
+
| rlnAmplitudeCorrelationUnmaskedMaps
rlnAutoLocalSearchesHealpixOrder (int)    : Healpix order (before oversampling) from which autosampling procedure will use local angular searches
+
| double
 
+
| Correlation coefficient between amplitudes in Fourier shells of unmasked maps
rlnAutopickFigureOfMerit (double) : Autopicking FOM for a particle
+
|-
 
+
| rlnAnglePsi
rlnAvailableMemory (double) : Available memory per computing node (i.e. per MPI-process)
+
| double
 
+
| Third Euler, or in-plane angle (psi, in degrees)
rlnAverageNrOfFrames (int)    : Number of movie frames that one averages over upon extraction of movie-particles
+
|-
 
+
| rlnAnglePsiFlipRatio
rlnAveragePmax (double) : Average value (over all images) of the maxima of the probability distributions
+
| double
 
+
| Flip ratio of bimodal psi prior (0~0.5, 0 means an ordinary prior, 0.5 means a perfect bimodal prior)
rlnAverageValue (double) : Average value for the pixels in an image
+
|-
 
+
| rlnAnglePsiPrior
rlnBeamTiltClass (int)    : Beam-tilt class of a particle
+
| double
 
+
| Center of the prior (in degrees) on the third Euler angle (psi)
rlnBeamTiltX (double) : Beam tilt in the X-direction (in mrad)
+
|-
 
+
| rlnAngleRot
rlnBeamTiltY (double) : Beam tilt in the Y-direction (in mrad)
+
| double
 
+
| First Euler angle (rot, in degrees)
rlnBestResolutionThusFar (double) : The highest resolution that has been obtained in this optimization thus far
+
|-
 
+
| rlnAngleRotPrior
rlnBfactorUsedForSharpening (double) : Applied B-factor in the sharpening of the map
+
| double
 
+
| Center of the prior (in degrees) on the first Euler angle (rot)
rlnBodyKeepFixed (int)    : Flag to indicate whether to keep a body fixed (value 1) or keep on refining it (0)
+
|-
 
+
| rlnAngleTilt
rlnBodyMaskName (string) : Name of an image that contains a [0,1] body mask for multi-body refinement
+
| double
 
+
| Second Euler angle (tilt, in degrees)
rlnBodyReferenceName (string) : Name of an image that contains the initial reference for one body of a multi-body refinement
+
|-
 
+
| rlnAngleTiltPrior
rlnBodyRotateDirectionX (double) : X-component of axis around which to rotate this body
+
| double
 
+
| Center of the prior (in degrees) on the second Euler angle (tilt)
rlnBodyRotateDirectionY (double) : Y-component of axis around which to rotate this body
+
|-
 
+
| rlnAngstromResolution
rlnBodyRotateDirectionZ (double) : Z-component of axis around which to rotate this body
+
| double
 
+
| Resolution (in Angstroms)
rlnBodyRotateRelativeTo (int)    : Number of the body relative to which this body rotates (if negative, use rlnBodyRotateDirectionXYZ)
+
|-
 
+
| rlnAreaId
rlnBodySigmaAngles (double) : Width of prior on all three Euler angles of a body in multibody refinement (in degrees)
+
| int
 
+
| ID (i.e. a unique number) of an area (i.e. field-of-view)
rlnBodySigmaOffset (double) : Width of prior on origin offsets of a body in multibody refinement (in pixels)
+
|-
 
+
| rlnAreaName
rlnBodySigmaPsi (double) : Width of prior on psi angles of a body in multibody refinement (in degrees)
+
| string
 
+
| Name of an area (i.e. field-of-view)
rlnBodySigmaRot (double) : Width of prior on rot angles of a body in multibody refinement (in degrees)
+
|-
 
+
| rlnAutoLocalSearchesHealpixOrder
rlnBodySigmaTilt (double) : Width of prior on tilt angles of a body in multibody refinement (in degrees)
+
| int
 
+
| Healpix order (before oversampling) from which autosampling procedure will use local angular searches
rlnBodyStarFile (string) : Name of STAR file with body masks and metadata
+
|-
 
+
| rlnAutopickFigureOfMerit
rlnChangesOptimalClasses (double) : The number of particles that changed their optimal clsas assignment in the last iteration
+
| double
 
+
| Autopicking FOM for a particle
rlnChangesOptimalOffsets (double) : The average change in optimal translation in the last iteration (in pixels)  
+
|-
 
+
| rlnAvailableMemory
rlnChangesOptimalOrientations (double) : The average change in optimal orientation in the last iteration (in degrees)  
+
| double
 
+
| Available memory per computing node (i.e. per MPI-process)
rlnChromaticAberration (double) : Chromatic aberration (in millimeters)
+
|-
 
+
| rlnAverageNrOfFrames
rlnClassDistribution (double) : Probability Density Function of the different classes (i.e. fraction of images assigned to each class)
+
| int
 
+
| Number of movie frames that one averages over upon extraction of movie-particles
rlnClassNumber (int)    : Class number for which a particle has its highest probability
+
|-
 
+
| rlnAveragePmax
rlnClassPriorOffsetX (double) : Prior in the X-offset for a class (in pixels)
+
| double
 
+
| Average value (over all images) of the maxima of the probability distributions
rlnClassPriorOffsetY (double) : Prior in the Y-offset for a class (in pixels)
+
|-
 
+
| rlnAverageValue
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)
+
| double
 
+
| Average value for the pixels in an image
rlnComment (string) : A metadata comment (This is treated in a special way)
+
|-
 
+
| rlnBeamTiltClass
rlnConvergenceCone (double) : Convergence cone (in mrad)
+
| int
 
+
| Beam-tilt class of a particle
rlnCoordinateX (double) : X-Position of an image in a micrograph (in pixels)
+
|-
 
+
| rlnBeamTiltX
rlnCoordinateY (double) : Y-Position of an image in a micrograph (in pixels)
+
| double
 
+
| Beam tilt in the X-direction (in mrad)
rlnCoordinateZ (double) : Z-Position of an image in a 3D micrograph, i.e. tomogram (in pixels)
+
|-
 
+
| rlnBeamTiltY
rlnCorrectedFourierShellCorrelationPhaseRandomizedMaskedMaps (double) : FSC value after masking of the randomized-phases maps
+
| double
 
+
| Beam tilt in the Y-direction (in mrad)
rlnCorrelationFitGuinierPlot (double) : The correlation coefficient of the fitted line through the Guinier-plot
+
|-
 
