7. Molecule
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7. Molecule

This section explains the functionalities in building/editing molecule(s).

7.1. Molecule editing window

  1. The window for editing molecules

    Click "Molecule" in the tool bar or select "Molecule(MOL)" from the menu bar dropdown menu, the molecule editing window opens.

    This window contains the "Molecules" side window section, the "Molecule Interactions" side window section, the graphical layout window section, the "Molecule Composition" window section, the property window sections, and the "Save", "Clear" and "Change Color" buttons.

  2. "Molecules" side window section

    This side window section displays a list of the molecule(s) in the current model and functionalities to manage them.

  3. "New" button in the "Molecules" side window section.

    Clicking this "New" button will setup all associated window sections and buttons in the empty editing mode for creating a new molecule. The "Add Component" is highlighted to remind the user that the first step is to add a molecule component when creating a new molecule. If there is another molecule currently being edited, the modeler application will try to save it first.

  4. "View" button in the "Molecules" side window section.

    If there is a molecule highlighted in the molecule list, clicking "View" button will load the molecule into the editing window. If there is another molecule currently being edited, the modeler application will try to save it first. The modeler application will do nothing if there is no molecule highlighted in the list.

  5. "Delete" button in the "Molecules" side window section.

    If a molecule is highlighted in the molecule list, clicking "Delete" button will send a request to the modeler application to delete the molecule from the current model. If there are no related entities found, the modeler application will delete this molecule. Otherwise, a message window will appear prompting the user to decide if to do a cascading deletion (deleting all related entities such as complexes containing the molecule) or to cancel the "Delete" action.

  6. The message window for the confirmation of cascaded deletion of the related items of a molecule

    For the details of individual items, click corresponding "Details" button.

  7. The window for the details of a list of "Molecule Interactions"

  8. The window for the details of a list of "Complex Species"

  9. The window for the details of a list of "Complexes"

  10. The window for the details of a list of "Complex Transformations"

  11. The window for the details of a list of "Complex Associations"

  12. The window for the details of a list of "Complex Dissociations"

  13. List in the "Molecules" side window section (highlighted in the screenshot below).

    This window section displays the list of molecule(s) in the current model. The list will be automatically updated when a molecule is added or deleted.

  14. Molecule preview in the "Molecules" side window section.

    When a molecule is highlighted in the molecule list, this window section shows the preview of the layout of the highlighted molecule. The user can zoom-into or zoom-out of the preview by using the mouse wheel when the mouse is over the preview window section.

  15. "Molecule Interactions" side window section.

    This window section is located at the right hand side of the whole window. When a saved molecule is loaded into the molecule editing window, the molecule interactions side window section becomes activated and shows a list of molecule interactions involving the currently loaded molecule. In the example screenshot below, the loaded molecule "A" is involved in three molecule interactions: "[A].[A]-interaction", "[A].[A]-interaction.1", and "[A].[A]-interaction.2". There are three buttons available in this side window section: "New", "View", and "Delete".

    • "New" button in the "Molecule Interactions" side window section

      Clicking the "New" button will open the "Molecule Interaction" editing window and preload the current molecule as the first molecule of an interaction between two molecules.

    • "View" button in the "Molecule Interactions" side window section

      If a molecule interaction is selected (highlighted) in the molecule interaction list, clicking the "Edit" button will open the "Molecule Interaction" editing window and load the selected molecule interaction. The modeler application will do nothing if there is no molecule interaction selected from the list.

    • "Delete" button in the "Molecule Interactions" side window section.

      If there a molecule interaction is selected(highlighted) in the molecule interaction list, when the "Delete" button is clicked, the modeler application will try to remove the selected molecule interaction from the current model. If the selected molecule interaction has no related entities such as complex species and complex associations, the molecule interaction will be removed and the molecule interaction list will be updated. Otherwise, a message window is will appear prompting the user to either cancel the removing action or confirm a cascading deletion. The screenshot below shows an example window asking the user to confirm the molecule interaction removing action.

  16. The graphical layout window section

    The user can customize the layout of a molecule. The user can also zoom-in or zoom-out by using the mouse wheel, and highlight a molecule component or binding site by clicking it.

    • Moving a binding site

      The user can press the left mouse button and move a binding site around its parent molecule component.

