Creating Molecules
When JChemPaint has been startet, you automatically get an empty document. In order to paint a structure the typical steps would be the following:
- Often it is the best to start with rings. Using the ring templates in the button bar (click on a button and then in the document) you can build the ring structures of the molecule. You can dock a ring to another ring by clicking on an existing ring (the docking atoms will be highlighted). If the molecule has no rings, go to the next step.
- The next step are typically the chains. Choose the
button, click on the atom where the chain starts and then on the
last atom of the chain to enlarge it. - After this, you can add double/triple bonds by using again and clicking on the bonds to make double or triple. You can use
and 
to make existing bonds wedge bonds or you can draw wedge bonds directly by clicking
on an existing bond. - Finally the atoms need to be set. Either use one of the symbol buttons and click on an atom to change it to this symbol. You can also use the periodic table
to choose an element. Finally with 
you can go through some common elements by clicking on an atom repeatedly. With
and 
you can change the charge.
Creating Reactions
Start a new document, by clicking the white paper with the yellow star on the top left corner. In the Draw mode (the bond button), draw methane on the left and methanol on the right. Right mouse click on the methane and choose "Reaction..." and "Make Reactant in new Reaction". Similarly, right mouse click on the methanol, and choose "Make Product in existing Reaction". Choose in the drop down box the reaction you want to add methanol as product to.