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scoreHistogram - plot histogram of cross-correlation scores  


scoreHistogram filename
scoreHistogram filename iterationNum
scoreHistogram filename iterationNum numBins
scoreHistogram filename iterationNum numBins colNum
scoreHistogram filename iterationNum numBins colNum numParticles  


Compute and plot a histogram of cross-correlation scores (or other columns from motive lists) corresponding to the specified iteration number. If called with only the name of the PEET parameter (aka prm) file, a histogram of the cross-correlation scores generated by the final alignment iteration will be plotted. Cross-correlation values plotted will be those from column 1 of the motive list(s), which have been adjusted according to any missing wedge compensation in effect.

By default, scoreHistogram includes values from all motive list rows not flagged as duplicates (classID = -9999 in motive list column 20). This behavior can be modifed by setting includeList, excludeList, and / or selectClassID, which scoreHistogram honors, in the prm file. See averageAll(1) for details on these parameters. Additionally, the total number particles / values to include can be specified using the optional numParticles runstring argument; particles to be included will be chosen using the same criteria as would apply during averaging when fewer than the total number of particles are specified.

The name of the parameter (*.prm) file.
iterationNumber (optional)
An integer specifying the alignment iteration whose output will be plotted. If omitted, the final alignment iteration specified by the prm file will be assumed.
numBins (optional, default = 100)
The number of bins desired in the histogram.
colNum (optional, default = 1)
Which column number of the motive list(s) to use in generating the histogram. The default, 1, is the adjusted cross-correlation score.
numParticles (optional)
An integer number of particles to include in the historgram, ordered according to prm file settings as if particles were being chosen for averaging. If omitted or <= 0, all available particles will be used.


John Heumann  


alignSubset(1), averageAll(1), PEET(1)




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Time: 16:44:59 GMT, March 05, 2018