Another feature of the MembraneEditor is the support of multiple bilayers in one generated pdb file. Through this feature, you may even build snippets of double- or even triple-membranes, such as they occur in nature in some special cases.
To insert an additional bilayer, use the 'Add Secondary Bilayer' option in the File menu.
After defining a height relative to the default layer, the new layer will be added and become available.
The handling of a multi-layered membrane is pretty much the same as usual; you can add molecules, draw microdomains and calculate the lipids as described earlier. The difference is that you have to switch the regarded layers and you have to handle possible intersections between them.
You can switch the currently active bilayer in the now visible lower toolbar. There you can also change the height, which is always relative to the default layer or remove the current layer from the model. Inactive layers will be rendered transparent.
When it comes to the calculation of the lipids, note that the calculation only regards the currently active layer. Nevertheless, intersections with elements of other layers will be noticed and avoided, which even makes it possible for you to place proteins that reach through multiple bilayers.
A finished multilayered membrane, displayed in Jmol, may look like this: