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Manpage of varianceMap
varianceMap
Section: User Commands (1)
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NAME
varianceMap  compute variance and standard deviation maps with missing wedge correction
SYNOPSIS
varianceMap prmFile iterationNumber numParticles trueFile
varianceMap prmFile iterationNumber numParticles
DESCRIPTION
Compute variance and standard deviation maps between the
particles contributing
to the 'numParticles' average at iteration 'iterationNumber'.
Systematic variation in missing tomographic information can
lead to bias and overestimation of variance when analyzing
tomograms averaged with PEET. When tilt ranges are provided in
the parameter file and a PEET average (or other estimate of the
true volume) is provided in 'trueFile' a missing wedge corrected
variance map will be constructed which attempts to eliminate
these errors.
The resulting maps will be stored in MRC format in
files named
<fnOutput>_<mapType>Map_Iter<iterationNummber>_<numParticles>.mrc
where <mapType> is either "Variance" or "StandardDeviation".
 prmFile

The file name of the parameter file. See PEET(1) and averageAll(1) man pages
and below for descriptions of applicable parameter file settings.
 iterationNumber

An integer specifying the alignment iteration whose output will determine
the rotations and translations used
to compute the reference and/or average volumes.
 numParticles

An integer specifying the number of particles used to compute
the variance map.
 trueFile

The name of the file containing a volume to be considered an estimate
of the true particle in MRC format. Typically, an average created by
averageAll would be used, although this is not required. A multiple
of the missing wedge masked true volume will be subtracted from each
particle prior to computing the variance.
varianceMap supports the
alignAveragesAngles,
debugLevel,
edgeShift,
excludeList,
flgFPWedgeMask,
flgNormalize,
flgRandomize,
flgVolNamesAreTemplates,
fnModParticle,
fnOutput,
fnVolume,
includeList,
maskType,
reference,
selectClassID,
szVol,
tiltRange,
yaxisType,
yaxisObjectNum,
and yaxisContourNum
parameter file settings,
described in the PEET(1) and averageAll(1) man pages.
AUTHORS
John Heumann
SEE ALSO
PEET(1), prepareEM(1), prepareRef(1), mergeEM(1), alignSubset(1),
averageAll(1), removeDuplicates(1), calcFSC(1), and calcSSNR(1)
Index
 NAME

 SYNOPSIS

 DESCRIPTION

 AUTHORS

 SEE ALSO

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Time: 18:16:05 GMT, January 11, 2021