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pipeline:localres:sxlocres [2018/02/26 16:42] moriya |
pipeline:localres:sxlocres [2018/05/15 12:01] moriya |
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Usage in command line | Usage in command line | ||
- | sxlocres.py | + | sxlocres.py |
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===== Input ===== | ===== Input ===== | ||
=== Main Parameters === | === Main Parameters === | ||
- | ; firstvolume : First half-volume: | + | ; firstvolume : First half-volume: |
- | ; secondvolume : Second half-volume: | + | ; secondvolume : Second half-volume: |
; maskfile : 3D mask: Defines the region where the local filtering should be applied. (default none) | ; 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 [[definitions: | ; outputfile : Output volume: Each voxel contains the resolution for this area in [[definitions: | ||
- | ; 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) | + | ; %%--%%wn : FSC window size [Pixels]: Defines the size of window where the local real-space FSC (i.e. real-space CCC; cross-correlation coefficient) |
- | ; wn : FSC window size [Pixels]: Defines the size of window where the local real-space FSC is computed. (default 7) | + | ; %%--%%step : Fourier shell step size [Pixels]: |
- | ; step : Fourier shell step size [Pixels]: (default 1.0) | + | ; %%--%%cutoff : Local resolution criterion: Specify local resolution criterion in terms of the real-space FSC (i.e. real-space |
- | ; cutoff : Local resolution criterion: Specify local resolution criterion in terms of the real-space FSC (i.e. 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) |
- | ; radius : Mask radius [Pixels]: In case no mask is provided, a hard sphere of this radius will be used. (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) | + | ; %%--%%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) |
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=== Advanced Parameters === | === Advanced Parameters === | ||
- | ; out_ang_res : Save Angstrom local resolution: Additionally creates a local resolution file in Angstroms. (default False) | + | ; %%--%%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) | + | ; %%--%%apix : Pixel size of half-volumes [A]: Effective only with %%--%%out_ang_res options. (default 1.0) |
- | ; MPI : Use MPI: (default False) | + | ; %%--%%MPI : Use MPI: (default False) |
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===== Description ===== | ===== Description ===== | ||
- | Local resolution values are computed within small windowed areas (size wn< | + | Local resolution values are computed within small windowed areas (size wn< |
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