+
| rlnBestResolutionThusFar
rlnCtfAstigmatism (double) : Absolute value of the difference between defocus in U- and V-direction (in A)
+
| double
 
+
| The highest resolution that has been obtained in this optimization thus far
rlnCtfBfactor (double) : B-factor (in A^2) that describes CTF power spectrum fall-off
+
|-
 
+
| rlnBfactorUsedForSharpening
rlnCtfDataAreCtfPremultiplied (bool)  : Flag to indicate that the input images have been premultiplied with their CTF
+
| double
 
+
| Applied B-factor in the sharpening of the map
rlnCtfDataArePhaseFlipped (bool)  : Flag to indicate that the input images have been phase-flipped
+
|-
 
+
| rlnBodyKeepFixed
rlnCtfFigureOfMerit (double) : Figure of merit for the fit of the CTF (not used inside relion_refine)
+
| int
 
+
| Flag to indicate whether to keep a body fixed (value 1) or keep on refining it (0)
rlnCtfImage (string) : Name of an image with all CTF values
+
|-
 
+
| rlnBodyMaskName
rlnCtfMaxResolution (double) : Estimated maximum resolution (in A) of significant CTF Thon rings
+
| string
 
+
| Name of an image that contains a [0,1] body mask for multi-body refinement
rlnCtfScalefactor (double) : Linear scale-factor on the CTF (values between 0 and 1)
+
|-
 
+
| rlnBodyReferenceName
rlnCtfValidationScore (double) : Gctf-based validation score for the quality of the CTF fit
+
| string
 
+
| Name of an image that contains the initial reference for one body of a multi-body refinement
rlnCtfValue (double) : Value of the Contrast Transfer Function
+
|-
 
+
| rlnBodyRotateDirectionX
rlnCurrentImageSize (int)    : Current size of the images used in the refinement
+
| double
 
+
| X-component of axis around which to rotate this body
rlnCurrentIteration (int)    : The number of the current iteration
+
|-
 
+
| rlnBodyRotateDirectionY
rlnCurrentResolution (double) : Current resolution where SSNR^MAP drops below 1 (in 1/Angstroms)
+
| double
 
+
| Y-component of axis around which to rotate this body
rlnDataDimensionality (int)    : Dimensionality of the data (2D/3D)
+
|-
 
+
| rlnBodyRotateDirectionZ
rlnDataType (int)    : Type of data stored in an image (e.g. int, RFLOAT etc)
+
| double
 
+
| Z-component of axis around which to rotate this body
rlnDefocusAngle (double) : Angle between X and defocus U direction (in degrees)
+
|-
 
+
| rlnBodyRotateRelativeTo
rlnDefocusU (double) : Defocus in U-direction (in Angstroms, positive values for underfocus)
+
| int
 
+
| Number of the body relative to which this body rotates (if negative, use rlnBodyRotateDirectionXYZ)
rlnDefocusV (double) : Defocus in V-direction (in Angstroms, positive values for underfocus)
+
|-
 
+
| rlnBodySigmaAngles
rlnDetectorPixelSize (double) : Pixel size of the detector (in micrometers)
+
| double
 
+
| Width of prior on all three Euler angles of a body in multibody refinement (in degrees)
rlnDiff2RandomHalves (double) : Power of the differences between two independent reconstructions from random halves of the data
+
|-
 
+
| rlnBodySigmaOffset
rlnDifferentialPhaseResidualMaskedMaps (double) : Differential Phase Residual in Fourier shells of masked maps
+
| double
 
+
| Width of prior on origin offsets of a body in multibody refinement (in pixels)
rlnDifferentialPhaseResidualUnmaskedMaps (double) : Differential Phase Residual in Fourier shells of unmasked maps
+
|-
 
+
| rlnBodySigmaPsi
rlnDoAutoRefine (bool)  : Flag to indicate that 3D auto-refine procedure is being used
+
| double
 
+
| Width of prior on psi angles of a body in multibody refinement (in degrees)
rlnDoCorrectCtf (bool)  : Flag to indicate that CTF-correction should be performed
+
|-
 
+
| rlnBodySigmaRot
rlnDoCorrectMagnification (bool)  : Flag to indicate that (per-group) magnification correction should be performed
+
| double
 
+
| Width of prior on rot angles of a body in multibody refinement (in degrees)
rlnDoCorrectNorm (bool)  : Flag to indicate that (per-image) normalisation-error correction should be performed
+
|-
 
+
| rlnBodySigmaTilt
rlnDoCorrectScale (bool)  : Flag to indicate that internal (per-group) intensity-scale correction should be performed
+
| double
 
+
| Width of prior on tilt angles of a body in multibody refinement (in degrees)
rlnDoFastSubsetOptimisation (bool)  : Use subsets of the data in the earlier iterations to speed up convergence
+
|-
 
+
| rlnBodyStarFile
rlnDoHelicalRefine (bool)  : Flag to indicate that helical refinement should be performed
+
| string
 
+
| Name of STAR file with body masks and metadata
rlnDoIgnoreCtfUntilFirstPeak (bool)  : Flag to indicate that the CTFs should be ignored until their first peak
+
|-
 
+
| rlnChangesOptimalClasses
rlnDoMapEstimation (bool)  : Flag to indicate that MAP estimation should be performed (otherwise ML estimation)
+
| double
 
+
| The number of particles that changed their optimal clsas assignment in the last iteration
rlnDoOnlyFlipCtfPhases (bool)  : Flag to indicate that CTF-correction should only comprise phase-flipping
+
|-
 
+
| rlnChangesOptimalOffsets
rlnDoRealignMovies (bool)  : Flag to indicate that individual frames of movies are being re-aligned
+
| double
 
+
| The average change in optimal translation in the last iteration (in pixels)
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
+
|-
 
+
| rlnChangesOptimalOrientations
rlnDoSkipRotate (bool)  : Flag to indicate that rotational searches will be omitted from the refinement, only marginalisation over classes and translations will take place
+
| double
 
+
| The average change in optimal orientation in the last iteration (in degrees)
rlnDoSolventFlattening (bool)  : Flag to indicate that the references should be masked to set their solvent areas to a constant density
+
|-
 
+
| rlnChromaticAberration
rlnDoSolventFscCorrection (bool)  : Flag to indicate that the FSCs should be solvent-corrected during refinement
+
| double
 
+
| Chromatic aberration (in millimeters)
rlnDoSplitRandomHalves (bool)  : Flag to indicate that the data should be split into two completely separate, random halves
+
|-
 
+
| rlnClassDistribution
rlnDoStochasticGradientDescent (bool)  : Flag to indicate that SGD-optimisation should be performed (otherwise expectation maximisation)
+
| double
 
