Map sharpening allows to correct for the contrast loss at high resolution, resulting in better interpretable maps.

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 data1) (“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.

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.
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 FourierShellCorrelation logic
Local resolution map Local resolution map (“Fourier shell correlation” output) from FourierShellCorrelation logic
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
New/Changed Header Values Description
pixelSize Pixel size in Å

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.

Gabashvili, I.S., et al. (2001). Solution Structure of the E. coli 70S Ribosome at 11.5 Å Resolution. Cell, 100(5), 537-49.