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--- pipeline:localres:sxlocres [2018/06/20 13:12]
127.0.0.1 external edit
+++ pipeline:localres:sxlocres [2018/08/22 10:52]
fmerino
@@ Line 21: / Line 21: @@
 ===== Input =====
 === Main Parameters ===
-  ; firstvolume : First half-volume: Typically, generated by sxmeridien. (default required string)
+  ; firstvolume : First half-map: A sub-map computed from about half of input projection data. In case of quasi-independent half-refinements, it has to one of the two generated structures. (default required string)
-  ; secondvolume : Second half-volume: Typically, generated by sxmeridien. (default required string)
+  ; secondvolume : Second half-map: A sub-map computed from about half of input projection data. In case of quasi-independent half-refinements, it has to one of the two generated structures. (default required string)
-  ; maskfile : 3D mask: Defines the region where the local filtering should be applied. (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 : Output volume: Each voxel contains the resolution for this area in [[definitions:absolute_frequency_units|absolute frequency]] units. (default required string)
+  ; outputfile : Output volume: Each voxel contains the associated resolution. It is expressed in [[definitions:absolute_frequency_units|absolute frequency]] units. (default required string)
-  ; %%--%%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 : 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]: Defines the finess of resolution measure. (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 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 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.  Low values (say 0.14) result in a noisy and tus difficult to interpret local resolution map. (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 (%%>=%%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. Use the absolute frequency corresponding to the standard FSC resolution estimation. 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)
-  ; %%--%%apix : Pixel size of half-volumes [A]: Effective only with %%--%%out_ang_res options. (default 1.0)
+  ; %%--%%apix : Pixel size of half-maps [A]: Effective only with %%--%%out_ang_res options. (default 1.0)
   ; %%--%%MPI : Use MPI: (default False)
@@ Line 44: / Line 44: @@
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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 window 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 half-maps. This value has to be independently obtained by the user. Command sximgstat.py computes (masked) FSC from half-maps and one can read the absolute frequency corresponding to 0.5 (or other) cut-off threshold.
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@@ Line 65: / Line 65: @@
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 ==== Files ====
-sparx/bin/sxlocres.py
+SPARX/bin/sxlocres.py
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@@ Line 80: / Line 80: @@
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