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eyes:logics:sharpen3d [2017/06/08 15:39] nfische [Usage] |
eyes:logics:sharpen3d [2017/06/13 15:17] (current) lschult |
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| =====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((Gabashvili, I.S., et al. (2001). Solution Structure of the E. coli 70S Ribosome at 11.5 Å Resolution. Cell, 100(5), 537-49.)) | 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 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. | + | ("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 | | ||
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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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