Content-type: text/html Manpage of alignSubset

alignSubset

Section: User Commands (1)
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NAME

alignSubset - align particles from a single tomogram with the reference  

SYNOPSIS

alignSubset file.prm tomogramNumber iterationNumber particleList  

DESCRIPTION

alignSubset aligns a specified set of particles in tomogram 'tomogramNumber' with the reference, using additional parameters specified in in parameter file 'file.prm'. 'IterationNumber' specifies the round of alignment performed. All numbering starts with 1. Alignment consists of choosing a translation and rotation for each particle to maximize a correlation-based measure of similarity with the reference. The parameters chosen for each particle are recorded in the motive list for the next iteration.

The parameter file is a MATLAB readable text file specifying parameter values in MATLAB syntax. See the man page of PEET for a description of the parameter file options and syntax. Sample parameter files are available in $PARTICLE_DIR/templates.

file.prm
The file name of the parameter file.
tomogramNumber
An integer specifying the number of the tomogram containing the particles to be aligned. Tomograms in the 'fnVolume' parameter are numbered from 1 according to the order in which they are listed in the parameter file.
iterationNumber
An integer specifying the round of alignment to perform.
particleList
A particle list specifies the particles that need to be aligned. The list should be an integer array in MATLAB syntax with the entries seperated by commas and should be double quoted. For example, "[5:10,2]" specifies the particles 5 through 10, and 2.
 

AUTHORS

Rick Gaudette
Quanren Xiong
John Heumann  

SEE ALSO

PEET(1), prmParser(1), prepareEM(1), prepareRef(1), mergeEM(1), averageAll(1), removeDuplicates(1), calcFSC(1), and calcSSNR(1)


 

Index

NAME
SYNOPSIS
DESCRIPTION
AUTHORS
SEE ALSO

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Time: 21:10:05 GMT, March 20, 2017