Atom Pop-up Menu

The Atom pop-up menu appears when you right-click on an atom on the canvas. It contains options for atom-specific activities that also can be accessed from the Atom Menu.

Menu Item



Assigns reaction stereo labels or enhanced stereo labels to atoms. See the Enhanced stereo specifications for details.


Applies a charge between [-128,128] to the atom. Marvin will let you set any of these values on any atom, highlighting the Valence Errors in red upon completion. In other words, Marvin will allow you to set a charge of -5 on hydrogen, despite the fact that this is chemically impossible.


Allows you to change the valence of any atom between [0, 8].


Sets the selected atom as a radical. You can select the type of radical - monovalent, divalent, divalent singlet, divalent triplet, trivalent, trivalent doublet, trivalent quartet. The Off option removes the radical designation.


The Isotope submenu contains a list of the isotopes of the selected element, dynamically generated based on the selected atom. Select an isotope to set or change the isotope number or choose Off to reset the default atom type (no isotope).


Set map labels/identifiers on the selected atoms that do not change while altering the molecule. They are useful when dealing with reactions, and can be saved in SMILES and MDL formats.


Changes the selected atom to an R-group label. R-groups symbolize alternative substituents.

R-group attachment

Adds R-group attachment point to the selected atom.

R-group attachment order

Defines the order of the R-group or deletes R-group attachment point.

Link Node

Link node specifies rings or chains of variable size.

Add S-group attachment

Creates an attachment point on the selected atom of an S-group.

Remove S-group attachment

Removes the last attachment point from the selected atom of an S-group.


Removes the atom from the canvas.


Creates a custom Substructure group

Edit Group

Modifies the properties of the selected group


Removes the abbreviated group association from the atom.

Contract group

Contracts the atom to its abbreviations.

Add < Data

Attaches data to the molecule.


Changes atom and bond drawing properties in the document

Edit properties...

Specifies the property of an atom.

Label Editor

Allows changing the atom label on the canvas. Atom label properties can be set on the appearing toolbar.