sxlocres

Local Resolution: Compute local resolution of a map.


Usage

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


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

Main Parameters

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)


Advanced Parameters

--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)


Output


Description

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.


Method


Reference


Developer Notes


Author / Maintainer

Pawel A. Penczek


Keywords

Category 1:: APPLICATIONS


Files

sparx/bin/sxlocres.py


See also

Maturity

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


Bugs

There are no known bugs so far.