The input and output files are controlled from the side panel, while the tools work from inside the OpenGL drawing area.

Lets begin with the control panel:
Control Panel

With the following buttons: open Open button , load Load button
and save Save button

The filename box:
Filename Box

The following Choice boxes:
input format Input Format Choice
output format Output Format Choice
input units Units Choice

And finally the output file options:
Output Options
check them when the number of atoms and fragments should be written in to the output file.

If you want more information please contact to the Molecular Explorer support team.