      The modeler application will prevent the user from moving the site into a position that conflicts with any other molecule component or binding site.

    • Moving a molecule component

      The user can press the mouse left button and move a molecule component. The associated child binding site(s) will move with the parent molecule component and keep their relative positions.

      If the moving molecule component has no neighbor molecule component, the user can freely move this molecule component and its binding site(s) within the graphical layout window section.

      If the moving molecule component has more than 1 neighbor molecule component(s), the whole molecule will move with this molecule component.

      If the moving molecule component has 1 and only 1 neighbor molecule component, this molecule component and its child binding site(s) will move around the neighbor molecule component.

      If the moving molecule component or any of its child binding sites is in a position conflicting with any other molecule component or binding site, the molecule component stops moving.

  17. "Molecule Composition" window section

    This window section shows the hiearchical structure of a molecule. There are three buttons in this window section: "Add Component", "Add Binding Site", and "Remove".

  18. "Add Component" button in the "Molecule Composition" window section

    Clicking this button will initialize an action to add a new molecule component to the current molecule. A window will appear prompting the user to specify the size of the new molecule component.

    If the molecule already has (a) molecule component(s), the new molecule component will be attached to the highlighted molecule component. Once the new molecule component is attached, the relationship is indicated by two dotted lines from the contact point of the two molecule components to the centers of the individual molecule components. The user can change the relative positions of molecule components and binding sites as described in the graphical layout section.

  19. "Add Binding Site" button in the "Molecule Composition" window section

    Clicking this button will add a new binding site to the selected molecule component. The modeler application labels new binding sites with a number automatically to distinguish different binding site within a molecule. Once the binding site is added, its position can be adjusted as described in the graphical layout section.

  20. "Remove" button in the "Molecule Composition" window section.

    If a binding site is highlighted, clicking the "Remove" button removes the highlighted binding site. If a molecule component is highlighted, clicking the "Remove" button removes the molecule components and all its binding site(s).

    Note

    The modeler application does not permit removing a molecule component with at more than one neighbor molecule component.

  21. "Change Color"

    Right clicking any molecule component or binding site and selecting "Change Color" will activate a color dialog window prompting the user to change the color of the molecule.

  22. Property window section: "Properties of Molecule"

    When the molecule is highlighted in the "Molecule Composition" window section, the window section on the right side of the "Molecule Composition" window section shows the properties of the molecule.

    The properties of a molecule include:

    • Name or Short Name

      To be provided by the user. If it is empty, the modeler application assigns the SimmID as the short name when the molecule is saved.

    • Full name

      To be provided by the user. If it is empty, the modeler application will assign the short name as the full name when the molecule is saved.

      Note

      See "Display Full Name Fields" in the preferences section.

    • Type

      Chosen from a list of "Protein", "DNA", "RNA", "Small Molecule", and "Other". The default is "Small Molecule".

      Note

      The type will be used in a forthcoming visualization module. It has no functional implications.

    • Membrane association status

      Be either "Freely Diffusing" or "Membrance Associated". Only when the status is "Membrane Associated", the user can define the molecule component location(s).

    • Diffusion coefficient (Diff_Coeff)

      The unit is microns2/s. For "Freely Diffusing", the default is 100 microns2/s. For "Membrane Associated", the default is 0.01 microns2/s for "Receptor" and 0.1 microns2/s for all other categories.

    • Category

      Chosen from a list of "Receptor", "GTPase", "Enzyme", "Kinase", "Phosphatase", "GEF", "GAP", "Adaptor", "Small Molecule", and "Other".

      Note

      The category will be used in a forthcoming visualization module. Only the receptor category has functional implications: specifying a molecule as "Receptor" makes it possible to assign different locations for its molecule components (see below).

    • Accession

      The user can use this field to provide the public accession number for reference.

    • Annotation

      This is a free text field for the user to provide annotation information.

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

    When a molecule component is highlighted in the "Molecule Composition" window section, the right hand side window section shows the properties of the molecule component.

    The properties include:

    • Short name or Name

      To be provided by the user. If it is empty, the modeler application will assign the SimmID as the short name when the molecule is saved.

    • Full name

      To be provided by the user. If it is empty, the modeler application will assign the short name as the full name when the molecule is saved.

      Note

      See "Display Full Name Fields" in the preferences section.

