Mass spectrometry is often unable to provide information about the exact position of a functional group on a chain or ring portion of a structure. In a number of application areas even incompletely characterized molecules can be sufficient to study a particular phenomenon. A typical example is metabolite characterization in an early drug discovery process, where knowledge of the precise location of biotransformation action is of less importance.

To allow the display and calculation of monoisotopic mass or the isotopic pattern of a fragment or molecule with an unspecified bond location, Structure Editor provides Ellipse as a graphical tool. Ellipse visually defines the region on a structure where a functional group could potentially be attached. So that the software can correctly interpret an unspecified bond location, the ellipse must enclose one or more atoms of the core structure and a single atom of a functional group that is not attached to the core structure. The ellipse is green, to facilitate better visual orientation.

Note: The Ellipse tool is only available in the Structure Editor module, so it is not possible to use a structure with an unspecified bond location in other modules. In addition the generation of fragments and mechanisms from such structures is not supported.