Compartment Editor Dialog
This dialog allows you to view and modify the contents of a compartment. This contents are presented as three pages, accessible by clicking the tabs at the top of the dialog with the left mouse button:
Reaction Steps Page
This page displays list of reaction steps that have been previously defined for this compartment; the list includes information about kinetic parameters for each step. Above the list is a tool bar with a row of push buttons that allow you to add, remove and edit reaction steps.
A single click of the right mouse button creates a pop-up context menu listing more available actions.
Using the Tool Bar
Generally, you first select one of the reaction steps from the list by a single-click with the left mouse button, then click the desired tool bar push button.
The push buttons and their functions are as follows:
- Add a new step.
- Clicking this push button adds a new empty reaction step to the list of reaction steps and opens the Reaction Step Editor Dialog where you may enter the new reaction equation and specify the kinetic parameters. The new reaction step is inserted in the list immediately after the currently selected step.
- Delete the selected step.
- Clicking this push button removes the currently selected reaction step from the compartment and discards it.
- Edit the selected step.
- Clicking this push button opens the Reaction Step Editor Dialog, allowing you to modify the chemical equation and kinetic parameters of the currently selected reaction step. A double-click with the left mouse button over a line in the list is equivalent to clicking this push button.
- Copy the selected step.
- When this push button is clicked, a copy of the currently selected reaction step is placed on Kinetiscope's internal clipboard. That copy may be pasted into this compartment, into another compartment, or into another reaction scheme that is loaded into memory.
- Cut the selected step.
- This action deletes the selected step from the compartment and places it on Kinetiscope's clipboard. It may be pasted into this compartment, into another compartment, or into another reaction scheme that is loaded into memory.
- Paste a step.
- This push button is only enabled when a reaction step is on the clipboard from a previous Cut/Copy action. When clicked, a copy of the reaction step on the clipboard is added to the compartment.
The Context Menu
All the tool bar actions also may be initiated using the context menu shown here. You may access this menu by a single click of the right mouse button over the list of reaction steps. Generally, you first select one of the reaction steps from the list by a single-click with the left mouse button, then click the desired menu item.
You may also export all the reaction steps from the compartment as a formatted text file, or import reaction steps from such a file, by choosing one of the last two items. These are intended to facilitate the construction of complex reaction schemes where an external script or spreadsheet is used to create or edit reaction steps and their rate parameters. The text files have a specific format. For more information, see Export and Import of Reaction and Transfer Steps.
Compartment Details Page
You use this page to set other characteristics of the compartment.
You may change the name and screen coloring here.
- To change the Compartment Name, type the new name in the data entry field.
- To change the Compartment Color or the Text Color, single-click the left mouse button on the colored squares to the right of the labels, and choose the new color from the dialog that appears.
The current compartment dimensions, and the volume calculated from those, are shown.
The Dimension Editor Dialog is displayed.
- Type the new dimensions in the data entry fields of the dialog.
OKto dismiss the Dimension Editor Dialog.
This group is only available when the reaction scheme has been set to be variable volume on the Reaction Conditions Page.
Indicate here by checking the appropriate check boxes which of the compartment's dimensions are free to increase or decrease when the contents of the compartment change due a reaction or a materials transfer event. Kinetiscope requires that all compartments in the plane perpendicular to the unconstrained direction also be free to change, so selecting a dimension here may affect the setting in other compartments.
Initial Concentrations Page
Use this page to set the initial concentrations for all species in the compartment. The table indicates for each species its current initial concentration, the number of moles as calculated using the compartment's volume, and the number of particles Kinetiscope will assign to represent the species population in this compartment.
This last value depends on the species concentration, the compartment volume and the value of the Total Number of Particles you set on the Simulation Settings Page. If a concentration entry is non-zero but you have not specified an adequate Total Number of Particles to represent this non-zero concentration, then the entry for the Calculated Initial Number of Particles in this table will be zero and will be highlighted in red.
You may set here the concentration of any species defined in the reaction scheme, even if it does not participate in any reaction in this compartment. Initially this table displays a list of all species that have been appeared in the equations on the Reaction Steps page, and adds any other species for which you have previously set a non-zero concentration. You may customize which species are listed using the drop-down list box above the table:
- Show ALL species in use in this compartment
- displays the default list of species;
- Show only REACTIVE species in use in this compartment
- excludes from the list any species which do not appear in any of the reaction equations of this Compartment;
- Show only REACTIVE species in use in this compartment with initial concentration >0
- additionally excludes species with initial concentrations of zero;
- Show all species defined in the reaction scheme
- list every species you have used somewhere in the scheme.