    • Location

      This field is only enabled to a molecule in the "Membrance Associated" status. There are 2 options: Outside-membrane and Inside-membrane.

    • States

      This field contains the state definition information which can be defined by clicking "Add/Modify/Remove" button to activate the molecule component state editing window.

      • "New Tag" editing field.

        This field allows the user to define a name for the new state tag. When the name is unique within the molecule component and is not empty, the "Add" button will be enabled.

        The tags are also used by the modeler to encode complex tag states in an xml file, some characters/string are not allowed to use, including ; ( ) < > ! = " and xml. If any one of them is used, a warning window appears and the forbidden character/string will be removed from the tag.

        Click the "Add" button to add the new state tag. A window will prompt the user whether the color for the tag representing the state in the molecule icon should be different from the default color.

        If the user chooses to change the color a color dialog window will open. (Depending on your system, the color dialog window may not be exactly the same as the screenshot below.)

        A tag with the selected color representing the new state displays in the molecule component.

      • The "Current Tag(s)" field.

        This field shows the list of the molecule component tag(s) already defined. When a tag is selected, the "Remove" and "Change Color" buttons on the right are enabled.

      • "Remove" button.

        When this button is enabled, clicking it will remove the selected molecule component state tag from the list.

      • "Change Color" button.

        When this button is enabled, clicking it will bring up the color dialog window again and the user can change the state tag color.

      • "Done" button.

        When this button is clicked, the modeler application will go back to the molecule component property window.

      • Tag display.

        In molecule, molecule interaction or complex species editing window, a tag is displayed in "half-filled" format, which is different from the tag state format of a complex.

        In complexes and transformation, association or dissociation editing windows, a tag has one of three different states, "On", "Off" or "Don't Care" and is displayed differently.

        Molecule component tag state "On":

        Molecule component tag state "Off":

        Molecule component tag state "Don't Care":

    • Annotation

      This is a free text field for the user to provide annotation information.

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

    Similar to the property window sections of molecule and molecule component, the property window section for binding site has the fields for "Short Name", "Full Name" and "Annotation".

  25. Control buttons

    • "Save" button

      When this button is clicked, the modeler application will check the completeness of the current molecule and save the molecule information to the model file, including the properties and graphical layout information of the molecule, molecule component(s) and binding site(s). If no short name is assigned yet, the modeler may try to use it internal ID as the default name with confirmation from the user.

      When there is any new content under current editing, the button displays with a start "Save*" to alert the user.

    • "Clear" button

      When this button is clicked, the modeler application will clear all the fields and graphics layouts.

      Note

      This operation does not make any change to the model file.

    • "Molecule Color" button

      Clicking this button has the same effect as clicking the "Change Color" from graphical layout.

    • "Center" button

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

    • "Related Item(s)" button

      When the current molecule is saved, the modeler application detects if there are related items. If there is no related item, this button is hidden. Otherwise, it is visible.

      When this button is clicked, a message window will show the related items.

    • "Delete" button.

      Delete the current molecule from the model. If there are related items detected, the user needs to confirm a cascade deletion.

7.2. Creating/editing a molecule

This section mainly introduces the details of individual graphical components within the molecule editing window and explains the how to create/edit a molecule.

  1. Add the first molecule component.

    Click the "Add Component" button from the "Molecule Composition" window section.

  2. Add a molecule component attached to an existing molecule component.

    Click a molecule component in the "Molecule Composition" window section or the graphical layout window section. Then, click the "Add Component" button from the "Molecule Composition" window section.

  3. Add a binding site to an existing molecule component.

    Click a molecule component in the "Molecule Composition" window section or the graphical layout window section. Then, click the "Add Binding Site" button from the "Molecule Composition" window section.

  4. Change the layout of the current molecule

    The layout of the current molecule can be changed in the graphical layout window section.

  5. Remove a binding site.

    Click "Remove" button in the "Molecule Composition" window section when the binding site is highlighted.

  6. Remove a molecule component.

    Click "Remove" button in the "Molecule Composition" window section when the molecule component is highlighted.

  7. Save a molecule.

    Click the "Save" button.

  8. Clear the molecule editing window

    Click the "Clear" button.

  9. Create/Edit/Remove molecule interaction

    Click the corresponding button in the "Molecule Interactions" side window section.

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6. Model summary Home 8. Molecule interaction