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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 over-estimation 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, 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: 21:10:06 GMT, March 20, 2017