+
| Probability Density Function of the different classes (i.e. fraction of images assigned to each class)
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
+
|-
 
+
| rlnClassNumber
rlnEnabled (bool)  : Not used in RELION, only included for backward compatibility with XMIPP selfiles
+
| int
 
+
| Class number for which a particle has its highest probability
rlnEnergyLoss (double) : Energy loss (in eV)
+
|-
 
+
| rlnClassPriorOffsetX
rlnEstimatedResolution (double) : Estimated resolution (in A) for a reference
+
| double
 
+
| Prior in the X-offset for a class (in pixels)
rlnExperimentalDataStarFile (string) : STAR file with metadata for the experimental images
+
|-
 
+
| rlnClassPriorOffsetY
rlnFinalResolution (double) : Final estimated resolution after postprocessing (in Angstroms)
+
| double
 
+
| Prior in the Y-offset for a class (in pixels)
rlnFittedInterceptGuinierPlot (double) : The fitted intercept of the Guinier-plot
+
|-
 
+
| rlnCoarseImageSize
rlnFittedSlopeGuinierPlot (double) : The fitted slope of the Guinier-plot
+
| 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 (bool)  : Flag to indicate that the estimates for the power spectra of the noise should be kept constant
+
|-
 
+
| rlnComment
rlnFixSigmaOffsetEstimates (bool)  : Flag to indicate that the estimates for the stddev in the origin offsets should be kept constant
+
| string
 
+
| A metadata comment (This is treated in a special way)
rlnFixTauEstimates (bool)  : Flag to indicate that the estimates for the power spectra of the signal (i.e. the references) should be kept constant
+
|-
 
+
| rlnConvergenceCone
rlnFourierCompleteness (double) : Fraction of Fourier components (per resolution shell) with SNR>1
+
| double
 
+
| Convergence cone (in mrad)
rlnFourierShellCorrelation (double) : FSC value (of unspecified type, e.g. masked or unmasked)
+
|-
 
+
| rlnCoordinateX
rlnFourierShellCorrelationCorrected (double) : Final FSC value: i.e. after correction based on masking of randomized-phases maps
+
| double
 
+
| X-Position of an image in a micrograph (in pixels)
rlnFourierShellCorrelationMaskedMaps (double) : FSC value after masking of the original maps
+
|-
 
+
| rlnCoordinateY
rlnFourierShellCorrelationUnmaskedMaps (double) : FSC value before masking of the original maps
+
| double
 
+
| Y-Position of an image in a micrograph (in pixels)
rlnFourierSpaceInterpolator (int)    : The kernel used for Fourier-space interpolation (NN=0, linear=1)
+
|-
 
+
| rlnCoordinateZ
rlnGoldStandardFsc (double) : Fourier shell correlation between two independent reconstructions from random halves of the data
+
| double
 
+
| Z-Position of an image in a 3D micrograph, i.e. tomogram (in pixels)
rlnGroupName (string) : The name of a group of images (e.g. all images from a micrograph)
+
|-
 
+
| rlnCorrectedFourierShellCorrelationPhaseRandomizedMaskedMaps
rlnGroupNrParticles (int)    : Number particles in a group of images
+
| double
 
+
| FSC value after masking of the randomized-phases maps
rlnGroupNumber (int)    : The number of a group of images
+
|-
 
+
| rlnCorrelationFitGuinierPlot
rlnGroupScaleCorrection (double) : Intensity-scale correction for a group of images
+
| double
 
+
| The correlation coefficient of the fitted line through the Guinier-plot
rlnHasConverged (bool)  : Flag to indicate that the optimization has converged
+
|-
 
+
| rlnCtfAstigmatism
rlnHasHighFscAtResolLimit (bool)  : Flag to indicate that the FSC at the resolution limit is significant
+
| double
 
+
| Absolute value of the difference between defocus in U- and V-direction (in A)
rlnHasLargeSizeIncreaseIterationsAgo (int)    : How many iterations have passed since the last large increase in image size
+
|-
 
+
| rlnCtfBfactor
rlnHealpixOrder (int)    : Healpix order for the sampling of the first two Euler angles (rot, tilt) on the 3D sphere
+
| double
 
+
| B-factor (in A^2) that describes CTF power spectrum fall-off
rlnHelicalCentralProportion (double) : Only expand this central fraction of the Z axis when imposing real-space helical symmetry
+
|-
 
+
| rlnCtfDataAreCtfPremultiplied
rlnHelicalKeepTiltPriorFixed (bool)  : Flag to indicate that helical tilt priors are kept fixed (at 90 degrees) in global angular searches
+
| bool
 
+
| Flag to indicate that the input images have been premultiplied with their CTF
rlnHelicalMaskTubeInnerDiameter (double) : Inner diameter of helical tubes in Angstroms (for masks of helical references and particles)
+
|-
 
+
| rlnCtfDataArePhaseFlipped
rlnHelicalMaskTubeOuterDiameter (double) : Outer diameter of helical tubes in Angstroms (for masks of helical references and particles)
+
| bool
 
+
| Flag to indicate that the input images have been phase-flipped
rlnHelicalOffsetStep (double) : Step size for the searches of offsets along helical axis (in Angstroms)
+
|-
 
+
| rlnCtfFigureOfMerit
rlnHelicalRise (double) : The helical rise (translation per subunit) in Angstroms
+
| double
 
+
| Figure of merit for the fit of the CTF (not used inside relion_refine)
rlnHelicalRiseInitial (double) : The initial helical rise (translation per subunit) in Angstroms before refinement
+
|-
 
+
| rlnCtfImage
rlnHelicalRiseInitialStep (double) : Initial step of helical rise search (in Angstroms)
+
| string
 
+
| Name of an image with all CTF values
rlnHelicalRiseMax (double) : Maximum helical rise (in Angstroms)
+
|-
 
+
| rlnCtfMaxResolution
rlnHelicalRiseMin (double) : Minimum helical rise (in Angstroms)
+
| double
 
+
| Estimated maximum resolution (in A) of significant CTF Thon rings
rlnHelicalSigmaDistance (double) : Sigma of distance along the helical tracks
+
|-
 
+
| rlnCtfScalefactor
rlnHelicalSymmetryLocalRefinement (bool)  : Flag to indicate that local refinement of helical parameters should be performed
+
| double
 
+
| Linear scale-factor on the CTF (values between 0 and 1)
rlnHelicalTrackLength (double) : Distance from the position of this helical segment to the starting point of the tube
+
|-
 
