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_CRITERION  --radius=RADIUS  --fsc=OUTPUT_FILE_PATH  --res_overall=RESOLUTION  --out_ang_res=OUTPUT_FILE_PATH  --apix=PIXEL_SIZE  --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

firstvolume

First half-volume: Typically, generated by sxmeridien. (default required string)

secondvolume

Second half-volume: Typically, generated by sxmeridien. (default required string)

maskfile

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

outputfile

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

--wn

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)

--step

Fourier shell step size [Pixels]: Defines the finess of resolution measure. (default 1.0)

--cutoff

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)

--radius

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

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)

--res_overall

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)

--out_ang_res

Save Angstrom local resolution: Additionally creates a local resolution file in Angstroms. (default False)

--apix

Pixel size of half-volumes [A]: Effective only with --out_ang_res options. (default 1.0)

--MPI

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 sximgstat.py to compute (masked) FSC from half-volumes and reading the absolute frequency corresponding to 0.5 (or other) cut-off value.

Pawel A. Penczek

Category 1:: APPLICATIONS

sparx/bin/sxlocres.py

sxmeridien, sxprocess, and sxfilterlocal.

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

There are no known bugs so far.