CellDesigner Help

To place the CompartmentAlias:

1. Select a desired compartment shape from the Compartment tool bar.
2. Click in the draw area and drag the mouse to specify the area to draw the shape.

* For the whole type, the area specified by dragging the mouse is the size of the CompartmentAlias
* For the partial close-up type, the point you click on the screen would become the corner of the shape.

3. Type the name of the compartment in the dialog box displayed.

Caution: As the default value, the compartment ID is displayed in the name box.
We recommend to retype the name to represent the physical entity of the compartment, such as "nucleus".

Relationship between CompartmentAlias and Compartment:

When the CompartmentAlias is created on the screen, the logically relevant Compartment is simultaneously created and stored as the local structure data in the model.

To review the logical Compartments stored in the model:

1. Check the "Compartment" list in the list window.

Note: For the details of the difference in CompartmentAlias and Compartment, the naming convention, please refer to the Modeling Guide.

To create multiple CompartmentAlias:

You can create as many CompartmentAlias as you like.
Note that If you specify the same name of the existing CompartmentAlias, it is regarded as the second alias of the same Compartment.
The compartment is identified and distinguished by its name only, not the shape.

Relationship between the compartment and the species enclosed inside the compartment:

The species placed inside the CompartmentAlias are belonged to the CompartmentAlias.
When you select the compartment, the species insides are also highlighted.
When you move the compartment, the enclosed species also move in the same layout.

To change the color and the thickness of the compartment:

You can change the color and the membranes thickness of the individual compartment.
1. Select [Change color & shape] icon from the tool bar, then change the property of the compartment in the dialog box.