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

• Local resolution values are computed within small windowed areas (size wn^15). Due to small sample size the values are inaccurate and outcome tends to be noisy. It is thus suggested to use broader Gaussian window when local resolution is computed, say sigmag=3.0.

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.