+
| rlnCtfValidationScore
rlnHelicalTubeID (int)    : Helical tube ID for a helical segment
+
| double
 
+
| Gctf-based validation score for the quality of the CTF fit
rlnHelicalTubePitch (double) : Cross-over distance for a helical segment (A)
+
|-
 
+
| rlnCtfValue
rlnHelicalTwist (double) : The helical twist (rotation per subunit) in degrees
+
| double
 
+
| Value of the Contrast Transfer Function
rlnHelicalTwistInitial (double) : The intial helical twist (rotation per subunit) in degrees before refinement
+
|-
 
+
| rlnCurrentImageSize
rlnHelicalTwistInitialStep (double) : Initial step of helical twist search (in degrees)
+
| int
 
+
| Current size of the images used in the refinement
rlnHelicalTwistMax (double) : Maximum helical twist (in degrees, + for right-handedness)
+
|-
 
+
| rlnCurrentIteration
rlnHelicalTwistMin (double) : Minimum helical twist (in degrees, + for right-handedness)
+
| int
 
+
| The number of the current iteration
rlnHighresLimitExpectation (double) : High-resolution-limit (in Angstrom) for the expectation step
+
|-
 
+
| rlnCurrentResolution
rlnHighresLimitSGD (double) : High-resolution-limit (in Angstrom) for Stochastic Gradient Descent
+
| double
 
+
| Current resolution where SSNR^MAP drops below 1 (in 1/Angstroms)
rlnIgnoreHelicalSymmetry (bool)  : Flag to indicate that helical symmetry is ignored in 3D reconstruction
+
|-
 
+
| rlnDataDimensionality
rlnImageDimensionality (int)    : Dimensionality of data stored in an image (i.e. 2 or 3)
+
| int
 
+
| Dimensionality of the data (2D/3D)
rlnImageId (int)    : ID (i.e. a unique number) of an image
+
|-
 
+
| rlnDataType
rlnImageName (string) : Name of an image
+
| int
 
+
| Type of data stored in an image (e.g. int, RFLOAT etc)
rlnImageOriginalName (string) : Original name of an image
+
|-
 
+
| rlnDefocusAngle
rlnImageSize (int)    : Size of an image (in pixels)
+
| double
 
+
| Angle between X and defocus U direction (in degrees)
rlnImageSizeX (int)    : Size of an image in the X-direction (in pixels)
+
|-
 
+
| rlnDefocusU
rlnImageSizeY (int)    : Size of an image in the Y-direction (in pixels)
+
| double
 
+
| Defocus in U-direction (in Angstroms, positive values for underfocus)
rlnImageSizeZ (int)    : Size of an image in the Z-direction (in pixels)
+
|-
 
+
| rlnDefocusV
rlnImageWeight (double) : Relative weight of an image
+
| double
 
+
| Defocus in V-direction (in Angstroms, positive values for underfocus)
rlnIncrementImageSize (int)    : Number of Fourier shells to be included beyond the resolution where SSNR^MAP drops below 1
+
|-
 
+
| rlnDetectorPixelSize
rlnIs3DSampling (bool)  : Flag to indicate this concerns a 3D sampling  
+
| double
 
+
| Pixel size of the detector (in micrometers)
rlnIs3DTranslationalSampling (bool)  : Flag to indicate this concerns a x,y,z-translational sampling  
+
|-
 
+
| rlnDiff2RandomHalves
rlnIsFlip (bool)  : Flag to indicate that an image should be mirrored
+
| double
 
+
| Power of the differences between two independent reconstructions from random halves of the data
rlnIsHelix (bool)  : Flag to indicate that helical refinement should be performed
+
|-
 
+
| rlnDifferentialPhaseResidualMaskedMaps
rlnJoinHalvesUntilThisResolution (double) : Resolution (in Angstrom) to join the two random half-reconstructions to prevent their diverging orientations (for C-symmetries)
+
| double
 
+
| Differential Phase Residual in Fourier shells of masked maps
rlnKullbackLeiblerDivergence (double) : Kullback-Leibler divergence for a particle
+
|-
 
+
| rlnDifferentialPhaseResidualUnmaskedMaps
rlnKurtosisExcessValue (double) : Kurtosis excess (4th moment - 3) for the pixel values in an image
+
| double
 
+
| Differential Phase Residual in Fourier shells of unmasked maps
rlnLensStability (double) : Lens stability (in ppm)
+
|-
 
+
| rlnDoAutoRefine
rlnLocalSymmetryFile (string) : Local symmetry description file containing list of masks and their operators
+
| bool
 
+
| Flag to indicate that 3D auto-refine procedure is being used
rlnLogAmplitudesIntercept (double) : Y-value for Guinier plot: the fitted plateau of the logarithm of the radially averaged amplitudes
+
|-
 
+
| rlnDoCorrectCtf
rlnLogAmplitudesMTFCorrected (double) : Y-value for Guinier plot: the logarithm of the radially averaged amplitudes after MTF correction
+
| bool
 
+
| Flag to indicate that CTF-correction should be performed
rlnLogAmplitudesOriginal (double) : Y-value for Guinier plot: the logarithm of the radially averaged amplitudes of the input map
+
|-
 
+
| rlnDoCorrectMagnification
rlnLogAmplitudesSharpened (double) : Y-value for Guinier plot: the logarithm of the radially averaged amplitudes after sharpening
+
| bool
 
+
| Flag to indicate that (per-group) magnification correction should be performed
rlnLogAmplitudesWeighted (double) : Y-value for Guinier plot: the logarithm of the radially averaged amplitudes after FSC-weighting
+
|-
 
+
| rlnDoCorrectNorm
rlnLogLikeliContribution (double) : Contribution of a particle to the log-likelihood target function
+
| bool
 
+
| Flag to indicate that (per-image) normalisation-error correction should be performed
rlnLogLikelihood (double) : Value of the log-likelihood target function
+
|-
 
+
| rlnDoCorrectScale
rlnLongitudinalDisplacement (double) : Longitudinal displacement (in Angstroms)
+
| bool
 
+
| Flag to indicate that internal (per-group) intensity-scale correction should be performed
rlnMagnification (double) : Magnification at the detector (in times)
+
|-
 
+
| rlnDoFastSubsetOptimisation
rlnMagnificationCorrection (double) : Magnification correction value for an image
+
| bool
 
+
| Use subsets of the data in the earlier iterations to speed up convergence
rlnMagnificationSearchRange (double) : Search range for magnification correction
+
|-
 
+
| rlnDoHelicalRefine
rlnMagnificationSearchStep (double) : Step size  for magnification correction
+
| bool
 
