Sub-Tomogram Averaging estimates the rotation and shift of each sub-tomogram relative to reference.
aiAveraging needs a configuration file provided by the -u argument. Some options can be overwritten using command line arguments.
Options are:
CudaDeviceIDs
The deviceIDs of the GPUs to use.
Argument for command line: -d or –CudaDeviceIDs
Type: List<int>, a list of integer values
Option is mandatory: true
LP
Low pass filter value.
Argument for command line: -lp or –LP
Type: float
Option is mandatory: true
LPS
Low pass filter sigma value.
Argument for command line: -lps or –LPS
Type: float
Option is mandatory: true
HP
High pass filter value.
Argument for command line: -hp or –HP
Type: float
Option is mandatory: false
Default value if not set: 0
HPS
High pass filter sigma value.
Argument for command line: -hps or –HPS
Type: float
Option is mandatory: false
Default value if not set: 0
MotiveList
The list of particles to average. Naming convention: filename_IterationNr.motl.
Type: string
Option is mandatory: true
Particles
Particle filename. Two naming conventions are possible: filename_PartNr.em/mrc or filename_TomoNr_PartInTomoNr.em/mrc.
Type: string
Option is mandatory: true
References
Reference filename. Naming convention: filename_RefNr_IterationNr.em/mrc.
Type: string
Option is mandatory: true
Wedges
Wedge filename. Naming convention: filename_WedgeNr.em/mrc.
Type: string
Option is mandatory: true
Mask
Mask filename. Naming convention: filename_MaskNr.em/mrc.
Type: string
Option is mandatory: true
RotateMask
Indicates if the reference mask has to be rotated with the particle orientation.
Type: bool
Option is mandatory: true
MaxShift
Maximum allowed shift (or set MaskCC filename)
Type: int
Option is mandatory: false
Default value if not set: 0
MaskCC
MaskCC filename. Naming convention: filename.em/mrc.
Type: string
Option is mandatory: true
Only applicable if MaxShift = -1.
RotateMaskCC
Indicates if the CC-Mask has to be rotated with the particle orientation.
Type: bool
Option is mandatory: true
Only applicable if MaxShift = -1.
StartIteration
The iteration to start with this run of averaging.
Type: int
Option is mandatory: true
IterationCount
The number of iterations to perform starting at ‘StartIteration’.
Type: int
Option is mandatory: true
AngIter
Number of angular search increments.
Type: int
Option is mandatory: true
AngIncr
Angular search increment.
Type: float
Option is mandatory: true
PhiAngIter
Number of angular search increments for phi angle.
Type: int
Option is mandatory: true
PhiAngIncr
Angular search increment for phi angle.
Type: float
Option is mandatory: true
BestParticleRatio
Only sum up the best ‘BestParticleRatio’ particles for each reference.
Type: float
Option is mandatory: false
Default value if not set: 1
CouplePhiToPsi
Indicates if the phi angle is coupled to psi (can be necessary for restricted search ranges).
Type: bool
Option is mandatory: true
Method
Defines the averaging method: ‘Standard’ for averaging on a single reference per class, ‘Gold-Standard’ for two independent references per class, ‘Multi-Reference’ for classification.
Type: one of [GOLDSTANDARD, MULTIREFERENCE, STANDARD]
Option is mandatory: true
Possible notations:
- GOLDSTANDARD: GOLDSTANDARD, GOLD-STANDARD, Gold-Standard, gold-standard, GoldStandard, goldstandard
- MULTIREFERENCE: MULTIREFERENCE, MULTI-REFERENCE, Multi-Reference, multi-reference, MultiReference, multireference
- STANDARD: STANDARD, Standard, standard
CorrelationMethod
Defines the correlation method to use: ‘Cross-Correlation’ or ‘Phase-Correlation’.
Type: one of [CROSSCORRELATION, PHASECORRELATION]
Option is mandatory: true
Possible notations:
- CROSSCORRELATION: CROSSCORRELATION, CROSS-CORRELATION, CROSS_CORRELATION, CrossCorrelation, Cross-Correlation, Cross_Correlation, crosscorrelation, cross-correlation, cross_correlation
- PHASECORRELATION: PHASECORRELATION, PHASE-CORRELATION, PHASE_CORRELATION, PhaseCorrelation, Phase-Correlation, Phase_Correlation, phasecorrelation, phase-correlation, phase_correlation
CompensateNoWBPWeighting
When particles are reconstructed without WBP weighting and when using cross-correlation, the amplified amplitudes due to reconstruction are corrected before cross-correlation, if set to ‘true’.
Type: bool
Option is mandatory: true
Only applicable if CorrelationMethod = CROSSCORRELATION.
SubPixelRatio
For values > 1, the shift is determined with sub-pixel precission. 2=0.5 pixel shift, 4=0.25 pixel shift, etc.
Type: int
Option is mandatory: false
Default value if not set: 1
PhaseRandomizationLimit
When assessing resolution, an additional FSC is performed with randomized phases for frequencies above the limit. This allows to quantify the influence of the mask on the FSC.
Type: int
Option is mandatory: true
AddParticles
If set, the particles are only summed up to create a new reference for the first given iteration.
Argument for command line: -add or –AddParticles
Type: bool
Option is mandatory: false
Default value if not set: false
DoseWeighting
Enabled by default, if set to false, no dose weighting is applied. If true, and the particles are reconstructed without dose weighting, the particle is weighted before summation.
Type: bool
Option is mandatory: false
Default value if not set: true
Symmetry
If provided, the average result is symmetrized with the provided symmetry (even, odd and summed volume).
Type: string
Option is mandatory: false
Default value if not set: ’’
RigidScan
Scan Psi angles with fixed angular distance (equal to PhiAngIncr).
Type: bool
Option is mandatory: false
Default value if not set: false
SaveFilteredReference
Indicates if additionally to the reference volume, a volume low pass filtered to the estimated resolution is saved, too.
Type: bool
Option is mandatory: false
Default value if not set: false