Name

sxlocres - Local Resolution: Compute local resolution of a map.

Usage

Usage in command lines:

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

Typical usage

sxlocres exists in for both MPI and non-MPI versions.

mpirun -np 32 sxlocres.py refinementdir/main002/vol0.hdf refinementdir/main002/vol2.hdf locres.hdf --cutoff=0.5 --radius=28 --res_overall=0.3 --fsc=fscvol.txt --MPI

Input

firstvolume

First half-volume: (default required string)

secondvolume

Second half-volume: (default required string)

maskfile

3D mask: Defines the region where the local filtering should be applied. (default none)

wn

FSC window size: Defines the size of window where the local real-space FSC is computed. (default 7)

step

Fourier shell step size [Pixels]: (default 1.0)

cutoff

Resolution cut-off [1/Pixel]: Cut-off for the FSC. By default it goes to the Nyquist frequencies. (default 0.5)

radius

Mask radius [Pixels]: In case no mask is provided, a hard sphere of this radius will be used. (default -1)

res_overall

Overall resolution calibration (0 to 0.5). See Description below for details. (default -1)

The remaining parameters are optional.

MPI

Use MPI: (default False)

Output

outputfile

Output volume: Each voxel contains the resolution for this area in absolute frequency units. (default required string)

fsc

FSC output file: Contains the overall FSC curve computed by rotational averaging of local resolution values. It is truncated to res_overall. (default no curve)

Description

• Local resolution values are computed within small windowed areas (size wn^3). Due to small sample size the values are inaccurate and tend to underestimate resolution. Therefore, option res_overall allows to calibrate the average value of all local resolutions to the overall resolution, as estimated by the FSC between two full size volumes. I This value has to be independently obtained by the user - for example using sximgstat.py to compute (masked) FSC from half-volumes and reading the absolute frequency crresponding to 0.5 (or other) cut-off value.

Method

Reference

Author / Maintainer

Pawel Penczek

Keywords

category 1

APPLICATIONS

Files

sxlocres.py

See also

Maturity

stable

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

Bugs

None. It is perfect.