usage: e2helixboxer.py --gui <micrograph1> <<micrograph2> <micrograph3> ... e2helixboxer.py --gui --helix-width=<width> <micrograph1> <<micrograph2> <micrograph3> ... e2helixboxer.py <options (not --gui)> <micrograph>
| Option | Type | Description |
|---|---|---|
| --version | None | show program's version number and exit |
| --gui | None | Start the graphic user interface for boxing helices. |
| --helix-coords, -X | str | Save coordinates for helices to the file specified, which will have the EMAN1 *.box format:\t\t\tx1-w/2 y1-w/2 w w -1 x2-w/2 y2-w/2 w w -2 |
| --helix-images, -x | str | Save images of the helices. The file name specified will have helix numbers added to it. |
| --ptcl-coords, -P | str | Save coordinates of the centers of particles to the specified formatted text file |
| --ptcl-images, -p | str | Save images of the particles. The file name specified will have helix numbers (and particle numbers if the file type does not support image stacks) added to it. |
| --ptcl-images-stack-mode | str | Options for saving particle images to stack files. 'single' uses one stack file, 'multiple' (default) uses one stack file per helix, 'none' uses a file for each particle and is always used when the output file format does not support image stacks. |
| --db-add-hcoords | str | Append any unique helix coordinates to the database from the specified file (in EMAN1 *.box format). Use --helix-width to specify a width for all boxes. |
| --db-set-hcoords | str | Replaces the helix coordinates in the database with the coordinates from the specified file (in EMAN1 *.box format). Use --helix-width to specify a width for all boxes. |
| --helix-width, -w | int | Helix width in pixels. Overrides widths saved in the database or in an input file. |
| --helix-length, -l | int | Helix length in pixels. Normally each filament can be an arbitrary length. This forces all new helices to a fixed size. |
| --ptcl-overlap | int | Particle overlap in pixels |
| --ptcl-length | int | Particle length in pixels |
| --ptcl-width | int | Particle width in pixels |
| --ptcl-not-rotated | None | Particles are oriented as on the micrograph. They are square with length max(ptcl_length, ptcl_width). |
| --ptcl-norm-edge-mean | None | Apply the normalize.edgemean processor to each particle. |
| --gridding | None | Use a gridding method for rotation operations on particles. Requires particles to be square. |
| --save-ext | str | The default file extension to use when saving 'particle' images. This is simply a convenience for improved workflow. If a format other than HDF is used, metadata will be lost when saving. |
| --ppid | int | Set the PID of the parent process, used for cross platform PPID |
For more information go to emanwiki/EMAN2/Programs/e2helixboxer.