Atom properties: various atom properties can be added to an atom in the drawing.
The property key and the value is free to set by the user in the Edit properties dialog.
Select an atom in the molecule.
Right-click and choose "Edit properties".
In the dialog box double-click the blue text field and type the property key then the value. Press Enter after each entry.
If invalid value is set, (after clicking OK) the backgound changes to pink and the wrong input can not be saved.
The display of the atom properties can be switched on and off: View > Advanced > Atom properties.
Query properties: You can define the chemical neighborhood for an atom within a query structure.
MarvinSketch allows you to set properties, such as
which must be matched by the corresponding atom in the target structure to produce a hit.
First select one or more atoms then go to the Advanced tab of Periodic Table to add the propertiy to every selected atom.
First go to the Periodic Table then click individual atoms to increase/decrease property value.
Each query property can be drawn typing .<query property name> (e.g., .H2) while the mouse pointer is over the relevant atom or there is active selection containing atoms.
The list of available query properties can be found here.