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.

e2helixboxer.png

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.

Box Editing

Draw box

Left click and drag

Move box

Left click near box center and drag

Move one box endpoint

Left click near box end and drag

Delete box

Hold shift and left click inside box

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 particlesyou extract from them.

e2helixboxer_write_dialog.png

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: