After you have constructed a membrane tree you can generate a membrane model. In the "Membrane Preview" tab you see the top of your membrane. By clicking on the Generate New button a the bottom of the tab, the proteins, which are displayed as rectangles, will be distributed onto the membrane.
In order to generate a consistent distribution of the proteins in the membrane, the proteins are placed by a random function onto the lipid bilayer. After the random placement you have the possibility to position a protein by dragging it through the membrane on a place you want. The assumption for dropping a protein is, that it doesn't overlap with a further protein. If this is the case, the protein remains in its old position.
When you move with the mouse over such a protein rectangle, proteins with the same pdb code will be highlighted. Besides you get some additional information about the protein:
By right-clicking on a protein, you can do a 90 degree rotation. Besides you are able to zoom in, zoom out or to retrieve the starting zoom-state of the membrane model by clicking on the corresponding buttons at the bottom of the tab.
After you have generated your membrane model, you can export it as a pdb file by clicking in the menu on Membrane Model->Generate Membrane Model.