Sharpen 3D

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

Use this module to sharpen a 3d map either in global mode and to filter it to a specific resolution, i.e. in the same way over the whole volume, or in local mode, i.e. by adapting the sharpening to the local resolution of the map. Sharpening will help in interpreting the map: dependent on resolution of the map domains, secondary structure elements or side-chains will be more clearly defined. However, sharpening will also increase the high-resolution noise, therefore “too much” sharpening may impede reliable interpretation, in particular in less-well resolved regions of the map. Therefore use the local mode to account for large variations in the resolution of the map. Sharpening can be either performed using an experimental curve from SAXS data (generally more conservative) or using a reference curve from another 3d volume, e.g. a theoretical density computed from an atomic model. In the latter case, the pixel size of the reference must be provided. If the target resolution is higher than the provided reference curve’s, the curve is extrapolated in a constant way.

The pixel size of the input “Optional experimental data” [in Angstrom]. If no experimental data input is given, this value is not used.

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.

Check this checkbox to normalize the corrected 3d volume to mean 0 and sigma 10.

The pixel size of the input “3d volume” [in Angstrom].

Cut off resolution in pixel (from 0 to volume radius). 0 = no cutoff

The target resolution level [in Angstrom]

Provides a reference 3d structure which is used instead of the spider x-ray curve for correction

Provides the 3d volume to be sharpened

1d curve showing the 1d averaged power spectrum of the input 3d volume

1d curve showing the 1d representation of the output “Amplitude filter”.

3d volume that shows the applied sharpening filter image.

Contains the corrected output 3d volume.

• resolutionLevel Resolution where cut off was performed
• pixelSize Pixel size of the volume

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.