+
| Flag to indicate that helical refinement should be performed
rlnMaskName (string) : Name of an image that contains a [0,1] mask
+
|-
 
+
| rlnDoIgnoreCtfUntilFirstPeak
rlnMatrix_1_1 (double) : Matrix element (1,1) of a 3x3 matrix
+
| bool
 
+
| Flag to indicate that the CTFs should be ignored until their first peak
rlnMatrix_1_2 (double) : Matrix element (1,2) of a 3x3 matrix
+
|-
 
+
| rlnDoMapEstimation
rlnMatrix_1_3 (double) : Matrix element (1,3) of a 3x3 matrix
+
| bool
 
+
| Flag to indicate that MAP estimation should be performed (otherwise ML estimation)
rlnMatrix_2_1 (double) : Matrix element (2,1) of a 3x3 matrix
+
|-
 
+
| rlnDoOnlyFlipCtfPhases
rlnMatrix_2_2 (double) : Matrix element (2,1) of a 3x3 matrix
+
| bool
 
+
| Flag to indicate that CTF-correction should only comprise phase-flipping
rlnMatrix_2_3 (double) : Matrix element (2,1) of a 3x3 matrix
+
|-
 
+
| rlnDoRealignMovies
rlnMatrix_3_1 (double) : Matrix element (3,1) of a 3x3 matrix
+
| bool
 
+
| Flag to indicate that individual frames of movies are being re-aligned
rlnMatrix_3_2 (double) : Matrix element (3,1) of a 3x3 matrix
+
|-
 
+
| rlnDoSkipAlign
rlnMatrix_3_3 (double) : Matrix element (3,1) of a 3x3 matrix
+
| 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 (int)    : Maximum number particles that are processed together to speed up calculations
+
|-
 
+
| rlnDoSkipRotate
rlnMaxValueProbDistribution (double) : Maximum value of the (normalised) probability function for a particle
+
| bool
 
+
| Flag to indicate that rotational searches will be omitted from the refinement, only marginalisation over classes and translations will take place
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)
+
|-
 
+
| rlnDoSolventFlattening
rlnMaximumValue (double) : Maximum value for the pixels in an image
+
| bool
 
+
| Flag to indicate that the references should be masked to set their solvent areas to a constant density
rlnMicrographBinning (double) : Micrograph binning factor
+
|-
 
+
| rlnDoSolventFscCorrection
rlnMicrographDefectFile (string) : Name of a defect list file
+
| bool
 
+
| Flag to indicate that the FSCs should be solvent-corrected during refinement
rlnMicrographDoseRate (double) : Dose rate in electrons per square Angstrom per frame
+
|-
 
+
| rlnDoSplitRandomHalves
rlnMicrographEndFrame (int)    : End frame of a motion model
+
| bool
 
+
| Flag to indicate that the data should be split into two completely separate, random halves
rlnMicrographFrameNumber (int)    : Micrograph frame number
+
|-
 
+
| rlnDoStochasticGradientDescent
rlnMicrographGainName (string) : Name of a gain reference
+
| bool
 
+
| Flag to indicate that SGD-optimisation should be performed (otherwise expectation maximisation)
rlnMicrographId (int)    : ID (i.e. a unique number) of a micrograph
+
|-
 
+
| rlnDoZeroMask
rlnMicrographMetadata (string) : Name of a micrograph metadata file
+
| 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 (string) : Name of a micrograph movie stack
+
|-
 
+
| rlnEnabled
rlnMicrographName (string) : Name of a micrograph
+
| bool
 
+
| Not used in RELION, only included for backward compatibility with XMIPP selfiles
rlnMicrographNameNoDW (string) : Name of a micrograph without dose weighting
+
|-
 
+
| rlnEnergyLoss
rlnMicrographOriginalPixelSize (double) : Pixel size of original movie before binning in Angstrom/pixel.
+
| double
 
+
| Energy loss (in eV)
rlnMicrographPreExposure (double) : Pre-exposure dose in electrons per square Angstrom
+
|-
 
+
| rlnEstimatedResolution
rlnMicrographShiftX (double) : X shift of a (patch of) micrograph
+
| double
 
+
| Estimated resolution (in A) for a reference
rlnMicrographShiftY (double) : Y shift of a (patch of) micrograph
+
|-
 
+
| rlnExperimentalDataStarFile
rlnMicrographStartFrame (int)    : Start frame of a motion model
+
| string
 
+
| STAR file with metadata for the experimental images
rlnMicrographTiltAngle (double) : Tilt angle (in degrees) used to collect a micrograph
+
|-
 
+
| rlnFinalResolution
rlnMicrographTiltAxisDirection (double) : Direction of the tilt-axis (in degrees) used to collect a micrograph
+
| double
 
+
| Final estimated resolution after postprocessing (in Angstroms)
rlnMicrographTiltAxisOutOfPlane (double) : Out-of-plane angle (in degrees) of the tilt-axis used to collect a micrograph (90=in-plane)
+
|-
 
+
| rlnFittedInterceptGuinierPlot
rlnMinRadiusNnInterpolation (int)    : Minimum radius for NN-interpolation (in Fourier pixels), for smaller radii linear int. is used
+
| double
 
+
| The fitted intercept of the Guinier-plot
rlnMinimumValue (double) : Minimum value for the pixels in an image
+
|-
 
+
| rlnFittedSlopeGuinierPlot
rlnModelStarFile (string) : STAR file with metadata for the model that is being refined
+
| double
 
+
| The fitted slope of the Guinier-plot
rlnModelStarFile2 (string) : STAR file with metadata for the second model that is being refined (from random halves of the data)
+
|-
 
+
| rlnFixSigmaNoiseEstimates
rlnMotionModelCoeff (double) : A coefficient of a motion model
+
| bool
 
+
| Flag to indicate that the estimates for the power spectra of the noise should be kept constant
rlnMotionModelCoeffsIdx (int)    : Index of a coefficient of a motion model
+
|-
 
+
| rlnFixSigmaOffsetEstimates
rlnMotionModelVersion (int)    : Version of micrograph motion model
+
| bool
 
+
| Flag to indicate that the estimates for the stddev in the origin offsets should be kept constant
rlnMovieFrameNumber (int)    : Number of a movie frame
+
|-
 
+
| rlnFixTauEstimates
rlnMovieFramesRunningAverage (int)    : Number of movie frames inside the running average that will be used for movie-refinement
+
| bool
 
