Name

sxihrsr - 3D structure determination of helical filaments using single-particle method

CODE UNDER DEVELOPMENT, no user support at the moment

Usage

usage in command line:

sxihrsr.py progname + stack ref_vol outdir mask.hdf --ir=inner_radius --ou=outer_radius --rs=ring_step --xr=x_range --yr=y_range --ts=translational_search_step --delta=angular_step --an=angular_neighborhood --maxit=max_iter --CTF --snr=1.0 --MPI --fourvar --dp --dphi --psi_max --rmin --rmax --fract --function --nise --npad --debug --datasym=symdoc

usage in python programming:

ihrsr(stack, ref_vol, outdir, maskfile, ir, ou, rs, xr, yr, ts, delta, an, maxit, CTF, snr, dp, dphi, psi_max, rmin, rmax, fract, nise, npad, sym, user_func_name, datasym, fourvar, debug = False, MPI = False)

Note: the helical symmetry axis is oriented to coincide with z-axis of the coordinate system. This implies in 2D images the symmetry axis is along y axis.

Input

stack

set of 2-D images in a stack file (format hdf or bdb), images have to be square (nx=ny)

maskfile

optional mask file to be used internally during alignment

The parameters preceded with -- are optional and default values are given in parenthesis.

inner_radius

inner radius for rotational correlation > 0 (set to 1) (in pixels)

outer_radius

outer radius for rotational correlation < nx/2-1 (set to nx/2-2, should be set to the radius of the particle) (in pixels)

ring_step

step between rings in rotational correlation > 0 (set to 1) (in pixels)

x_range

range for translation search in x direction, search is +/xr (is set to "4 2 1 1", if set to "0" it corresponds to rotational alignment only) (in pixels, can be fractional)

y_range

range for translation search in y direction, search is +/yr (is set to same as x_range, if set to "0" it corresponds to rotational alignment only) (in pixels, can be fractional)

translation_step

step of translation search in both directions, (set to "2 1 0.5 0.25", larger value increase the speed, but decrease the accuracy) (in pixels, can be fractional)

delta

angular step of reference projections. Only projections perpendicular to the symmetry axis z will be generated. Thus, delta=1 results in 180 reference projections.

angular_neighborhood

angular neighborhood for local searches (not implemented)

max_iteration

maximum number of iterations the program will perform (default is 10)

CTF

if this flag is set, the program will use 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)

MPI

use MPI version

Fourvar

compute Fourier variance

dp

delta z - translation in Angstroms (first of the parameters defining initial guess of the helical symmetry)

dphi

delta phi - rotation in degrees (second of the parameters defining initial guess of the helical symmetry)

psi_max

maximum psi - how far rotation in-planeof the input projection can can deviate from 90 or 270 degrees

rmin

minimal radius for the helical symmetry search (in pixels)

rmax

maximal radius for the helical symmetry search (in pixels)

fract

fraction of the volume used for helical search (reasonable number os 0.67)

function

name of the reference preparation function

datasym

symdoc - output ASCII file stored in the output directory which will contain symmetry parameters found for each iteration.

nise

start refining helical symmetry after nise steps. During first nise steps, the program will enforce helical symmetry defined by parameters dp and dphi.

npad

padding size for 3D reconstruction (default npad=4, for larger window sizes set napd=2). debug::if present, the program will output additional information.

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 files will be written to this directory. The program will write two kind of files: the average of the aligned image series (aqc_***.hdf), (aqf_***.hdf).

Description

Method

Reference

Egelman, E. H. (2000). A robust algorithm for the reconstruction of helical filaments using single- particle methods. Ultramicroscopy, 85, 225–234

Author / Maintainer

Pawel A. Penczek

Keywords

category 1

APPLICATIONS

Files

sparx/bin/sxihrsr.py, applications.py

See also

Maturity

beta

works for author, often works for others.

Bugs

---