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Name

sxresolution - FSCM resolution measures: Compute overall and local resolution measures using a pair of half-maps.

Usage

Usage in command lines:

sxresolution.py firstvolume secondvolume maskfile outputdir --wn=window_size --step=shell_step_size --cutoff=res_cutoff --res_overall=overall_resolution --radius=radius --fsc=output_file_name --MPI

Typical usage

sxresolution.py refinementdir/main002/vol0.hdf refinementdir/main002/vol2.hdf outputdir --radius=28

Input

firstvolume
First half-volume: (default required string)
secondvolume
Second half-volume: (default required string)
maskfile
3D mask: Defines the region within which FSCM will be computed. (default none)
outputdir
Output directory: results will be written to this directory. If it does not exist it will be created.
wn
FSCM box size: Defines the size of a 3D box within which local FSCM values will be computed. (default 15)
step
Fourier shell step size [Pixels]: (default 1.0)
lfi
LFI: Low Fourier index to begin calculations from (default 1)
hfi
HFI: High Fourier index to end calculations on (default nx//2-2)
significance
SIGNIFICANCE: Significance level for the Upper Confidence Interval. (default 0.99, which corresponds to 1%)
sigmag
SIGMAG: sigma of the Fourier space Gaussian window in pixels (default 1.0)
ndf_reduce
NDF_REDUCE: Reduction of ndf due to point group symmetry, for example for D3 set to 6 (default 1.0)
cutoff
Resolution cut-off [1/Pixel]: Cut-off for the Local FSCM CI. (default 0.143)
radius
Mask radius [Pixels]: If there is no maskfile, sphere with r=radius will be used. (default -1)
local_fsc
LOCAL_FSC: Set to 1 to compute local resolution volume (default 0).
nthreads
NTHREADS: Number of threads (mainly for 3D FFT) (default 4)

Output

outputdir
results will be written to this directory
  • Output volume: Each voxel contains the resolution for this area in absolute frequency units. (default required string)

Description

Method

Reference

Author / Maintainer

Pawel Penczek

Keywords

category 1
APPLICATIONS

Files

sxresolution.py

See also

Maturity

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

Bugs

None. It is perfect.