Pymol is divided into two separate windows: the main gui and an external gui. In theory, a user could create their own external gui, but I am not aware of any widely used variants.

 ![Screen Shot 2013-01-16 at 8 36 05](https://f.cloud.github.com/assets/171628/69774/77da7696-5f6c-11e2-9167-eb7332277e15.png)

When tk is installed with `enable-threads` AND python is installed with `with-brewed-tk` then the default pymol external gui should show up. If they are not installed, then pymol will only show the main gui. The external gui will be silently lost to mysterious hidden threads that apple tk ignores.

Pymol without an external gui can do almost everything. It has a single line input for commands, but command history cannot be scrolled (if opened from the terminal, you can scroll there). Also, there is no file, edit, build, etc. menus because these are attached to the external gui. In order to perform any task without the external gui requires prior knowledge of the pymol commands. I think most users will want the external gui on by default. Unfortunately, this requires these dependencies as far as I can tell.