8.6 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.
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.