In order to rename the membrane, click on the membrane once, and then with the right mouse button, select Properties . Use the dialog box to enter the appropriate name for the membrane, press OK . Once you have created the compartments, you need to create the molecular species for those compartments. The molecular species represent any distinct state necessary to describe the biochemistry of the cell, for example molecular conformation, receptor bound versus receptor unbound. The species can be separately defined in multiple compartments, membranes or filaments.
Species can participate in reactions, fluxes, and diffusion.
Species diffusion is defined separately for each cellular compartment, membrane or filament, and is specified by diffusion constants. Species may have directed motion along filaments, there may be a flux of species through a membrane separating two neighboring compartments and species may be involved in binding reactions between compartments, membranes or filaments. Select the Species Tool and then click once with the left mouse button in the appropriate compartment. Initially a Species Selection dialog will appear. If this is the first species to be created, you will have to click the Add button first, prompting a Create New Species dialog box to appear.