Name

sxrecons3d_f - 3D reconstruction and calculation of FSC curve

Usage

Usage in command lines:

[ mpirun -np 4 ] sxrecons3d_f.py prj_stack volume fsc_curve <mask> --CTF --snr=signal_noise_ratio --list=file --group=ID --sym=symmetry -verbose=(0|1) --MPI

Usage in python programming:

recons3d_f(prj_stack, volume, fsc_file, mask=None, CTF=True, snr=1.0, sym="c1", listfile = "", group = -1, verbose=1, MPI=False)

Input

prj_stack

projection stack file, each image should have the following attributes set in the header: (1) xform.projection - transform object defining orientation of a given projection image, (2) ctf - a ctf object if CTF flag is used, (3) ctf_applied - a flag indicating whether given image was pre-multiplied by the ctf (0 - no; 1 - yes).

maskfile

file containing a 3D mask. Odd and even volumes will have average outisde of this mask subtracted and will be multiplied by this mask for the calculation of the FSC statistics

npad

padding size, default is 2

Output

volume

reconstructed volume file

fsc_curve

text file contains fsc data

Options

CTF

the data is CTF or not

snr

Singal-to-Noise Ratio of input data

sym

symmetry of input data (default is "c1")

verbose

verbose level (0:no verbose, 1: verbose) default is 0

Description

• Weighted nearest neighbour algorithm, works on data that contains CTF information in headers

Author / Maintainer

Wei Zhang

Keywords

category 1

APPLICATIONS

category 2

FOURIER

Files

sxrecons3d_f.py

See also

Maturity

stable

works for most people, has been tested; test cases/examples available.

Bugs

None. It is perfect.