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SAVR: Semi-Automated Virus Reconstruction

SAVR consists of five major components:

I. IMIRS

ortAll	Finds initial orientation candidates using self common line algorithm
eliminateOrt	Eliminates incorrect orientations found by *ortAll* using cross common line method
globalRefine	Global refinement of orientations with cross common line between all particle pairs
refineAll	Refines orientations with cross common line against a set of projections of a 3D model
buildTemplate	Generates a orientation data file for reconstruction from a given set of log files outputted by *ortAll*
reconstructParallel	Reconstructs a 3D map from a list of particle orientations outputted by *refineAll, globalRefine, or buildTemplate*. Originally parallelized for shared memory platforms. We recently parallelized this for distributed memory systems using MPI
ctfForAll	Generates CTF curves for all micrographs at different defocuses, B factors

II. EMAN

proc2d	Miscellaneous operations of 2D images
proc3d	Miscellaneous operations of 3D maps
boxer	A graphical program for locating particles within micrographs
ctfit	A graphical utility for determining CTF parameters
ftictf	Automatic fitting of CTF parameters
iminfo	Return basic information about image files
volume	Finds the density value threshold of a 3D map for a given mass or the mass for a density threshold
runpar	Run a list of programs in parallel on one or several machines

III. New Algorithmic Programs

WaveOrt	Wavelet transform assisted projection matching for initial orientation determination
cenalign	Initial center determination using correlation with a rotational averaged particle image
symmetrize	Applys symmetries (C_n, D_n, icosahedral) in real space for a full map or a half map
icosmask	Masks internal and external areas by following the icosahedral geometry
projecticos	Generates 2D projections in random, even distribution, or specified list of orientations in icosahedral asymmetric unit

IV. Glue Programs

fftimagic	Performs FFT of input images in IMAGIC format and saves in individual MRC files. FFTW library is used.
Imagic2OrtCen	Convert the orientation and center parameters stored in IMAGIC file header into the data file format used in IMIRS
OrtCen2Imagic	Convert the orientation and center parameters in the data file format used in IMIRS into IMAGIC file header

V. Top Level Python Scripts

EM.py	The core module that provides all the automated processing and statistics. Not an executable program
virus.py	The master program a user runs to start the automated processing. Automatically calls *gui_virus.py* if no data file is provided
gui_virus.py	Graphic interface for data and option input to SAVR and job submission
refineStats.py	Computes the refinement statistics
plotort.py	Plots the particle orientation distribution using *xmgrace*
icos5fTo3f.py	Transform the "5fold" oriented map to "3fold" orientation. Works for half map and full map in ICOS or MRC formats
buildIM.py	Automatically build an initial model from raw images using self common line method

While SAVR is still under active development, public release of a snapshot is currently available at NCMI Software page

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