If you have a window with some empty space in it that you can't seem to get rid of, something that looks like this:
then you have been bitten by this open Issue:
You can fix the problem by doing the following:
Save all your work
- Completely exit Atom using Cmd+Q on macOS or Ctrl+Q on other platforms
- Launch Atom again from the command line using
You may also want to subscribe to the Issue linked above for updates.