Microdomains are limited areas inside a membrane that contain different lipid buildups. One common form of a microdomain, for example is a cholesterol enriched area which is also known as a "Raft".
A typical lipid raft, seen in the middle of the membrane (Jmol)
The MembraneEditor provides the option to define such microdomains inside your membrane. Those will be considered by the algorithms that build your membrane later on, as long as they support this feature.
A microdomain's boundary has to be defined 2-dimensionally on the XZ-plane of a membrane. To start, press the 'New Microdomain' item located inside the 'File' menu or inside the toolbar.
The program will now be in the domain painting mode. A small dialog will become visible where you can select a painting tool.
The Membrane View while drawing domain boundaries
You will most likely use the polygonal tool which enables you to paint free-hand. Alternatively, you can use the rectangular and the oval paint mode. Draw your desired boundaries while holding down the left mouse button and release it in order to finish. You can redraw your area as often as you wish. As soon as you are satisfied, press 'Ok' inside the dialog to accept your new domain.
Each microdomain in the membrane provides a separate list of molecules inside the Component View. It is accessible through its particular number, the so-called 'Domain ID' on the left.
The contents of such a list refers only to the microdomain it belongs to, while from now, the contents of the 'Default Area' only refers to the rest of the membrane, excluding all defined microdomains.
What you'll have to do is to set up the lipid configuration in each list separately. Adding molecules into a microdomain works the same way as usual and can still be done from the Database View. The only difference is that you'll have to choose the domain you want to add into.
You will have to choose a domain now
Assigning proteins explicitly to a microdomain is not necessary at all. This happens automatically depending on a protein's location and is updated dynamically when you move it around.
There are two options for each microdomain located at the top of its list:
Allows you to repaint the boundaries of the domain.
Removes the entire microdomain from the membrane. All sample lipids that were included will be discarded, remaining proteins will be transferred to the default area.
Another benefit of using microdomains is that you are able to exclude parts of the membrane surface, if required.
You could create a non-rectangular membrane, for instance, by placing your contents in a domain and leaving the default area empty. Additionally, you will get the option to exclude areas when you attempt to write the output file.
See also "Generating the output file"
Example of a non-rectangular membrane