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 quartet

The 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.