usage: prog [options] This program is designed to generate a reconstruction via the random conical tilt technique. Starting from a tilted and untilted dataset. Thce program interfaces with e2refine2d.py to find the azimuthal angles from the untilited dataset and e2make3d.py to make the 3D model from the untilted dataset combined with the azimuthal angles and stage tilt. A model is made foreach e2refine2d.py class(used for alignment)
| Option | Type | Description |
|---|---|---|
| --version | None | show program's version number and exit |
| --path | str | Path for the rct reconstruction, default=auto |
| --untiltdata | str | Name of the tilted dataset |
| --tiltdata | str | Name of the tilted dataset |
| --classavg | str | Name of classavg file created by e2refine2d.py |
| --stagetilt | float | Amount of tiliting of the cryo stage, default=0, get the stage tilt from particle attributes. Only possible if e2RCTboxer was used for particle picking |
| --careject | str | class averages to reject, default=None |
| --minproj | int | Minimum number of projections/images in a class average, for a class average to be used for a reconstruction, default=auto |
| --align | None | Switch on image alignment. This is only translational alignment for the tilted images, and uses a iterative method similar to EMAN1 centalignint |
| --tiltaxis | None | Do a tiltaxis correction(Takes into account variations in tilt axis from micrograph to micrograph. Only possible if e2RCTboxer was used for particle picking |
| --maxshift | int | Maximun amount to shift the images during alignment |
| --process | str | process RCT recons. Usually used to filter RCTS |
| --avgrcts | None | If set recons from each CA will be alinged and averaged. |
| --reference | str | Reference used to align RCT recons to, needs to be aligned to symetry axis is --sym is specified |
| --sym | None | Set the symmetry; if no value is given then the model is assumed to have no symmetry.\nChoices are: i, c, d, tet, icos, or oct. |
| --cuda | None | Use CUDA for the alignment step. |
| --aligngran | float | Fineness of global search in e2align3d.py, default=10.0 |
| --weightrecons | None | Weight the reconstruction by particle numbers. |
| --ppid | int | Set the PID of the parent process, used for cross platform PPID |
| --verbose | int | verbose level [0-9], higher number means higher level of verboseness |
For more information go to emanwiki/EMAN2/Programs/e2rct.