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--- eyes:logics:sharpen3d [2017/06/08 09:54]
nfische created
+++ eyes:logics:sharpen3d [2017/06/13 15:17] (current)
lschult
@@ Line 1: / Line 1: @@
-======Sharpen 3D ======
+======Sharpen3D ======
+Map sharpening allows to correct for the contrast loss at high resolution, resulting in better interpretable maps.
+=====Usage=====
+Use this module to sharpen and subsequently low-pass filter a 3d map. Sharpening helps in interpreting the map: dependent on resolution of the map domains, secondary structure elements or side-chains will be more clearly defined. Sharpening can be either performed using a standard curve from SAXS data((Gabashvili, I.S., et al. (2001). Solution Structure of the E. coli 70S Ribosome at 11.5 Å Resolution. Cell, 100(5), 537-49.))
+ ("Do not use custom experimental data"; generally more conservative) or using a reference curve from a custom 3d volume ("Use custom experimental data"), e.g. a theoretical density computed from an atomic model. In the latter case, the pixel size of the reference must be provided. Sharpening also increases the high-resolution noise, which may impede reliable interpretation, in particular in less-well resolved regions of the map. Consequently, homogeneously well-resolved maps may subsequently be filtered in global mode, i.e. every part of the map is low-pass filtered to the same resolution. Heterogeneously resolved maps may be be filtered in local mode, i.e. individual regions are filtered according to the respective local resolution.
+===== Process =====
+|< 100% 30% >|
+^ Parameters                 ^ Description     ^
+|Amplitude source  - //Simulated SAXS data from ribosome// | Use standard curve for sharpening  |
+| Amplitude source - //Custom experimental data//| Use reference curve from custom 3d volume for sharpening  |
+| -> Experimental sampling        | Pixel size of reference 3d volume in Å|
+| Filtering mode - //global// | Low-pass filter sharpened 3d volume everywhere to the same resolution level |
+| -> Resolution level        | Value for global low-pass filtering in Å|
+| Filtering mode - //local// | Low-pass filter sub-regions of the 3d volume map according to local resolution |
+| -> Kernel radius        | Edge-length of cubic sub-regions in pixels |
+| -> Resolution threshold        | Lowest resolution to which sub-regions are low-pass filtered  |
+| Filtering mode - //none// | Omit low-pass filtering of resulting sharpened map |
+| Normalize | Check this box to normalize the sharpened 3d volume to mean 0 and sigma 10.  |
+| Pixel size | Pixel size of the 3d volume to be sharpened.  |
+|< 100% 30% >|
+^ Input   ^ Description ^
+| 3d volume  | 3d volume to be sharpened |
+| //Optional experimental data//  | Custom 3d volume to be used as reference for sharpening |
+| //Resolution levels// | Local resolution values ("Resolution levels" output) from [[:eyes:logics:FourierShellCorrelation]] logic |
+| //Local resolution map//  | Local resolution map ("Fourier shell correlation" output) from [[:eyes:logics:FourierShellCorrelation]] logic  |
+|< 100% 30% >|
+^ Output   ^ Description ^
+| 1d power spec of input | 1d curve showing the rotationally averaged power spectrum of the input 3d volume |
+| 1d power spec of output | 1d curve showing the rotationally averaged power spectrum of the sharpened 3d volume |
+| Sharpened 3D | Sharpened and possibly filtered 3d volume |
+|< 100% 30% >|
+^ New/Changed Header Values ^ Description ^
+| pixelSize | Pixel size in Å |
+===== Additional Information =====
+This logic is not computationally heavy but needs a lot of RAM for execution. The biggest tested dimensions were 1024x1024x1024 which occupied roughly 12gb of RAM. If not enough RAM is available, this logic will fail to execute.