Create

Atoms

Draw an atom

Place an atom on the canvas by selecting one of the frequently used atoms from the Atoms toolbar (or from the Periodic table )
Type its chemical symbol and click on the canvas where you want to put it.

Changing atom type
Select the atom/atoms you would like to change with the Select tool, and then type the chemical symbol on your keyboard, or use the buttons on the Atoms toolbar.
Right-click on the atom and Change the atom type in the Atom properties dialog in Marvin JS window.

Draw a bond

To create a bond between two atoms select the appropriate bond type from the Bonds combo box on the Tools toolbar, click on one of the two atoms, and drag the bond to the other atom or to an empty place.

Changing bond type
Select another bond type from the Bonds combo-box and click on the bond to be changed.
Right-click on the bond and choose another bond Type in the Bond properties dialog window.
Move the mouse over the bond and type a keyboard shortcut.

Drawing a chain is possible by clicking on the Chain button on the Tools toolbar and drag on the canvas, or using one of the Bonds .
Place a template on the canvas by selecting a template on the Template Toolbar and click on the canvas.
Predefined abbreviated groups can be also useful to create complex molecular structures. For selecting an abbreviated group, use the Abbreviated Groups button of the Template toolbar.