In Molecular Editor, a pre-written three dimensional graphics package is used to generate the coordinates of the on-screen representation of the molecules. The coordinate system used is right-handed, with the Z axis coming out of the plane of the screen. All rotations and translations applied to the molecule are held in a matrix known as the transformation matrix. This matrix modifies the original coordinates so that they appear to be rotated or moved. The matrix is pre-multiplied by the homogeneous three dimensional point to give it the effect of the transformations, and then the modified point is converted into screen coordinates which can then be displayed. All options in the Draw Menu, as well as some of the screen editing options, affect this matrix.
