We have now created four molecule types and - automatically - four molecule complex species based on these molecule types. Click on 'Model' in the navigation header to go to the model overview page - that should look like this. Note that you can select icon size preferences here by clicking on S (small), M or L in the navigation header.

Click on 'Complex' in the navigation header to open the complex editing page.

Load the Receptor complex species by double-clicking it.

Click 'New' under 'Relations' (on the right). Select 'Create/Edit Association', click 'Go'.

The list on the left contains complex species that can be selected as binding partners.

Double-click the "Ligand" entry in the complex species list on the right to load it into the 'Source Complexes' view. Next, we want to specify an interaction between the extracellular binding site of the Receptor and the Ligand. However, the binding sites face opposite sides on the molecules. To fix this, double-click the Receptor.

The Receptor is now highlighted and we can click the 'Flip' button to make it face the other side.

Draw a line from the binding site at the Receptor's extracellular domain to the binding site of the Ligand.

The Modeler will prompt you to confirm that you want to establish a new interaction between two molecules. This prompt can help you to make sure you use the right binding sites for the associations you specify.

Once you have established the interaction, you have to define the shape of the result complex species. The Modeler displays the corresponding button in orange to remind you of this.

Note, that defining the result complex is necessary only to allow the Modeler to display it (iconographically) as a user-defined (through the definition of the association) complex. You don't have to define all multi-molecular complexes that can be built based on the associations in the model. Simmune will automatically build complexes A:B:C if you define associations A:B and B:C between molecules A, B and C and if the bimolecular complexes can still interact with each other (A could, for instance, occupy the same binding site on B as C would use to interact with it. Then, A:B:C would not be possible.).

Clicking the 'define result complex species' button will take you here:

Move the Receptor and Ligand species together until they touch at the binding sites. The Modeler will make a link between the sites. You can specify a name for the complex species (e.g. "Ligated Receptor") or keep the suggested concatenation of the molecule type names ("Ligand.Receptor"). Click 'Save' and 'Back'.

Back on the page for definining the association properties, please assign an association rate (e.g. 1.0e7 l/Mol*s) and (optionally) a name for the reaction. Then click 'Save' and 'Back'.

On the page describing the properties of the receptor, you will now see the association we just defined, listed on the right hand side.

The file "G_protein_3.14.dbf" represents the model as it should be at this stage of the tutorial.

To define the dissociation of the Ligand from the receptor, please select the Ligand.Receptor complex species by double-clicking it in the complex species list on the left.

Click the 'New' button on top of the right-hand-side list of relations of the complex species. Select 'Create/Edit Dissociation'.

If the view components in the window are sized in a sub-optimal way (as shown here) they can be resized.

Now, please select the interaction that will be broken by the dissociation in the combo box underneath the complex.

Here, it is the (only) interaction between the Ligand and the extracellular binding site of the Receptor.

Click 'split' and specify the dissociation rate and (optionally) a name for the dissociation. Then, click 'Save' and 'Back'. Back on the complex page, double-click the Galpha complex species to load it for editing.

The file "G_protein_3.20.dbf" represents the model as it should be at this stage of the tutorial.