Local Resolution: Compute local resolution of a map.
Usage in command line:
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
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
- First half-volume: (default required string)
- Second half-volume: (default required string)
- 3D mask: Defines the region where the local filtering should be applied. (default none)
- FSC window size: Defines the size of window where the local real-space FSC is computed. (default 7)
- Fourier shell step size [Pixels]: (default 1.0)
- Resolution cut-off [1/Pixel]: Cut-off for the FSC. By default it goes to the Nyquist frequencies. (default 0.5)
- Mask radius [Pixels]: In case no mask is provided, a hard sphere of this radius will be used. (default -1)
- Overall resolution [1/Pixel]: A value between 0 to 0.5 for calibration of the average local resolution. See Description section in the wiki page for details. (default -1.0)
- Use MPI: (default False)
- Output volume: Each voxel contains the resolution for this area in absolute frequency units. (default required string)
- 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)
Local resolution values are computed within small windowed areas (size wn<sup>3<\sup>). Due to small sample size the values are inaccurate and tend to underestimate resolution. Therefore, the 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. 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 corresponding to 0.5 (or other) cut-off value.
Author / Maintainer
Category 1:: APPLICATIONS
Stable:: works for most people, has been tested; test cases/examples available.