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pipeline:localres:sxlocres [2018/08/22 10:52] fmerino |
pipeline:localres:sxlocres [2019/04/02 10:11] lusnig |
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~~NOTOC~~ | ~~NOTOC~~ | ||
- | ===== sxlocres | + | ===== sp_locres |
Local Resolution: Compute local resolution of a map. | Local Resolution: Compute local resolution of a map. | ||
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Usage in command line | Usage in command line | ||
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\\ | \\ | ||
===== Typical usage ===== | ===== Typical usage ===== | ||
- | sxlocres | + | sp_locres |
- | mpirun -np 32 | + | mpirun -np 32 |
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; secondvolume : Second half-map: A sub-map computed from about half of input projection data. In case of quasi-independent half-refinements, | ; secondvolume : Second half-map: A sub-map computed from about half of input projection data. In case of quasi-independent half-refinements, | ||
; maskfile : 3D mask: Defines the region for which local resolution will be computed. It is advisable to eliminate irrelevant regions surrounding the structure. (default none) | ; maskfile : 3D mask: Defines the region for which local resolution will be computed. It is advisable to eliminate irrelevant regions surrounding the structure. (default none) | ||
- | ; outputfile | + | ; directory |
+ | ; %%--%%prefix : Output prefix: Prefix for output files. (default localres) | ||
+ | ; %%--%%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) : maskfile==none | ||
; %%--%%wn : Window size [Pixels]: Size of window within which local real-space CCC (equivalent to FSC) is computed. (default 7) | ; %%--%%wn : Window size [Pixels]: Size of window within which local real-space CCC (equivalent to FSC) is computed. (default 7) | ||
; %%--%%step : Fourier shell step size [Pixels]: Values larger than 1.0 increase the speed and stability of the local resolution map, but decrease its reciprocal space resolvability. (default 1.0) | ; %%--%%step : Fourier shell step size [Pixels]: Values larger than 1.0 increase the speed and stability of the local resolution map, but decrease its reciprocal space resolvability. (default 1.0) | ||
- | ; %%--%%cutoff : Local resolution criterion: Specify the resolution cut-off of the local resolution map. The map will contain, for each voxel, the value of spatical frequency at which local resolution at this voxel dropped below the specified cut-off level. | + | ; %%--%%cutoff : Local resolution criterion: Specify the resolution cut-off of the local resolution map. The map will contain, for each voxel, the value of spatical frequency at which local resolution at this voxel dropped below the specified cut-off level. |
- | ; %%--%%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) | ; %%--%%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 | + | ; %%--%%out_ang_res |
+ | ; %%--%%apix : Pixel size of half-maps [A]: Effective only with %%--%%out_ang_res options. (default 1.0) : %%--%%out_ang_res==True | ||
\\ | \\ | ||
=== Advanced Parameters === | === Advanced Parameters === | ||
- | ; %%--%%out_ang_res | + | ; %%--%%res_overall |
- | ; %%--%%apix : Pixel size of half-maps [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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==== Files ==== | ==== Files ==== | ||
- | SPARX/bin/sxlocres.py | + | SPARX/bin/sp_locres.py |
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==== See also ==== | ==== See also ==== | ||
- | [[pipeline: | + | [[pipeline: |
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