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eyes:logics:sharpen3d [2017/06/08 15:28] nfische [Process] |
eyes:logics:sharpen3d [2017/06/13 15:17] lschult |
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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 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. | + | 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.)) |
+ | ("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. | ||
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^ Parameters ^ Description ^ | ^ Parameters ^ Description ^ | ||
- | | //Use custom experimental data - Do not use// | Use standard curve for sharpening | | + | |Amplitude source - //Simulated SAXS data from ribosome// | Use standard curve for sharpening | |
- | | //Use custom experimental data - Use//| Use reference curve from custom 3d volume 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| | | -> 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 | | + | | 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| | | -> 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 | | + | | 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 | | | -> Kernel radius | Edge-length of cubic sub-regions in pixels | | ||
| -> Resolution threshold | Lowest resolution to which sub-regions are low-pass filtered | | | -> Resolution threshold | Lowest resolution to which sub-regions are low-pass filtered | | ||
- | | //Filtering mode - none// | Omit low-pass filtering of resulting sharpened map | | + | | 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. | | | 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. | | | Pixel size | Pixel size of the 3d volume to be sharpened. | | ||
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| //Optional experimental data// | Custom 3d volume to be used as reference for sharpening | | | //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 | | | //Resolution levels// | Local resolution values ("Resolution levels" output) from [[:eyes:logics:FourierShellCorrelation]] logic | | ||
- | | //ThirdInput// | Local resolution map ("Fourier shell correlation" output) from [[:eyes:logics:FourierShellCorrelation]] logic | | + | | //Local resolution map// | Local resolution map ("Fourier shell correlation" output) from [[:eyes:logics:FourierShellCorrelation]] logic | |
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^ Output ^ Description ^ | ^ Output ^ Description ^ | ||
- | | 1d power spec of input | 1d curve showing the 1d averaged power spectrum of the input 3d volume | | + | | 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 1d averaged power spectrum of the sharpened 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 | | | Sharpened 3D | Sharpened and possibly filtered 3d volume | | ||
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| pixelSize | Pixel size in Å | | | pixelSize | Pixel size in Å | | ||
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- | =====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. | ||
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- | ===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] | ||
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- | =====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 ===== | ===== 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. |