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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 half-volumes and reading the absolute frequency crresponding
to 0.5 (or other) cut-off 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.
sxresolution - FSCM resolution measures: Compute overall and local resolution measures using a pair of half-maps.
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
sxresolution.py refinementdir/main002/vol0.hdf refinementdir/main002/vol2.hdf outputdir --radius=28
- First half-volume: (default required string)
- Second half-volume: (default required string)
- 3D mask: Defines the region within which FSCM will be computed. (default none)
- Output directory: results will be written to this directory. If it does not exist it will be created.
- FSCM box size: Defines the size of a 3D box within which local FSCM values will be computed. (default 15)
- Fourier shell step size [Pixels]: (default 1.0)
- LFI: Low Fourier index to begin calculations from (default 1)
- HFI: High Fourier index to end calculations on (default nx//2-2)
- SIGNIFICANCE: Significance level for the Upper Confidence Interval. (default 0.99, which corresponds to 1%)
- SIGMAG: sigma of the Fourier space Gaussian window in pixels (default 1.0)
- NDF_REDUCE: Reduction of ndf due to point group symmetry, for example for D3 set to 6 (default 1.0)
- Resolution cut-off [1/Pixel]: Cut-off for the Local FSCM CI. (default 0.143)
- Mask radius [Pixels]: If there is no maskfile, sphere with r=radius will be used. (default -1)
- LOCAL_FSC: Set to 1 to compute local resolution volume (default 0).
- NTHREADS: Number of threads (mainly for 3D FFT) (default 4)
- results will be written to this directory
Output volume: Each voxel contains the resolution for this area in absolute frequency units. (default required string)
- 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.
Author / Maintainer
- category 1
- works for most people, has been tested; test cases/examples available.
None. It is perfect.