The Atom pop-up menu appears when you right-click on an atom on the canvas. It contains options for atom-specific functions that also can be accessed from the Atom Menu.
| Menu item | Description |
|---|---|
| Stereo | Assigns reaction stereo labels or enhanced stereo labels to atoms. For more information, see Stereochemistry. |
| Charge | 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 allows you to set chemically impossible charges. |
| Valence | Allows you to change the valence of an atom between [0, 8]. |
| Radical | Sets the selected atom as a radical. You can select from the following radical types: Off Monovalent Divalent Divalent singlet Divalent triplet Trivalent Trivalent doublet Trivalent quartetThe Off option removes the radical designation. |
| Isotope | 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). |
| Map | Sets 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. |
| R-group | 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 the 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. |
| Delete | Removes the atom from the canvas. |
| Group | Creates a custom substructure group |
| Edit Group | Modifies the properties of the selected group |
| Ungroup | Removes the abbreviated group association from the atom. |
| Contract group | Contracts the atom to its abbreviations. |
| Add > Data | Attaches data to the molecule. |
| Format | 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. |