PEET 1.11.0 Program Descriptions

(with links to man pages)


Notes:

  1. While most common PEET operations can be performed from IMOD's eTomo graphical user interface, some programs and advanced options are only available from the command line.
  2. The links below are to html pages converted automatically from the original Linux man pages. Formatting of the converted version is not always perfect; if in doubt, refer to the original Linux man page by running "man" in a shell window.
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 Signal-to-noise 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
k-means 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
generate a dual-tilt-axis Fourier domain missing/present data mask
convert a .em format motive list to csv
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
modify a a rotation axes file to reflect rotations in a motive list
generate an initial motive list for a twisted filament by tracing subfilaments
convert Z-X-Z Euler angles to Z-Y-X "Slicer" angles
generate a mutl-tilt-axis Fourier domain missing/present data mask
perform principal components analysis on a set of aligned subvolumes
single-precision 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 Signal-to-noise ratio
generate a motive list for the first iteration of a PEET alignment search
generate a multi-particle 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
find and mark particles with nearly identical positions and orientations from averages
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 Z-Y-X "Slicer" angles to Z-X-Z Euler angles and optionally generate a motive list
model structures protruding from a sphere or cylinder (e.g. retrovirus spikes)
model structures defined by oriented 2-point contours (e.g. phage particles)
decompose aligned subvolumes using a previous principal components analysis
single-precision version of usePreviousPca
generate a variance map from a set of aligned particles and the corresponding average