13. Complex dissociation
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13. Complex dissociation

13.1. Complex dissociation editing window

  1. The window for editing complex dissociation

  2. The window section for "Source Complex"

    This window section displays the information about the source complex and the options.

    • graphical layout window section: displaying layout of the source complex.

    • "Select Binding Site Interaction to Split"

      A dropdown menu has a list of binding site interactions that can be split depending on the structure of the source complex. Once an interaction is highlighted, click the "Split" button to split the complex. If the source complex is successfully splitted, the dropdown menu is disabled and the "Split" button becomes the "Reset" button.

    • Complex Information:

      Similar to the "Source" complex in the complex association editing, this information for the complex to decay can be edited or automatically assigned.

      • Complex Name

      • Species ID

      • Species Name

      • States of molecule component tags and statuses of binding sites

      • "Save Complex" button

      • "Select Complex" button

  3. The window section for "Result Complex 1"

    The fields and the usage of this window section are the same as for the "Source" complex in the transformation editing window.

    In case the splitted complex can't be identified as belonging to any defined complex species, the modeler application displays a reminder for the user to define a new complex species first.

    Once the "Define" button is clicked, the modeler application displays a window to create a new complex species.

    Once the complex species has been configured, click the "Save" button. The complex is loaded as default from the new defined complex species with all "Don't Care" molecule component tag state(s) and binding site status(es).

  4. The window section for "Result Complex 2"

    The fields and the usage of this window section are the same as for the "Result Complex 1".

  5. Properties

    This window section contains the parameters for the dissociation, including "Short Name", "Full Name", "Dissoc Rate", "Orientation", "Intra Complex" and "Annotation". The orientation is selected from "No orientation", "trans-binding" and "cis-binding". Similarly as for associations, an orientation property can be specified for dissociations. Dissociations with no orientation will be applied to all complexes matching the structural and state properties specified here. Dissociations with trans-binding orientation will only be applied to complexes between two adjacent membranes whereas dissociations with cis-binding property will be applied only to bindings between molecules located in the same membrane.

    The dissociation rate unit is always " /s ".

  6. Control buttons

    • "Save" button

      When this button is clicked, a saving request is sent to the modeler application. The moder will first check the completeness of the data for the dissociation. If the check is passed, the modeler application saves the data to the model file.

      The modeler application will dectect if there is any confilicting data for saving. If the modeler application finds an conflicting situation, a message window prompts the user to decide how to handle the conflict.

      • Conflicting case 1: the current dissociation has orientation conflicting with saved dissociation rule(s).

        "No orientation" conflicts to "trans-binding" or "cis-binding", and verse visa.

        The user may click "No" to keep the model file unchanged, or click "Yes" to save anyway.

        Note

        See the note in association.

      • Conflicting case 2: a complex has been changed for an existing dissociation and the dissociation with the changed complex has not been defined yet.

      • Conflicting case 3: a complex has been changed for an existing dissociation and the dissociation with changed complex has been defined.

      • Conflicting case 4: the current dissociation is created as new, but it has been defined before.

    • "Back" button

      When this button is clicked, the modeler application goes back to the previous window without saving.

    • "Delete" button

      The modeler application will delete the current dissociation and then go back to previous window.

    • "Display Molecule Mapping"

      If this checkbox is checked, the all graphcal window sections will show the molecule mapping relationship between source and result complexes.

13.2. Creating/editing a complex dissociation

  1. Create a new dissociation

    The user can create a new dissociation using the "New" button in the "Relations" in either the complex species editing window or the complex editing window.

    If the dissociation is created from an complex species, the modeler application will set default "Don't care" for the states of all molecule component tag(s) and status(es) of all binding sites not involving in-complex binding and the user can make change(s) afterwards.

  2. Load an existing dissociation

    An existing dissociation can be loaded:

  3. Edit

    The fields which can be edited include:

    • "Short Name"

    • "Full Name"

    • "Dissoc Rate": dissociation rate

    • States of "Source Complex" molecule component tag(s) and status(es) of binding site(s)

    • States of "Result Complex 1" molecule component tag(s) and status(es) of binding site(s)

    • States of "Result Complex 2" molecule component tag(s) and status(es) of binding site(s)

    • Orientation: "No orientation", "trans-binding", or "cis-binding".

    • "Intra Complex": checkbox to indicate if the dissociation is "Intra Complex" or not.

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