Name

sxlocal_ali3dm - Perform local refinement of 3-D projection alignment of image series.

Usage

usage in command line

sxlocal_ali3dm.py stack ref_vol outdir <maskfile> --ou=outer_radius --delta=angular_bracket --ts --nassign --nrefine --MPI --function --fourvar --maxit=max_iter --termprec=percentage_to_stop --npad --debug --CTF --snr=SNR --sym=symmetry

usage in python programming

local_ali3dm_MPI(stack, refvol, outdir, maskfile, ou=-1, delta=2, ts=0.25, maxit=10, nassign=4, nrefine=1, CTF = None,snr=1.0, sym="c1", user_func_name="ref_ali3d", fourvar=False, npad = 4, debug=False, termprec = 0.0 )

Input

input_stack

set of 2-D images in a stack file, images have to be squares (nx=ny)

ref_vol
initial reference volume
output_directory
name of the output directory where the results and debug information will be placed
maskfile
filename used to create the mask
  • The parameters preceded with -- are optional and default values are given in parenthesis.

    ou

    outer radius of a circular mask used to calculate correlation between 2-D data and projections of the structure< int(nx/2)-1 (set to int(nx/2)-2, should be set to the radius of the particle)

    delta
    angular bracket for the search of orientation parameters (each parameter will be checked +/- delta) (set to 2.0)
    max_iter

    maximum number of iterations the program will perform (set to 10). Within each iteration the 3-D reference structure will be updated after each chunk of 2-D dat.

    ts
    step size of the translation search in both directions, search is -xr, -xr+ts, 0, xr-ts, xr, can be fractional.
    CTF

    if this flag is set, the program will use during the alignment CTF information provided in file headers (for details see I_O). (default no CTF)

    snr
    Signal-to-Noise Ratio of the data (default SNR=1.0)
    sym
    symmetry of the volume under reconstruction (set to c1)
    function

    user-supplied-function that prepares the reference volume during each iteration (default: ref_ali3d)

    MPI
    run program in MPI mode
  • Output

    output_directory
    directory name into which the output files will be written. If it does not exist, the directory will be created. If it does exist, the program will crash and an error message will come up. Please change the name of directory and restart the program . The program will write two kind of files: the average of the aligned image series (aqe***.spi) and the Fourier Resolution Criterion curve (dre***). Both files are numbered by the iteration number.
    header
    the alignment parameters of each 2D projection (Euler angles and two in-plane translations) are stored in the headers of input files as xform.projection

    Description

    Method

    Program uses simplex optimization method to refine for each image five orientation parameters such that the inner product between the image and the average of remaining images is maximized.

    Reference

    Yang and Penczek, Ultramicroscopy 2008.

    Author / Maintainer

    Pawel A. Penczek

    Keywords

    category 1
    APPLICATIONS
    category 3
    GRIDDING

    Files

    sparx/bin/sxali3d_em.py

    See also

    sxali3d

    Maturity

    beta
    works for author, often works for others.

    Bugs

    The centering may fail.

    sxlocal_ali3dm (last edited 2014-09-05 19:20:24 by penczek)