The `open` command is part of OS X and uses Finder's default “Open With…” application to open the file, just like double-clicking it in Finder. `$EDITOR` is used for things like `fc` where it is used as the default command-line editor (a replacement for `vim` or `emacs`).

To use Atom with the `open` command, you can select a file of the type you want in Finder, press <kbd>⌘ command</kbd>+<kbd>`I`</kbd> for “Get Info”, and then change “Open With:” to Atom, and click “Change All…”.

Alternatively you can define an alias like

    alias e="atom -nw"

in your `.bashrc` and then run `e file-to-edit.txt` whenever you want to edit a file in Atom.