8.7 Molecular similarity

In order to analyze the similarity between molecules, VEGA ZZ can superimpose them and calculate the RMS (Root Mean Square) value. This function is available choosing Calculate -> Similarity in the main menu.

Molecular similarity

To superimpose two molecules, you must click at least on three atom pairs: one of the source and one of the target molecule. Please remember that the source molecule is moved on the target molecule and the source is defined at first atom click. If you want swap the source with the target, you must click the Swap button. To remove a single pair, you must select it in the list and than click the Remove button. To restart the selection of the atom pairs, you must click the New button. To perform the superimposition of the two molecules, you must click the Superimpose button and to revert the source molecule to the starting position after the superimposition, use the undo function.
When you perform the superimposition, the RMS value is reported in the VEGA ZZ console.