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eyes:logics:sharpen3d [2017/06/08 11:39] nfische [Usage] |
eyes:logics:sharpen3d [2017/06/13 15:17] (current) lschult |
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| - | ======Sharpen 3D ====== | + | ======Sharpen3D ====== |
| Map sharpening allows to correct for the contrast loss at high resolution, resulting in better interpretable maps. | Map sharpening allows to correct for the contrast loss at high resolution, resulting in better interpretable maps. | ||
| =====Usage===== | =====Usage===== | ||
| - | 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. | + | 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.)) |
| - | =====Parameters===== | + | ("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. |
| - | ===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===== | + | ===== Process ===== |
| - | ===Optional experimental data=== | + | |
| - | Provides a reference 3d structure which is used instead of the spider x-ray curve for correction | + | |< 100% 30% >| |
| - | ===3d volume=== | + | ^ Parameters ^ Description ^ |
| - | Provides the 3d volume to be sharpened | + | |Amplitude source - //Simulated SAXS data from ribosome// | Use standard curve for sharpening | |
| - | =====Outputs===== | + | | Amplitude source - //Custom experimental data//| Use reference curve from custom 3d volume for sharpening | |
| - | ===1d rot avg of power spec=== | + | | -> Experimental sampling | Pixel size of reference 3d volume in Å| |
| - | 1d curve showing the 1d averaged power spectrum of the input 3d volume | + | | Filtering mode - //global// | Low-pass filter sharpened 3d volume everywhere to the same resolution level | |
| - | ===Enhancement curve=== | + | | -> Resolution level | Value for global low-pass filtering in Å| |
| - | 1d curve showing the 1d representation of the output “Amplitude filter”. | + | | Filtering mode - //local// | Low-pass filter sub-regions of the 3d volume map according to local resolution | |
| - | ===Amplitude filter=== | + | | -> Kernel radius | Edge-length of cubic sub-regions in pixels | |
| - | 3d volume that shows the applied sharpening filter image. | + | | -> Resolution threshold | Lowest resolution to which sub-regions are low-pass filtered | |
| - | ===Amplitude Corrected 3d volume=== | + | | Filtering mode - //none// | Omit low-pass filtering of resulting sharpened map | |
| - | Contains the corrected output 3d volume. | + | | Normalize | Check this box to normalize the sharpened 3d volume to mean 0 and sigma 10. | |
| - | ==Written Header Values== | + | | Pixel size | Pixel size of the 3d volume to be sharpened. | |
| - | * **resolutionLevel** Resolution where cut off was performed | + | |
| - | * **pixelSize** Pixel size of the volume | + | |< 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 ===== | ===== 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. | 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. | ||