Click the "objects" button and select "ReactionKinetics" from the menu. This makes a new, empty, reaction kinetics object. There should be an object on the left labelled "ReactionKinetics" with four children, three green and one blue. The green labels are for lists of AppletConfig objects, Profiles and ReactionSchemes. The blue object labelled "rscalc" is for computing the behaviour of reaction schemes. As objects are added to the green lists they should appear in the diagram.
Move the mouse over the "ReactionScheme" label so it turns yellow and click. This brings up an empty window for constructing reaction schemnes.
In the new window click the button at the top left labelled "ReactionScheme". It brings up a menu with a number of options.
Select "new". A new window should appear about where the mouse is asking for a name for this new scheme.
For now just click "accept" to accept the default name. You are now editing a scheme called "Reactio-0".
Go to the main Catacomb window - the first one that appeared - and make a few short clicks with the right mouse button. This should rescale the object tree which is looking a bit more interesting. Try clicking at the bottom of the window to squeeze it left-right only, and dragging the mouse with the right button held down to move it around. Note that this requires the right mouse button. As with all the rescalable windows, the left button zooms in and the right one zooms out, so clicking with the left button will soon leave you looking at a highly enlarged patch of nothing. Most windows have a button to recenter them. This one does it automatically any time an item is added or deleted anywhere in the tree. Alternatively, press "f" with the mouse over the window to reframe the data. A number of other key actions are possible as indicated by the capital letters in the options of the menu atthe the top right of the dispaly.
Now return to the squarish reaction scheme window, move the mouse over the colored blob at the top left so a red dot appears, press the left mouse button and drag. Release somewhere on the window. This should add a new pool to the current scheme. At the left of this window you can set its name, and initial concentration.
Do the same again so you have two pools. They will have the default names P_0 and P_1.
Go to the first double arrow on the top row, pull one off and drag it onto the window. Holding it by the middle, move it so the ends stick to the two separate pools. When the arrow appeared, a few more sliders should have appeared on the right of the diagram for setting the forward and reverse rates of this transition. Now you have a simple reaction scheme.
Drag the slider for k-f to the left so its value is about 0.1.
To see what this scheme does, go to the main Catacomb window and click on the "rscalc" box. Two new windows should appear - a little stubby one with a couple of sliders and some buttons in it, and a bigger one with the axes of a graph in.
In the window with the sliders, select "Reactio_0" from the "scheme" selection at the bottom. This tells the calculation to work on the reaction scheme you have just created. When you do this the results of the calculation should appear on the graph. Now go to the reaction scheme window and change the sliders on the right. Whenever anything changes, the model is recalculated and the results displayed. To change the colors, click on a pools so it is highlighted and then click the button "RSpool" at the top left. A menu appears of which the first option is "set color". Selecting this should bring up a color editor, and when you choose "apply" at the bottom the new color should propagate through.
Finally, click the "file" button on the main window and select "save". A dialog should appear asking where you want to save this model. The preferred extension for Catacomb models is .ccm, but any name will do.
That's about it. You should have four windows on the screen by now, which cover all you need to make models: