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_cutoff --res_overall=overall_resolution --radius=radius  --fsc=output_file_name  --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: (default required string)
secondvolume
Second half-volume: (default required string)
maskfile
3D mask: Defines the region where the local filtering should be applied. (default none)
wn
FSC window size: Defines the size of window where the local real-space FSC is computed. (default 7)
step
Fourier shell step size [Pixels]: (default 1.0)
cutoff
Resolution cut-off [1/Pixel]: Cut-off for the FSC. By default it goes to the Nyquist frequencies. (default 0.5)
radius
Mask radius [Pixels]: In case no mask is provided, a hard sphere of this radius will be used. (default -1)
res_overall
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)
MPI
Use MPI: (default False)


Output

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


Description

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

Pawel Penczek


Keywords

Category 1:: APPLICATIONS


Files

sxlocres.py


Maturity

Stable:: works for most people, has been tested; test cases/examples available.


Known Bugs

None.