+
| Flag to indicate that the estimates for the power spectra of the signal (i.e. the references) should be kept constant
rlnMtfValue (double) : Value of the detectors modulation transfer function (between 0 and 1)
+
|-
 
+
| rlnFourierCompleteness
rlnNormCorrection (double) : Normalisation correction value for an image
+
| double
 
+
| Fraction of Fourier components (per resolution shell) with SNR>1
rlnNormCorrectionAverage (double) : Average value (over all images) of the normalisation correction values
+
|-
 
+
| rlnFourierShellCorrelation
rlnNrBodies (int)    : The number of independent rigid bodies to be refined in multi-body refinement
+
| double
 
+
| FSC value (of unspecified type, e.g. masked or unmasked)
rlnNrClasses (int)    : The number of references (i.e. classes) to be used in refinement
+
|-
 
+
| rlnFourierShellCorrelationCorrected
rlnNrGroups (int)    : The number of different groups of images (each group has its own noise spectrum, and intensity-scale correction)
+
| double
 
+
| Final FSC value: i.e. after correction based on masking of randomized-phases maps
rlnNrHelicalAsymUnits (int)    : How many new helical asymmetric units are there in each box
+
|-
 
+
| rlnFourierShellCorrelationMaskedMaps
rlnNrOfFrames (int)    : Number of movie frames that were collected for this particle
+
| double
 
+
| FSC value after masking of the original maps
rlnNrOfSignificantSamples (int)    : Number of orientational/class assignments (for a particle) with sign.probabilities in the 1st pass of adaptive oversampling
+
|-
 
+
| rlnFourierShellCorrelationUnmaskedMaps
rlnNumberOfIterWithoutChangingAssignments (int)    : Number of iterations that have passed without large changes in orientation and class assignments
+
| double
 
+
| FSC value before masking of the original maps
rlnNumberOfIterWithoutResolutionGain (int)    : Number of iterations that have passed without a gain in resolution
+
|-
 
+
| rlnFourierSpaceInterpolator
rlnNumberOfIterations (int)    : Maximum number of iterations to be performed
+
| int
 
+
| The kernel used for Fourier-space interpolation (NN=0, linear=1)
rlnOffsetRange (double) : Search range for the origin offsets (in Angstroms)
+
|-
 
+
| rlnGoldStandardFsc
rlnOffsetStep (double) : Step size for the searches in the origin offsets (in Angstroms)
+
| double
 
+
| Fourier shell correlation between two independent reconstructions from random halves of the data
rlnOrientSamplingStarFile (string) : STAR file with metadata for the orientational sampling
+
|-
 
+
| rlnGroupName
rlnOrientationDistribution (double) : Probability Density Function of the orientations  (i.e. fraction of images assigned to each orient)
+
| string
 
+
| The name of a group of images (e.g. all images from a micrograph)
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)  
+
|-
 
+
| rlnGroupNrParticles
rlnOrientationsID (int)    : ID (i.e. a unique number) for an orientation
+
| int
 
+
| Number particles in a group of images
rlnOriginX (double) : X-coordinate (in pixels) for the origin of rotation
+
|-
 
+
| rlnGroupNumber
rlnOriginXPrior (double) : Center of the prior on the X-coordinate (in pixels) for the origin of rotation
+
| int
 
+
| The number of a group of images
rlnOriginY (double) : Y-coordinate (in pixels) for the origin of rotation
+
|-
 
+
| rlnGroupScaleCorrection
rlnOriginYPrior (double) : Center of the prior on the X-coordinate (in pixels) for the origin of rotation
+
| double
 
+
| Intensity-scale correction for a group of images
rlnOriginZ (double) : Z-coordinate (in pixels) for the origin of rotation
+
|-
 
+
| rlnHasConverged
rlnOriginZPrior (double) : Center of the prior on the X-coordinate (in pixels) for the origin of rotation
+
| bool
 
+
| Flag to indicate that the optimization has converged
rlnOriginalImageSize (int)    : Original size of the images (in pixels)
+
|-
 
+
| rlnHasHighFscAtResolLimit
rlnOriginalParticleName (string) : Original name for a particles
+
| bool
 
+
| Flag to indicate that the FSC at the resolution limit is significant
rlnOutputRootName (string) : Rootname for all output files (this may include a directory structure, which should then exist)
+
|-
 
+
| rlnHasLargeSizeIncreaseIterationsAgo
rlnOverallAccuracyRotations (double) : Overall accuracy of the rotational assignments (in degrees)
+
| int
 
+
| How many iterations have passed since the last large increase in image size
rlnOverallAccuracyTranslations (double) : Overall accuracy of the translational assignments (in pixels)
+
|-
 
+
| rlnHealpixOrder
rlnOverallFourierCompleteness (double) : Fraction of all Fourier components up to the current resolution with SNR>1
+
| int
 
+
| Healpix order for the sampling of the first two Euler angles (rot, tilt) on the 3D sphere
rlnPaddingFactor (double) : Oversampling factor for Fourier transforms of the references
+
|-
 
+
| rlnHelicalCentralProportion
rlnParticleDiameter (double) : Diameter of the circular mask to be applied to all experimental images (in Angstroms)
+
| double
 
+
| Only expand this central fraction of the Z axis when imposing real-space helical symmetry
rlnParticleFigureOfMerit (double) : Developmental FOM for a particle
+
|-
 
+
| rlnHelicalKeepTiltPriorFixed
rlnParticleId (int)    : ID (i.e. a unique number) for a particle
+
| bool
 
+
| Flag to indicate that helical tilt priors are kept fixed (at 90 degrees) in global angular searches
rlnParticleName (string) : Name for a particle
+
|-
 
+
| rlnHelicalMaskTubeInnerDiameter
rlnParticleNumber (int)    : Number of particles
+
| double
 
+
| Inner diameter of helical tubes in Angstroms (for masks of helical references and particles)
rlnParticleSelectZScore (double) : Sum of Z-scores from particle_select. High Z-scores are likely to be outliers.
+
|-
 
+
| rlnHelicalMaskTubeOuterDiameter
rlnPerFrameCumulativeWeight (double) : Sum of the resolution-dependent relative weights from the first frame until the given frame
+
| double
 
+
| Outer diameter of helical tubes in Angstroms (for masks of helical references and particles)
rlnPerFrameRelativeWeight (double) : The resolution-dependent relative weights for a given frame
+
|-
 
+
| rlnHelicalOffsetStep
rlnPhaseShift (double) : Phase-shift from a phase-plate (in degrees)
+
| double
 
+
| Step size for the searches of offsets along helical axis (in Angstroms)
rlnPipeLineEdgeFromNode (string) : Name of the origin of an edge
+
|-
 
