Local Resolution: Compute local resolution of a map.

Usage in command line

sp_locres.py  firstvolume  secondvolume  maskfile  directory --prefix=PREFIX  --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

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

mpirun -np 32  sp_locres.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-map: A sub-map computed from about half of input projection data. In case of quasi-independent half-refinements, it has to one of the two generated structures. (default required string)

secondvolume

Second half-map: A sub-map computed from about half of input projection data. In case of quasi-independent half-refinements, it has to one of the two generated structures. (default required string)

maskfile

3D mask: Defines the region for which local resolution will be computed. It is advisable to eliminate irrelevant regions surrounding the structure. (default none)

directory

Output directory: Each voxel contains the associated resolution. It is expressed in absolute frequency units. (default required string)

--prefix

Output prefix: Prefix for output files. (default localres)

--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)

maskfile==none

--wn

Window size [Pixels]: Size of window within which local real-space CCC (equivalent to FSC) is computed. (default 7)

--step

Fourier shell step size [Pixels]: Values larger than 1.0 increase the speed and stability of the local resolution map, but decrease its reciprocal space resolvability. (default 1.0)

--cutoff

Local resolution criterion: Specify the resolution cut-off of the local resolution map. The map will contain, for each voxel, the value of spatical frequency at which local resolution at this voxel dropped below the specified cut-off level. Low values (say 0.14) result in a noisy and tus difficult to interpret local resolution map. (default 0.143)

--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)

--out_ang_res

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

--apix

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

--out_ang_res==True

--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. Use the absolute frequency corresponding to the standard FSC resolution estimation. See Description section in the wiki page for details. By default, the program will not calibrate the average local resolution. (default -1.0)

--MPI

Use MPI: (default False)

Local resolution values are computed within small windowed areas (size wn³). Due to small window 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 half-maps. This value has to be independently obtained by the user. Command sp_imgstat.py computes (masked) FSC from half-maps and one can read the absolute frequency corresponding to 0.5 (or other) cut-off threshold.

Pawel A. Penczek

Category 1:: APPLICATIONS

SPARX/bin/sp_locres.py

sp_meridien, sp_process, and sp_filterlocal.

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

There are no known bugs so far.