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--- pipeline:localres:sxlocres [2018/02/26 16:50]
moriya
+++ pipeline:localres:sxlocres [2018/05/15 12:01]
moriya
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 Usage in command line
-  sxlocres.py  firstvolume  secondvolume  maskfile  outputfile  --fsc=OUTPUT_FILE_PATH  --wn=WINDOW_SIZE  --step=SHELL_STEP_SIZE  --cutoff=RES_CRITERION  --radius=RADIUS  --res_overall=RESOLUTION  --out_ang_res=OUTPUT_FILE_PATH  --apix=PIXEL_SIZE  --MPI
+  sxlocres.py  firstvolume  secondvolume  maskfile  outputfile  --wn=WINDOW_SIZE  --step=SHELL_STEP_SIZE  --cutoff=RES_CRITERION  --radius=RADIUS  --fsc=OUTPUT_FILE_PATH  --res_overall=RESOLUTION  --out_ang_res=OUTPUT_FILE_PATH  --apix=PIXEL_SIZE  --MPI
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   ; outputfile : Output volume: Each voxel contains the resolution for this area in [[definitions:absolute_frequency_units|absolute frequency]] units. (default required string)
-  ; 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) is computed. (default 7)
-  ; 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)
-  ; 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)
-  ; 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)
-  ; 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 ===
-  ; 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 =====
-Local resolution values are computed within small windowed areas (size wn<sup>3<\sup>). Due to small sample size the values are inaccurate and tend to underestimate resolution. 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.
+Local resolution values are computed within small windowed areas (size wn<sup>3</sup>). Due to small sample size the values are inaccurate and tend to underestimate resolution. 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.
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