e2helixboxer.py: Overview

e2helixboxer.py is used to select rectangular 2D projections of helices from a micrograph, and extract overlapping particles from the boxed helices. The boxing must be done in GUI mode, but extracting particles from boxed regions may be done from the GUI or from the command line.

GUI mode

To start the program's graphic user interface, use the "--gui" option. You can follow this with a micrograph filename, a list of micrograph filenames, or nothing.

$ e2helixboxer.py --gui <micrograph1> <micrograph2> <...>

$ e2helixboxer.py --gui
$ e2helixboxer.py --gui 101.mrc
$ e2helixboxer.py --gui *.mrc micrograph.hdf *.img abc.dm3

The left window is the helix viewer, the middle is the micrograph viewer, and the right is the main window.

The main window shows a list of open micrographs and how many helices you have boxed in each one. (Actually, only one micrograph is loaded in memory at a time, but this allows for quick switching between particles.) Any micrographs you specified after the "--gui" option will be listed.

After you have boxed the helices in a micrograph, you can go to "File->Save" to save the coordinates and image data of the helices and the particles you extract from them.

Command-line mode

In command-line mode, you can only work with one micrograph at a time. You should have already boxed particles in the GUI mode; if that is done the box coordinates should be saved in the EMAN2 database.

e2helixboxer.py <options (not --gui)> <micrograph>

Options:

--version

• show program's version number and exit

-h, --help

• show this help message and exit

-X HELIX_COORDS, --helix-coords=HELIX_COORDS

• Save coordinates for helices in EMAN1 *.box format: x1-w/2 y1-w/2 w w -1 x2-w/2 y2-w/2 w w -2

-x HELIX_IMAGES, --helix-images=HELIX_IMAGES

• Save images of the helices. The file name specified will have helix numbers added to it.

-P PTCL_COORDS, --ptcl-coords=PTCL_COORDS

• Save coordinates of the centers of particles with the specified overlap in pixels

-p PTCL_IMAGES, --ptcl-images=PTCL_IMAGES

• Save images of the particles with the specified overlap in pixels. The file name specified will have helix numbers (and particle numbers if the file type does not support image stacks) added to it.

-w HELIX_WIDTH, --helix-width=HELIX_WIDTH

• Helix width in pixels

--ptcl-overlap=PTCL_OVERLAP

• Particle overlap in pixels

--ptcl-length=PTCL_LENGTH

• Particle length in pixels

--ptcl-width=PTCL_WIDTH

• Particle width in pixels

--ptcl-not-rotated Particles are oriented as on micrograph. They are

• square with length max(ptcl_length, ptcl_width).

--ptcl-norm-edge-mean

• Apply the normalize.edgemean processor to each particle.