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 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.