+
| rlnHelicalRise
rlnPipeLineEdgeProcess (string) : Name of the destination of an edge
+
| double
 
+
| The helical rise (translation per subunit) in Angstroms
rlnPipeLineEdgeToNode (string) : Name of the to-Node in an edge
+
|-
 
+
| rlnHelicalRiseInitial
rlnPipeLineJobCounter (int)    : Number of the last job in the pipeline
+
| double
 
+
| The initial helical rise (translation per subunit) in Angstroms before refinement
rlnPipeLineNodeName (string) : Name of a Node in the pipeline
+
|-
 
+
| rlnHelicalRiseInitialStep
rlnPipeLineNodeType (int)    : Type of a Node in the pipeline
+
| double
 
+
| Initial step of helical rise search (in Angstroms)
rlnPipeLineProcessAlias (string) : Alias of a Process in the pipeline
+
|-
 
+
| rlnHelicalRiseMax
rlnPipeLineProcessName (string) : Name of a Process in the pipeline
+
| double
 
+
| Maximum helical rise (in Angstroms)
rlnPipeLineProcessStatus (int)    : Status of a Process in the pipeline (running, scheduled, finished or cancelled)
+
|-
 
+
| rlnHelicalRiseMin
rlnPipeLineProcessType (int)    : Type of a Process in the pipeline
+
| double
 
+
| Minimum helical rise (in Angstroms)
rlnPixelSize (double) : Size of the pixels in the references and images (in Angstroms)
+
|-
 
+
| rlnHelicalSigmaDistance
rlnPsiStep (double) : Step size (in degrees) for the sampling of the in-plane rotation angle (psi)
+
| double
 
+
| Sigma of distance along the helical tracks
rlnRadiusMaskExpImages (int)    : Radius of the circular mask to be applied to all experimental images (in Angstroms)
+
|-
 
+
| rlnHelicalSymmetryLocalRefinement
rlnRadiusMaskMap (int)    : Radius of the spherical mask to be applied to all references (in Angstroms)
+
| bool
 
+
| Flag to indicate that local refinement of helical parameters should be performed
rlnRandomSeed (int)    : Seed (i.e. a number) for the random number generator
+
|-
 
+
| rlnHelicalTrackLength
rlnRandomSubset (int)    : Random subset to which this particle belongs
+
| double
 
+
| Distance from the position of this helical segment to the starting point of the tube
rlnRandomiseFrom (double) : Resolution (in A) from which the phases are randomised in the postprocessing step
+
|-
 
+
| rlnHelicalTubeID
rlnReconstructImageName (string) : Name of an image to be used for reconstruction only
+
| int
 
+
| Helical tube ID for a helical segment
rlnReferenceDimensionality (int)    : Dimensionality of the references (2D/3D)
+
|-
 
+
| rlnHelicalTubePitch
rlnReferenceImage (string) : Name of a reference image
+
| double
 
+
| Cross-over distance for a helical segment (A)
rlnReferenceSigma2 (double) : Spherical average of the estimated power in the noise of a reference
+
|-
 
+
| rlnHelicalTwist
rlnReferenceSpectralPower (double) : Spherical average of the power of the reference
+
| double
 
+
| The helical twist (rotation per subunit) in degrees
rlnReferenceTau2 (double) : Spherical average of the estimated power in the signal of a reference
+
|-
 
+
| rlnHelicalTwistInitial
rlnRefsAreCtfCorrected (bool)  : Flag to indicate that the input references have been CTF-amplitude corrected
+
| double
 
+
| The intial helical twist (rotation per subunit) in degrees before refinement
rlnResolution (double) : Resolution (in 1/Angstroms)
+
|-
 
+
| rlnHelicalTwistInitialStep
rlnResolutionInversePixel (double) : Resolution (in 1/pixel, Nyquist = 0.5)
+
| double
 
+
| Initial step of helical twist search (in degrees)
rlnResolutionSquared (double) : X-value for Guinier plot: squared resolution in 1/Angstrom^2
+
|-
 
+
| rlnHelicalTwistMax
rlnSGDGradientImage (string) : Name of image containing the SGD gradient
+
| double
 
+
| Maximum helical twist (in degrees, + for right-handedness)
rlnSamplingPerturbFactor (double) : Factor for random perturbation on the orientational sampling (between 0 no perturbation and 1 very strong perturbation)
+
|-
 
+
| rlnHelicalTwistMin
rlnSamplingPerturbInstance (double) : Random instance of the random perturbation on the orientational sampling
+
| double
 
+
| Minimum helical twist (in degrees, + for right-handedness)
rlnSamplingRate (double) : Sampling rate of an image (in Angstrom/pixel)
+
|-
 
+
| rlnHighresLimitExpectation
rlnSamplingRateX (double) : Sampling rate in X-direction of an image (in Angstrom/pixel)
+
| double
 
+
| High-resolution-limit (in Angstrom) for the expectation step
rlnSamplingRateY (double) : Sampling rate in Y-direction of an image (in Angstrom/pixel)
+
|-
 
+
| rlnHighresLimitSGD
rlnSamplingRateZ (double) : Sampling rate in Z-direction of an image (in Angstrom/pixel)
+
| double
 
+
| High-resolution-limit (in Angstrom) for Stochastic Gradient Descent
rlnSelected (int)    : Flag whether an entry in a metadatatable is selected (1) in the viewer or not (0)
+
|-
 
+
| rlnIgnoreHelicalSymmetry
rlnSgdFinalIterations (int)    : Number of final SGD iterations (at rlnSgdFinalResolution and with rlnSgdFinalSubsetSize)
+
| bool
 
+
| Flag to indicate that helical symmetry is ignored in 3D reconstruction
rlnSgdFinalResolution (double) : Resolution (in A) to use during the final SGD iterations
+
|-
 
+
| rlnImageDimensionality
rlnSgdFinalSubsetSize (int)    : Number of particles in a mini-batch (subset) during the final SGD iteration
+
| int
 
+
| Dimensionality of data stored in an image (i.e. 2 or 3)
rlnSgdInBetweenIterations (int)    : Number of SGD iteration in between the initial ones to the final ones (with linear interpolation of resolution and subset size)
+
|-
 
+
| rlnImageId
rlnSgdInitialIterations (int)    : Number of initial SGD iterations (at rlnSgdInitialResolution and with rlnSgdInitialSubsetSize)
+
| int
 
+
| ID (i.e. a unique number) of an image
rlnSgdInitialResolution (double) : Resolution (in A) to use during the initial SGD iterations
+
|-
 
