Name

sxhelicon - 3D structure determination of helical filaments with helical symmetry based constraints (under construction...)

Description

To run the program:

sxheader.py bdb:stack --zero --params=xform.projection

mpirun -np 12 sxhelicon.py bdb:stack start1.hdf ehelix128 --seg_ny=128 --fract=0.50 --psi_max=12.0 --delta=1.0 --maxit=900 --function="'[.,helicalusfjia,helical7_lonestar]'" --searchxshift=11.0 --xwobble=1.84 --ywobble=0.0 --dp=27.6 --dphi=166.5 --apix=1.84 --rmin=0.0 --rmax=128.8 --MPI --CTF

The image dimensions of the input stack should always be square. The desired segment length is specified through the --seg_ny option, and it should be no larger than the y dimension of the input images.

The z dimension of the reference volume should be the same as the y-dimension of the input images, and the x and y dimensions of the reference volume should not be larger than the x-dimension of the input images. If the reference volume is not cubic, the program will internally pad it to a cube.

The attributes xform.projection (Transform object containing the projection orientation parameters of an image: three Euler angles and two in-plane shifts) have to be set in the header of each image in the input stack. If the projection orientations are not known, then set them to zero. For more information on how to set projection orientation parameters, see I_O and Euler_angles.

Input

stack: set of 2-D images in a stack file (in bdb format), images have to be square (nx=ny).
ref_vol: Starting volume; x and y dimensions of the volume should not exceed x dimension of input images, and nz should be the same as x dimension of input images.
seg_ny: y dimension of desired segment size, should be related to fract in that fract ~ seg_ny/ny, where ny is dimension of input projections.
fract: fraction of the volume used for applying helical symmetry.
dp: rise [Angstrom] (helical symmetry parameter)
dphi: azimuthal angle [degrees] (helical symmetry parameter)
apix: pixel size [Angstroms]
rmin: minimal radius for hsearch (Angstroms)
rmax: maximal radius for hsearch (Angstroms)
sym: point-group symmetry of the structure
function: name of the reference preparation function
psi_max: maximum psi - how far rotation in plane can can deviate from 90 or 270 degrees
delta: angular step of reference projections
maxit: maximum number of iterations performed for each angular step (set to 30)
CTF: CTF correction (default is False)
MPI: use MPI version (default is False)
npad: padding size for 3D reconstruction (default 2)
debug: debug mode
searchxshift: search range for x-shift determination: +/- searchxshift (Angstroms), default 0.0
xwobble: wobble in x-directions (Angstroms), default 0.0 - It is the distance by which x-shift is allowed to deviate from the rigid helix-based prediction.
ywobble: wobble in y-directions (Angstroms), default 0.0 - It is the distance by which y-shift is allowed to deviate from the rigid helix-based prediction.
phiwobble: wobble of azimuthal angle (default = 0.0) (degrees) - It is the angle by which phi is allowed to deviate from the rigid helix-based prediction.
nopsisearch: Block searching for in-plane angle psi (default False) - If set, psi will be set to either 90 or 270 degrees.

Author / Maintainer

Pawel A. Penczek

Keywords

category 1: APPLICATIONS

Files

sparx/bin/sxhelicon.py, applications.py

Maturity

alpha: works for author, often works for others.

Bugs

Plenty