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← Revision 7 as of 20200915 14:37:28 ⇥
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Local resolution values are computed within small windowed areas (size wn^3). Due to small sample size the values are inaccurate and tend to underestimate resolution. Therefore, 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. I This value has to be independently obtained by the user  for example using sximgstat.py to compute (masked) FSC from halfvolumes and reading the absolute frequency crresponding to 0.5 (or other) cutoff value. 
Local resolution values are computed within small windowed areas (size wn^15). Due to small sample size the values are inaccurate and outcome tends to be noisy. It is thus suggested to use broader Gaussian window when local resolution is computed, say sigmag=3.0. 
Name
sxresolution  FSCM resolution measures: Compute overall and local resolution measures using a pair of halfmaps.
Usage
Usage in command lines:
sxresolution.py firstvolume secondvolume maskfile outputdir wn=window_size step=shell_step_size cutoff=res_cutoff res_overall=overall_resolution radius=radius fsc=output_file_name MPI
Typical usage
sxresolution.py refinementdir/main002/vol0.hdf refinementdir/main002/vol2.hdf outputdir radius=28
Input
 firstvolume
 First halfvolume: (default required string)
 secondvolume
 Second halfvolume: (default required string)
 maskfile
 3D mask: Defines the region within which FSCM will be computed. (default none)
 outputdir
 Output directory: results will be written to this directory. If it does not exist it will be created.
 wn
 FSCM box size: Defines the size of a 3D box within which local FSCM values will be computed. (default 15)
 step
 Fourier shell step size [Pixels]: (default 1.0)
 lfi
 LFI: Low Fourier index to begin calculations from (default 1)
 hfi
 HFI: High Fourier index to end calculations on (default nx//22)
 significance
 SIGNIFICANCE: Significance level for the Upper Confidence Interval. (default 0.99, which corresponds to 1%)
 sigmag
 SIGMAG: sigma of the Fourier space Gaussian window in pixels (default 1.0)
 ndf_reduce
 NDF_REDUCE: Reduction of ndf due to point group symmetry, for example for D3 set to 6 (default 1.0)
 cutoff
 Resolution cutoff [1/Pixel]: Cutoff for the Local FSCM CI. (default 0.143)
 radius
 Mask radius [Pixels]: If there is no maskfile, sphere with r=radius will be used. (default 1)
 local_fsc
 LOCAL_FSC: Set to 1 to compute local resolution volume (default 0).
 nthreads
 NTHREADS: Number of threads (mainly for 3D FFT) (default 4)
Output
 outputdir
 results will be written to this directory
Output volume: Each voxel contains the resolution for this area in absolute frequency units. (default required string)
Description
 Local resolution values are computed within small windowed areas (size wn^15). Due to small sample size the values are inaccurate and outcome tends to be noisy. It is thus suggested to use broader Gaussian window when local resolution is computed, say sigmag=3.0.
Method
Reference
Author / Maintainer
Pawel Penczek
Keywords
 category 1
 APPLICATIONS
Files
sxresolution.py
See also
Maturity
 stable
 works for most people, has been tested; test cases/examples available.
Bugs
None. It is perfect.