8. Molecule interaction
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8. Molecule interaction

8.1. Molecule interaction editing window

  1. The window for editing molecule interactions

    Note: Interactions specified at the molecular level define structural interactions possibilities. The specific conditions under which a certain reaction takes place and with which rates will usually depend on the states of molecular components as part of complexes. Accordingly, rates will be defined in the course of defining associations between complexes.

  2. "Add Molecule" side window section

    This window section is similar to the "Molecules" side window section in the molecule editing window, except that this window section does not have the "New", "View" and "Edit" buttons. If the current molecule interaction window only has one molecule loaded, double clicking on a molecule in the list will load the second molecule to define the molecule interaction.

  3. Molecule interaction graphical layout window section

    When there are two molecules loaded and there is no interaction line between any binding sites, the user can link a pair of binding sites between the two molecules. Depending on the "Edit Options", the user can change the layout of individual molecules and keep the relative positions of the molecule component(s) and binding site(s), or move an individual molecule as whole.

  4. Molecule interaction "Composition" window section

    This window section shows the hiearchy structures of the current molecule interaction and the molecules involved. When an item is highlighted in this window section, the modeler application will display the corresponding properties in the window section at the right.

    If the second molecule is highlighted, the "Remove" button is enabled. If the "Remove" button is clicked, the modeler application will reset the interaction parameters and remove the second molecule from the current molecule interaction.

  5. Molecule interaction parameter window section

    This window section includes the information about the pair of molecules and the pair of binding sites involved in the interaction.

    If enabled, clicking the "Reset Interaction" button will clear "Binding Site 1" and "Binding Site 2". The line linking the two binding sites in the graphical layout window section will also be removed.

  6. Molecule interaction "Edit Options" window section

    • The radio buttons "Edit Interaction and Move" and "Change Layout"

      Control the mouse behavior in the graphical layout window section.

    • "Rotate +90o" button

      When a molecule is highlighted, this button is enabled. Click to rotate the molecule as a whole by +90o (clockwise). If there will be a conflict between the two molecules for the position after rotation, the rotation action will not be executed. If there is a line linking two binding sites, it will be updated accordingly after the rotation.

    • "Rotate -90o"

      Similar to "Rotate +90o" the "Rotate -90o" button allows the user to rotate the molecule by -90o (counterclockwise) if possible sterically.

    • "Flip"

      The "Flip" allows the user to flip the molecule (mirror along its vertical axis).

  7. Property window section: "Properties of Molecule Interaction"

    When the "Molecule interaction" is highlighted in the "Composition" window section, the modeler application displays the "Properties of Molecule Interaction".

    Similar to the properties of molecule, the molecule interaction properties include: "SimmID", "Short Name", "Full Name", and "Annotation"

  8. Property window section: "Properties of Molecule"

    The same as the "Properties of Molecule" in the molecule editing window, except that this window section is read-only.

  9. Property window section: "Properties of Molecule Component"

    The same as the "Properties of Molecule Component" in the molecule editing window, exept that this window section is read-only.

  10. Property window section: "Properties of Binding Site"

    The same as the "Properties of Binding Site" in the molecule editing window, except that this window section is read-only.

  11. Control buttons

    • "Save" button:

      When this button is clicked, the modeler application will check the completeness of the information for the molecule interaction and, if complete, save the data including the graphical layout information to the model file. If the SimmID is empty, the modeler application will assign one.

    • "Back" button:

      When this button is clicked, the modeler application will go back to the previous window.

      Note

      The modeler application will neither discard unsaved changes nor save data to the model file.

    • "Center" button

      See "Display 'Center' buttons" in preference settings.

    • "Delete" button:

      When this button is clicked, the modeler application's response is the same as when clicking "Deletee" button under the molecule interaction side window section of the molecule editing window, and then clear the content of the current window and go back the previous window.

8.2. Creating/editing a molecule interaction

8.2.1. Creating a molecule interaction

  1. Activate the molecule interaction editing window

    From the molecule editing window, click the "New" button in its molecule interaction side window section. The current molecule in the molecule editing window will be loaded as the first molecule for a new molecule interaction.

  2. Add the second molecule

    Double click a molecule in the "Add Molecule" window to load it as the second molecule for the new molecule interaction.

  3. Create an interaction between two binding sites.

    In the graphical layout window section, the user can draw a line to link two binding sites of the molecules to establish an interaction.

  4. Change layout and rotate a molecule

    The user can change the layout of an individual molecule by setting the mode as "Change Layout" in the "Edit Options" window section.

    If a molecule is highlighted, the user can rotate or flip it from the "Edit Options" window section.

  5. "Reset" molecule interaction.

    In case the user wants to change to a different pair of binding sites for the molecule interaction, in the parameter window section, click the "Reset" button.

  6. "Remove" a molecule.

    In case the user want to change a molecule for the interaction, in the "Composition" window section, click the "Remove" button when the molecule is highlighted.

  7. "Save" data

    Click the "Save" button.

  8. Confirm to add a new molecule interaction.

    A process such as saving a complex species, an association or a dissociation, may require a new molecule interaction. The modeler application will prompt the the user to confirm the new molecule interaction.

    No graphical information is saved. The modeler application will take default positions for the molecules when this new added molecule interaction is loaded to the molecule interaction editing window and the user can make manual changes of the graphical layout afterwards.

8.2.2. Editing an existing molecule interaction

  1. Load a molecule interaction.

    A molecule interaction can be loaded either from the Model Summary window by double clicking the molecule interaction, or from the molecule interaction side window section in the molecule editing window by clicking "Edit" button or double clicking the interaction in the list.

  2. Edit the interaction data.

    The user can edit the data in the parameter window section and the property window section for molecule interaction.

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7. Molecule Home 9. Complex species