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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 (“Do not use custom experimental data”; generally more conservative) or using a reference curve from another 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. Therefore, for homogeneously well-resolved maps subsequent filtering can performed in global mode, i.e. every part of the map is low-pass filtered to the same resolution. Heterogeneously resolved maps should be filtered in local mode, i.e. individual regions are filtered according to the respective local resolution.
Process
| Parameters | Description |
|---|---|
| Use custom experimental data - Do not use | Use standard curve for sharpening |
| Use custom experimental data - Use | 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 |
| ThirdInput | Local resolution map (“Fourier shell correlation” output) from FourierShellCorrelation logic |
| Output | Description |
|---|---|
| 1d power spec of input | 1d curve showing the 1d averaged power spectrum of the input 3d volume |
| 1d power spec of output | 1d curve showing the 1d 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 |
Parameters
Experimental Sampling [Å]
The pixel size of the input “Optional experimental data” [in Angstrom]. If no experimental data input is given, this value is not used.
Fill filter with zeros
Check this checkbox to fill the filter image with zeros at indexes that are outside the important diameter. Otherwise the filter image will be filled using constant extrapolation.
Normalize
Check this checkbox to normalize the corrected 3d volume to mean 0 and sigma 10.
Pixel size [Å]
The pixel size of the input “3d volume” [in Angstrom].
Resolution Cutoff [px]
Cut off resolution in pixel (from 0 to volume radius). 0 = no cutoff
Resolution level [Å]
The target resolution level [in Angstrom]
Inputs
Optional experimental data
Provides a reference 3d structure which is used instead of the spider x-ray curve for correction
3d volume
Provides the 3d volume to be sharpened
Outputs
1d rot avg of power spec
1d curve showing the 1d averaged power spectrum of the input 3d volume
Enhancement curve
1d curve showing the 1d representation of the output “Amplitude filter”.
Amplitude filter
3d volume that shows the applied sharpening filter image.
Amplitude Corrected 3d volume
Contains the corrected output 3d volume.
Written Header Values
- resolutionLevel Resolution where cut off was performed
- pixelSize Pixel size of the volume
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.