Selecting a species in the Reaction Diagram or the Species will activate the Species Properties pane in the lower right quadrant of the workspace. Within this pane, the Species Name can be editing, Linked Pathway Object(s) are displayed, and annotations cans be added.
For rule-based models, the Object Properties tab provides a graphical editor to specify and edit the molecular details of Species using drop-down menus.
Specify a molecule previously created in the Molecules Table as a component of a species in a rule-based model.
Add additional species information. When a molecule is added, if additional information is required the species will be highlighted in red and errors may appear in the Problems tab. In the figure shown, three errors were identified. Two errors arise from the fact that two binding sites have unspecified states; one error arises because molecules within the species are not connected with a bond.
Specify connections between molecules in the species by right click on binding site shape and selecting from the drop-down menu
Specify states for binding sites by mouse right click on state shape and selecting the cognate binding site. In the figure shown, the number of errors is now one; bounds between molecules are specified connected and only one site has unspecified states.
