The default coloring scheme is carbons are green, hydrogens white, oxygen red, nitrogens are blue, fluorine is cyan, phosphorous is magenta, sulfur is yellow, chorine is light green, bromine brown and iodine is purple. Other atom types are other colors.

The "Perspect" button found near the top of the screen turns perspective on and off. When perspective is on, the atoms closest appear larger and their bonds thicker.

From the format menu you can color the atoms by partial charge. Partial charge color scheme: Red = partial charge < -0.15, yellow 0 to -0.15, green 0 to 0.15 and blue >0.15. The default method use in the calculation is a modified DelRe method, but if you have run the CNDO or a MOPAC calculations, the charges from these programs are used instead.

If you open a Brookhaven protein database file (.pdf) you may also color the molecule by residue from the Format menu (if this information is available in the file).

Clipping Planes: Clipping planes hide parts of molecules in front of or some defined distance in back of the viewing screen. Clipping planes are set through the Display menu. You can set a front clipping plane on or off (it is 1 angstrom in front of the screen). You can also set a back clipping planes. In this case you specify how many angstroms behind the screen the clipping plane is. Setting both clipping planes gives you a slice through a molecule. This can be useful for investigating large biopolymers.

Molecule Rotation: Holding the right mouse button down is the easiest way to rotate the molecules. Holding the right mouse button down near the left or right side of the screen will cause the molecule to rotate around the Y axis and holding it down near the top or bottom of the screen will cause rotation around the X axis. To speed up or slow down the rotation, hit the ">" or "<" buttons that appear near the upper left of the screen during rotations. To continuously rotate the molecule briefly hold down the right mouse button, then click on the "X", "Y" or "Z" buttons that appear near the top of the screen, or type the X, Y or Z key on your keyboard. To rotate the molecule some specified number of degrees, select X Y or Z from the Rotate menu and type in the degrees when prompted.

The "Rotation Options" tool on the Rotate menu allows you to specify rotation around the screen center versus rotation around the molecule centers and also allows you to choose between rotating all the molecules or a single molecule.

Orienting Molecules: You can orient the molecule in a specific way using tools found on the Geometry menu. To place an atom or a bond at the center of the screen, choose "Place atom at origin" from the Geometry menu. You can also place an atom or bond on the x axis and the x-y plane.

To orient the molecule so its length is along the x axis, and its widest point perpindicular to that length is along the y axis, select Dimensions from the Calculate menu and select the Yes button when it asks you if you want to do this.

Orienting two molecules the same way is accomplished from the Geometry menu. Select "Dock (compare) molecule on molecule" from this menu. The program will prompt you for the number of atoms to compare in the two molecules and then will ask you to select the atoms in each molecule for comparison. Make sure that you select the atoms in the same order in both molecules as it will compare the first atom selected in molecule one, with the first atom selected in molecule two etc. At completion of this routine, the two molecules will be displayed on top of each other so you can visually see how similar they are and will also give you the sum of the distances of the atom pairs from each other. You can separate the two molecules on the screen by selecting "Space molecules evenly and Reactions" from the Geometry menu, and they will maintain the new orientation.

Displaying Reactions: To display a reaction draw in the molecules in the reaction. To start a new molecule, hit the "New Mol" button near the top of the screen and click anywhere on the drawing surface. When you have drawn all the molecules in the reaction section go to the Tools menu and select "Reactor...". The Reaction Editor will appear. Edit the molecule names. If a molecule in the grid at the top is not a starting material, double click on the value in the Step column until "intermediate" or "product" appears. Type in any descriptions that you want to appear above or below the reaction arrows. Type in the molar ratios of the components. The program will also tell you if the reaction is balanced. When done, hit the "Draw" button. The MMEd Reaction editor is limited to two step reactions. Its output is not publication quality. An example of its output appears below.