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.