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Reconstruction
This logic is needed to create a 3D structure from 2D projections with assigned Euler angles.
Usage
Here, a general/generic description of HOW the logic is USED should be given. Try to be as general as possible, but also mention prerequisites, restrictions, advantages, requirements which are specific of this logic. Basically everything the user needs to know to successfully use this logic.
Modes
Fourier
This mode makes reconstruction in Fourier space and is generally faster than Real space reconstruction
Parameters | Description |
---|---|
Pixel in Angstrom | Pixel size of the microscope |
With gridding | Use gridding reconstruction algorithm |
Normalize 3D | Normalizes the obtained 3D structure (mean=0) |
→ 3D normalization sigma | Sigma value for normalization |
Padding factor | |
Already phase flipped | Indicate whether phase flipping was applied on the previous steps |
Reproject 3D | Gives additional output of 2D reprojections of the obtained 3D structure |
Symmetry | Symmetry of the complex studied (if known) |
With CTF | Indicate whether header files with CTF are available |
Input | Description |
---|---|
Input | Class averages with assigned angular info or alisums |
Output | Description |
---|---|
3D | 3D structure reconstructed from projections |
Reprojections (if Reproject 3D parameter is enabled) | 2D projections obtained from 3D structure |
Real Space
This mode makes reconstruction in Real space
Parameters | Description |
---|---|
Normalize 3D | Normalizes the obtained 3D structure (mean=0) |
→ 3D normalization sigma | Sigma value for normalization |
Reproject 3D | Gives additional output of 2D reprojections of the obtained 3D structure |
Symmetry | Symmetry of the complex studied (if known) |
Input | Description |
---|---|
Input | Class averages with assigned angular info or alisums |
Output | Description |
---|---|
3D | 3D structure reconstructed from projections |
Reprojections (if Reproject 3D parameter is enabled) | 2D projections obtained from 3D structure |
Concept
Real Space mode uses the Filtered Back-Projection method, but applies 2D filtering instead of 1D, that reduces sensitivity to noise. Fourier Space Mode uses Fourier inversion method based on central slice theorem. More information about the reconstruction in Real and Fourier space can be found in Chapter 7 of the following review.