Manpage of calcFSC
Section: User Commands (1)
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calcFSC - calculate the Fourier Shell Correlation of an alignment
calcFSC file.prm repCount
calcFSC file.prm repCount flgShuffle
calcFSC calculates the Fourier Shell Correlation (FSC) resulting from the
particle alignment specified in parameter file 'file.prm'.
Particles to be processed are selected using an approach similar to that
used by averageAll. The primary difference is that the number
of particles to process is specified by parameter "nParticles", rather
than "lstThresholds". Particles selected for processing are divided
into 2 equal-sized groups after alignment, and the FSC computed by
comparing their averages in Fourier space.
Result are stored in text files and can be graphed using plotFSC.
Like 'lstThresholds', 'nParticles' can be a vector, in which case
an FSC curve will be calculated for each entry.
Computing an FSC in this fashion (i.e. based on a common, mutual
alignment) can lead to bias and overly optimistic results. For a more
reliable estimate, consider manually splitting the data prior to
alignment and then using calcUnbiasedFSC(1).
is the name of the PEET parameter file.
is an optional positive integer specifying the number of times the FSC
calculation should be repeated. If 1 or greater, time-based initialization
of the pseudo-random number generator will be used, so subsequent runs
will give different results. If greater than 1, the caculated FSC curve
will be the average of 'repCount' runs with different pseudo-random assortment
for each run. If greater than 2, the standard deviation of
the mean estimated FSC will also be computed and saved to file
arrFSCC.txt, for use by plotFSC.
If flgShuffle is non-zero, return different results one each invocation,
even if repCount is 1. (Default = 0).
The parameter file is a MATLAB readable text file that specifies the parameter
values in MATLAB syntax. See the PEET man page for a description of the
parameter file options and syntax. calcFSC uses the 'flgNormalize'
, 'fnVolume', 'fnModParticle', 'fnOutput', 'dPhi', 'lstThresholds', 'szVol'
, 'tiltRange', 'edgeShift', 'flgRemoveDuplicates', flgRandomize,
flgVolNamesAreTemplates, and 'debugLevel'
parameters described there. In addition, calcFSC supports
the 'includeList', 'excludeList', and 'selectClassID' parameters described
on the averageAll man page. It also supports additional, optional
parameters specific to calcFSC listed below.
These optional parameters, some of which are shared with calcSSNR, all
have reasonable default values. Extra parameters used to control the other
programs are ignored by calcFSC and vice versa, so a single parameter file
should suffice even when modifying some parameters. Sample parameter files
are available in $PARTICLE_DIR/templates.
calcFSC needs to be run in the same directory where alignSubset and averageAll
- nParticles = < int | vector >
The number of particles in each group; a vector indicates that multiple
results are requested. If there are n particles specified by the alignment
structure, the maximum value in nParticles should be floor(n/2). The default
is an arithmetic sequence of 5 integers that start from 1/10 of the last entry
in the 'lstThresholds' array described in PEET man page and go up to
- freqShells = vector
The upper limit of each frequency shell. The default is [0.025:0.025:0.5].
- windowName = string
The type of the mask window to apply to the data, 'gaussian', 'hamming', etc.
The default is 'gaussian'. If windowName is 'file', windowParams must be
a string with the name of an MRC file containing the mask. A windowName
of 'none' can be used to disable masking.
- windowParams = vector
The parameters to pass to the window generation function. For a gaussian
window the parameters are [radius sigma]; see gaussianMask in MATLAB help. The
default is [0.35 0.05].
- windowCenter = vector
The center of the mask window (default: [ ] = volume center). The default is
- fnHalfVolume = string
The base name of the half volumes to write out (default: '', don't write out
the half volumes).
- fscMaskOrigin = vector
Specifies the origin of your FSC mask in the average volume coordinate system
that has the X-Y origin at lower left corner and Z origin at slice 0. The
center of the average volume will have coordinates szVol/2.
- fscMaskSize = vector
Specifies the FSC mask size in the X, Y, and Z dimension. Only voxels inside
this rectangular mask are included in the
Sample parameter files are available in $PARTICLE_DIR/templates.
calcFSC stores results in 4 or 5text files in the current working
directory. 'szVoxel.txt' contains the pixel size in
Angstroms. 'nParticles.txt' contains the the number of particles
used, which may differ from those requested in
parameter 'nParticles'. 'freqShells.txt' has the value for
parameter 'freqShells'. 'arrFSCC.txt' contains a 2 dimensional array of
correlation scores. Each of its columns corresponds to a number of
particles used, with rows corresponding to frequencies in 'freqShells'.
If repCount is greater than 1, pointwise standard deviations of the mean
will be stored in an optional 'arrSigma.txt' file.
PEET(1), plotFSC(1), prmParser(1), prepareEM(1), prepareRef(1), mergeEM(1),
alignSubset(1), averageAll(1), calcUnbiasedFSC(1), and calcSSNR(1)
- SEE ALSO
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using the manual pages.
Time: 16:44:59 GMT, March 05, 2018