Local Resolution: Compute local resolution of a map.


Usage in command line  firstvolume  secondvolume  maskfile  outputfile  --wn=WINDOW_SIZE  --step=SHELL_STEP_SIZE  --cutoff=RES_CRITERION  --radius=RADIUS  --fsc=OUTPUT_FILE_PATH  --res_overall=RESOLUTION  --out_ang_res=OUTPUT_FILE_PATH  --apix=PIXEL_SIZE  --MPI

Typical usage

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

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


Main Parameters

First half-volume: Typically, generated by sxmeridien. (default required string)
Second half-volume: Typically, generated by sxmeridien. (default required string)
3D mask: Defines the region where the local filtering should be applied. (default none)
Output volume: Each voxel contains the resolution for this area in absolute frequency units. (default required string)
FSC window size [Pixels]: Defines the size of window where the local real-space FSC (i.e. real-space CCC; cross-correlation coefficient) is computed. (default 7)
Fourier shell step size [Pixels]: Defines the finess of resolution measure. (default 1.0)
Local resolution criterion: Specify local resolution criterion in terms of the real-space FSC (i.e. real-space CCC; cross-correlation coefficient). (default 0.5)
Mask radius [Pixels]: In case no mask is provided, a hard sphere of this radius will be used. By default, radius = box_size/2 - (--wn). (default -1)
FSC output file: Contains the overall FSC curve computed by rotational averaging of local resolution values. It is truncated to --res_overall. By default, the program does not save the FSC curve. (default no curve)
Overall resolution [1/Pixel]: Specify overall (or global) resolution in absolute frequency (>=0.0 and <=0.5) for calibration of the average local resolution. Typically, use the absolute frequency corresponding to the conventional FSC resolution obtained by 3D refinement. See Description section in the wiki page for details. By default, the program will not calibrate the average local resolution. (default -1.0)

Advanced Parameters

Save Angstrom local resolution: Additionally creates a local resolution file in Angstroms. (default False)
Pixel size of half-volumes [A]: Effective only with --out_ang_res options. (default 1.0)
Use MPI: (default False)



Local resolution values are computed within small windowed areas (size wn3). 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 to compute (masked) FSC from half-volumes and reading the absolute frequency corresponding to 0.5 (or other) cut-off value.



Developer Notes

Author / Maintainer

Pawel A. Penczek





See also


Stable:: Has been evaluated and tested. Please let us know if there are any bugs.


There are no known bugs so far.