Bsoft program

borient

Usage: borient [options] input.star [input.star]

Determines the orientations and origins of single particles with respect to a reference.

Actions:

-mode scc	Mode: 0,pps: polar power spectrum only (fast, default),
	1,scc: polar power spectrum with selected cross correlation.
	2,ccc: polar power spectrum with all cross correlation (slow).
	3,ori: origin determination by cross correlation.
-all	Reset selection to all particles before other selections (default not).
-side 15	Generate side view projections within the given angle from the equator.

Parameters:

-verbose 1	Verbosity of output.
-select 14	Selection number of particles to process (default all selected).
-symmetry C5	Point group symmetry.
-fullasu	Full asymmetric unit (default half).
-angles 2.5,5.2	Step size for theta and phi, one value sets both (default 45 degrees).
-sampling 1.5,1.5,1.5	Sampling (A/pixel; a single value can be given.)
-resolution 20,360	High and low resolution limits (angstrom).
-bands 250,-1,150,1,30,0	Bands for anlysis in reciprocal space (pairs of numbers: angstrom,value).
	Band with 0: Not used.
	Band with 1: Use for orientation determination.
	Band with -1: Use for cross-validation.
-annuli 2,95	Real space annular limits (default 0,inf pixels).
-multiple	Flag to generate multiple projection files (default one multi-image file).
-fom 0.3	Set FOM threshold for selection (default 0).

Input:

-reference file.ext	Input 3D reference map or projection file.

Output:

-output file.star	Output parameter file.
-TwoD file.ext	File name for 2D real space reconstruction.
-oriented	Output oriented images with file names ending with "_proj.spi".
	(must be used with the -TwoD option).

Bsoft version 1.5.7-20090605 (64 bit)

Generated by bdoc.pl on Mon Jun 15 11:47:11 2009

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