+
| rlnImageName
rlnSgdInitialSubsetSize (int)    : Number of particles in a mini-batch (subset) during the initial SGD iterations
+
| string
 
+
| Name of an image
rlnSgdMaxSubsets (int)    : Stop SGD after doing this many subsets (possibly spanning more than 1 iteration)
+
|-
 
+
| rlnImageOriginalName
rlnSgdMuFactor (double) : The mu-parameter that controls the momentum of the SGD gradients
+
| string
 
+
| Original name of an image
rlnSgdSigma2FudgeHalflife (int)    : After processing this many particles the multiplicative factor for the noise variance will have halved
+
|-
 
+
| rlnImageSize
rlnSgdSigma2FudgeInitial (double) : The variance of the noise will initially be multiplied with this value (larger than 1)
+
| int
 
+
| Size of an image (in pixels)
rlnSgdSkipAnneal (bool)  : Option to switch off annealing of multiple references in SGD
+
|-
 
+
| rlnImageSizeX
rlnSgdStepsize (double) : Stepsize in SGD updates)
+
| int
 
+
| Size of an image in the X-direction (in pixels)
rlnSgdSubsetSize (int)    : The number of particles in the random subsets for SGD
+
|-
 
+
| rlnImageSizeY
rlnSgdWriteEverySubset (int)    : Every this many iterations the model is written to disk in SGD
+
| int
 
+
| Size of an image in the Y-direction (in pixels)
rlnSigma2Noise (double) : Spherical average of the standard deviation in the noise (sigma)
+
|-
 
+
| rlnImageSizeZ
rlnSigmaOffsets (double) : Standard deviation in the origin offsets (in Angstroms)
+
| int
 
+
| Size of an image in the Z-direction (in pixels)
rlnSigmaPriorPsiAngle (double) : Standard deviation of the prior on the psi (i.e. third Euler) angle
+
|-
 
+
| rlnImageWeight
rlnSigmaPriorRotAngle (double) : Standard deviation of the prior on the rot (i.e. first Euler) angle
+
| double
 
+
| Relative weight of an image
rlnSigmaPriorTiltAngle (double) : Standard deviation of the prior on the tilt (i.e. second Euler) angle
+
|-
 
+
| rlnIncrementImageSize
rlnSignalToNoiseRatio (double) : Spectral signal-to-noise ratio for a reference
+
| int
 
+
| Number of Fourier shells to be included beyond the resolution where SSNR^MAP drops below 1
rlnSkewnessValue (double) : Skewness (3rd moment) for the pixel values in an image
+
|-
 
+
| rlnIs3DSampling
rlnSmallestChangesClasses (int)    : Smallest changes thus far in the optimal class assignments (in numer of particles).
+
| bool
 
+
| Flag to indicate this concerns a 3D sampling
rlnSmallestChangesOffsets (double) : Smallest changes thus far in the optimal offset assignments (in pixels).
+
|-
 
+
| rlnIs3DTranslationalSampling
rlnSmallestChangesOrientations (double) : Smallest changes thus far in the optimal orientation assignments (in degrees).
+
| bool
 
+
| Flag to indicate this concerns a x,y,z-translational sampling
rlnSolventMask2Name (string) : Name of a secondary solvent mask (e.g. to flatten density inside an icosahedral virus)
+
|-
 
+
| rlnIsFlip
rlnSolventMaskName (string) : Name of an image that contains a (possibly soft) mask for the solvent area (values=0 for solvent, values =1 for protein)
+
| bool
 
+
| Flag to indicate that an image should be mirrored
rlnSortedIndex (int)    : Index of a metadata entry after sorting (first sorted index is 0).
+
|-
 
+
| rlnIsHelix
rlnSpectralIndex (int)    : Spectral index (i.e. distance in pixels to the origin in Fourier space)  
+
| bool
 
+
| Flag to indicate that helical refinement should be performed
rlnSpectralOrientabilityContribution (double) : Spectral SNR contribution to the orientability of individual particles
+
|-
 
+
| rlnJoinHalvesUntilThisResolution
rlnSphericalAberration (double) : Spherical aberration (in millimeters)
+
| double
 
+
| Resolution (in Angstrom) to join the two random half-reconstructions to prevent their diverging orientations (for C-symmetries)
rlnSsnrMap (double) : Spectral signal-to-noise ratio as defined for MAP estimation (SSNR^MAP)
+
|-
 
+
| rlnKullbackLeiblerDivergence
rlnStandardDeviationValue (double) : Standard deviation for the pixel values in an image
+
| double
 
+
| Kullback-Leibler divergence for a particle
rlnStarFileMovieParticles (string) : Filename of a STAR file with movie-particles in it
+
|-
 
+
| rlnKurtosisExcessValue
rlnSymmetryGroup (string) : Symmetry group (e.g., C1, D7, I2, I5, etc.)
+
| double
 
+
| Kurtosis excess (4th moment - 3) for the pixel values in an image
rlnTau2FudgeFactor (double) : Regularisation parameter with which estimates for the power in the references will be multiplied (T in original paper)
+
|-
 
+
| rlnLensStability
rlnTauSpectrumName (string) : Name of a STAR file that holds a tau2-spectrum
+
| double
 
+
| Lens stability (in ppm)
rlnTiltAngleLimit (double) : Values to which to limit the tilt angles (positive for keeping side views, negative for keeping top views)
+
|-
 
+
| rlnLocalSymmetryFile
rlnTransversalDisplacement (double) : Transversal displacement (in Angstroms)
+
| string
 
+
| Local symmetry description file containing list of masks and their operators
rlnUnfilteredMapHalf1 (string) : Name of the unfiltered map from halfset 1
+
|-
 
+
| rlnLogAmplitudesIntercept
rlnUnfilteredMapHalf2 (string) : Name of the unfiltered map from halfset 2
+
| double
 
+
| Y-value for Guinier plot: the fitted plateau of the logarithm of the radially averaged amplitudes
rlnUseTooCoarseSampling (bool)  : Flag to indicate that the angular sampling on the sphere will be one step coarser than needed to speed up calculations
+
|-
 
+
| rlnLogAmplitudesMTFCorrected
rlnVoltage (double) : Voltage of the microscope (in kV)
+
| double
 
+
| Y-value for Guinier plot: the logarithm of the radially averaged amplitudes after MTF correction
rlnWidthMaskEdge (int)    : Width (in pixels) of the soft edge for spherical/circular masks to be used for solvent flattening
+
|-
 +
| 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15日 (水) 13:12時点における版

  • 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
  • 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