Notes:
add points to an IMOD model at specified intervals along each contour  
align particle subvolumes with a specified reference  
apply a binary mask t a 3D volume in the Fourier domain  
create an average volumes from aligned particle subvolumes  
refine a subvolume using blind deconvolution  
calculate the Fourier Shell Correlation for a set of aligned subvolumes  
calculate the Spectral Signaltonoise Ratio for a set of aligned subvolumes  
calculate a gold standard Fourier Shell Correlation from a pair of PEET alignments  
scan the alignment log files for indications of poorly chosen search parameters  
kmeans clustering using principal components computed by program pca  
generate a Combine two motive lists into one  
save aligned positions, orientations, and rotations axes for each particle  
create explicit rotation axes files for particles in each tomogram  
generate a dualtiltaxis Fourier domain missing/present data mask  
convert a .em format motive list to csv  
search for an nfold rotational axis in projections along x, y, or z  
generate an IMOD model with a regular grid of points over a specified volume  
generate a summary of all warnings and errors in PEET log files  
combine temporary files created by parallel alignment into a single motive list  
model particles orthogonal to membranes defined by meshed IMOD surfaces  
generate a new motive list by rotating and / or translating an existing one  
please see entry for updateRotAxes instead  
generate
an initial motive list for a twisted filament by tracing
subfilaments 

convert ZXZ motive list angles to ZYX Relion (or other) angles  
convert ZXZ motive list angles to ZYX "Slicer" angles  
generate a mutltiltaxis Fourier domain missing/present data mask  
perform principal components analysis on a set of aligned subvolumes  
singleprecision version of principal components analysis  
this
entire suite of programs. Overall operation and global options
are described. 

delete log, intermediate, and (optionally) output files  
open this index to the PEET man pages in a browser  
print the version of PEET currently in use  
plot a previously computed Fourier Shell Correlation  
3D quiver plot showing location and rotation axis orientation for each particle  
plot a previously computed Spectral Signaltonoise ratio  
generate a motive list for the first iteration of a PEET alignment search  
generate
a multiparticle initial reference with reduced bias 

generate a single particle initial reference  
generate scripts for running a PEET alignment using processchunks  
randomize phase of fft componenents above a specified frequency  
convert ZYZ Relion (or other) angles to ZXZ motive list angles  
find and mark particles with nearly identical positions and orientations from averages  
generate a new rotation axes file by rotating each axis in an existing one  
plot a histogram of crosscorrelation scores (or other values from motive lists)  
seed a model for finding spikes protruding from a sphere or cylinder (e.g. viral spikes)  
plot Fourier Shell Correlation from a pair of MRC volumes  
convert ZYX "Slicer" angles to ZXZ motive list angles  
model structures protruding from a sphere, cylinder, or helix (e.g. retrovirus spikes)  
seed a model for finding spikes protruding from a sphere or cylinder (e.g. viral spikes)  
Split a linear model and motive list into equallysized segments  
update a rotation axes file to reflect rotations in a motive list  
decompose aligned subvolumes using a previous principal components analysis  
singleprecision version of
usePreviousPca 

generate a variance map from a set of aligned particles and the corresponding average 