Molecules generated with a 3D scorer are scored using the 3D Shape score and the 3D Pharmacophore score.
In the card widget of the result page of your generator, you will find the molecules optimized against the 3D ligand-based parameters previously mentioned. Molecules can be sorted using these scores.
By clicking the "Show 3D view" icon on any result, Maky will display a sidebar where you can find the 3D conformation of the selected molecule superimposed to the reference ligand.
To visualize the 3D conformation of multiple molecules, select the desired molecules and click "See 3D multiple poses". Makya will display a sidebar with the superimposed structures.