When you have completed your membrane, you should finally generate its pdb-file (which is the main objective of this program, after all).
You will only be able to generate the file if your membrane is not empty and not exceeding any limits.
If a microdomain is currently selected, then only the molecules inherited by it will be regarded. To generate the entire membrane, deselect the eventual microdomain first.
Press 'Generate the Pdb File' , found in the 'File' menu or in the toolbar.
You are now able to choose a file that your membrane will be written into:
The filechooser that prompts you to select a file for the membrane
On the right side you can see a little overview about compatibilities and of the contents that is sure to be included inside the file.
After you've made your selection, press 'Save' in order to finally generate your membrane file.