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pipeline:localres:sxlocres [2018/02/16 10:11] 127.0.0.1 external edit |
pipeline:localres:sxlocres [2018/05/15 12:01] moriya |
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===== Usage ===== | ===== Usage ===== | ||
- | Usage in command line: | ||
- | | + | Usage in command line |
+ | |||
+ | | ||
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===== Typical usage ===== | ===== Typical usage ===== | ||
+ | |||
sxlocres exists in for both MPI and non-MPI versions. | sxlocres exists in for both MPI and non-MPI versions. | ||
- | mpirun -np 32 sxlocres.py refinementdir/ | + | mpirun -np 32 sxlocres.py |
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===== Input ===== | ===== Input ===== | ||
+ | === Main Parameters === | ||
+ | ; firstvolume : First half-volume: | ||
+ | ; secondvolume : Second half-volume: | ||
+ | ; 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: | ||
+ | |||
+ | ; %%--%%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 (%%> | ||
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- | === Main Parameters=== | + | === Advanced |
- | ; firstvolume : First half-volume: (default required string) | + | ; %%--%%out_ang_res |
- | ; secondvolume : Second half-volume: (default required string) | + | ; %%--%%apix |
- | ; maskfile | + | ; %%--%%MPI : Use MPI: (default False) |
- | ; 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 | + | |
- | ; radius : Mask radius [Pixels]: In case no mask is provided, a hard sphere of this radius will be used. (default | + | |
- | ; 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 | + | |
- | ; MPI : Use MPI: (default False) | + | |
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===== Output ===== | ===== Output ===== | ||
- | ; outputfile : Output volume: Each voxel contains the resolution for this area in [[: | ||
- | ; 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) | ||
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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< |
- | 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 ==== | ||
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==== Author / Maintainer ==== | ==== Author / Maintainer ==== | ||
- | Pawel Penczek | + | Pawel A. Penczek |
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==== Files ==== | ==== Files ==== | ||
- | sxlocres.py | + | sparx/bin/sxlocres.py |
+ | |||
+ | \\ | ||
+ | ==== See also ==== | ||
+ | [[pipeline: | ||
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==== Maturity ==== | ==== Maturity ==== | ||
- | Stable:: | + | Stable:: |
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- | ==== Known Bugs ==== | + | ==== Bugs ==== |
- | None. | + | There are no known bugs so far. |
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+ |