Chemistry on the Desktop

If you are using a laptop touch panel, you need to click the left and right buttons together and then scroll with the touch pad itself. As an example, if you click on an atom, you can change the atom in this location or even replace it with some type of atomic group, such as an alcohol group.

You also can edit all kinds of display options, such as colors used, fonts for text, text placement and line widths.

The third icon on the top icon row pulls up a list of available templates for larger commonly used atomic structures, such as benzene rings.

Figure 3. You can add larger commonly used structures with templates.

The fourth icon on the top row lets you pull up a list of templates that you have created previously, allowing you to add templates for those substructures that you use most often.

You may need to play with the display in order to be able to see everything clearly while you are working. The appropriate instructions are under the Object menu item. The first option on that menu is Scale. Selecting either a portion of your structure or the whole thing, you essentially can zoom in or out to see the structure better as you work on it.

Figure 4. You can scale parts of your molecular structure to make it easier to work on.

You also can make changes to the display, such as altering the stack layers or mirroring horizontally or vertically.

The last option available is the Object→Configure menu item. This will pop up another window where you easily can change atom, bond, font or common details for the display. This is also the same window that appears when you click on the Properties item on the Edit menu (which you get when clicking the middle mouse button).

Figure 5. A configuration window allows you to edit properties of your structure's elements easily.


Joey Bernard has a background in both physics and computer science. This serves him well in his day job as a computational research consultant at the University of New Brunswick. He also teaches computational physics and parallel programming.