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eyes:logics:fouriershellcorrelation [2017/06/02 12:32] jschlie1 created |
eyes:logics:fouriershellcorrelation [2017/06/12 18:32] (current) jschlie1 |
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| This logic applies the "gold standard" FSC calculation for resolution determination of a 3D structure reconstruction where the data had been split into two randomly chosen halves earlier. After independent reconstruction of both halves, the FSC fall-off at different resolution levels can be used to determine the reconstruction quality. Additionally, a mask can be supplied to limit the 3D volume to be calculated with. | This logic applies the "gold standard" FSC calculation for resolution determination of a 3D structure reconstruction where the data had been split into two randomly chosen halves earlier. After independent reconstruction of both halves, the FSC fall-off at different resolution levels can be used to determine the reconstruction quality. Additionally, a mask can be supplied to limit the 3D volume to be calculated with. | ||
| - | ===== Modes/Processes ===== | + | ===== Parameters and I/O ===== |
| - | ==== thisIsTheNameOfMode1 ==== | + | |
| - | This is just a little text, where you can explain the given mode a bit. | + | |
| |< 100% 30% >| | |< 100% 30% >| | ||
| ^ Parameters ^ Description ^ | ^ Parameters ^ Description ^ | ||
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| | resolutionVariance | Variance of the resolution in the local map | | | resolutionVariance | Variance of the resolution in the local map | | ||
| | abscissaIsLogarithmical , abscissaMin, abscissaMax | For internal 1D viewer use only, to be hidden | | | abscissaIsLogarithmical , abscissaMin, abscissaMax | For internal 1D viewer use only, to be hidden | | ||
| - | |||
| - | ==== thisIsTheNameOfMode1 ==== | ||
| - | |< 100% 30% >| | ||
| - | ^ Parameters ^ Description ^ | ||
| - | | Calculate resolution | Picks the resolution mode to be used | | ||
| - | | -> Plot threshold curves | Enabling results in all possible threshold curves being included in the output | | ||
| - | | Mask | Enables use of an input mask | | ||
| - | | -> invert mask | Invert the selected/not selected volume of the mask | | ||
| - | | -> Mask Threshold | Threshold for counting mask voxel for mean calculation | | ||
| - | | Asymmetric units (3 sigma) | Number of asymmetric units in the 3D | | ||
| - | | Pixel size | Used pixel size in the 3Ds (Pixel/Angstrom) | | ||
| - | |||
| - | |< 100% 30% >| | ||
| - | ^ Input ^ Description ^ | ||
| - | | First3D | First 3D Structure/Reconstructed 3D from first half of data | | ||
| - | | Mask | Optional input, can be used to restrict 3D volume to only look at certain parts of the reconstruction | | ||
| - | | Second3D | Second 3D Structure/Reconstructed 3D from second half of data | | ||
| - | |||
| - | |< 100% 30% >| | ||
| - | ^ Output ^ Description ^ | ||
| - | | FourierShellCorrelation | A Graph showing the calculated FSC (y-axis, ranging from 0 to 1) against resolution (x-axis, Angstrom) | | ||
| - | |||
| - | === #Written Header Values === | ||
| - | * **resolutionAt0.143** Estimated resolution for FSC cut off at 0.143 | ||
| - | * **resolutionAt0.3** Estimated resolution for FSC cut off at 0.3 | ||
| - | * **resolutionAt0.5** Estimated resolution for FSC cut off at 0.5 | ||
| - | * **resolutionAt0.9** Estimated resolution for FSC cut off at 0.9 | ||
| - | * **resolutionAt3Sigma** Estimated resolution for FSC cut off at 3 Sigma | ||
| - | * **resolution** Estimated resolution at the user chosen cut off value | ||
| - | * **maxResolution** Maximum resolution in the local map | ||
| - | * **meanResolution** Mean resolution in the local map | ||
| - | * **minResolution** Minimum resolution in the local map | ||
| - | * **resolutionVariance** Variance of the resolution in the local map | ||
| - | * **abscissaIsLogarithmical , abscissaMin, abscissaMax** For internal 1D viewer use only, to be hidden | ||
| ===== Concept ===== | ===== Concept ===== | ||
| - | Paper about FSC theory and applications can be found [[http://www.sciencedirect.com/science/article/pii/S1047847705001292|here]] | + | A Paper about FSC theory and applications can be found [[http://www.sciencedirect.com/science/article/pii/S1047847705001292|here]] |