Context Menus

    The following context menus are available in MarvinSketch:

    The menu items fall into three categories. Some context menu items do not require the corresponding atom, bond, or object to be selected, however, some additional menu elements appear only when they are selected.

    Please note that when a context menu appears, it is usually the combination of these menus. For example, when selecting an atom and pressing the right mouse button, a context menu appears that contains elements of the context context menu, in this case, the atom context menu, the edit context menu, and the selection context menu.

    Context menus of MarvinSketch

    Atom Context Menu

    The Atom context 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, and 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.

    Bond Context Menu

    The bond context menu appears when you right-click on a bond within the molecule. It allows you to make changes to the selected bond. It contains options for bond-specific activities that also can be accessed from the Bond menu.

    Menu item Description
    Type Changes the selected bond type to Single. Changes the type of the selected bond. For more information regardingbonds, see Draw Bonds.
    Bold Thickens the selected bond.
    Hashed Changes the selected bond hashed.
    Topology > None Removes defined bond topologies.
    Topology > In Ring The specified bond must be in a ring to score a hit.
    Topology > In Chain The specified bond must be in a chain to score a hit.
    Reacting Center > None Removes added bond property.
    Reacting Center > Center Specifies that the bond takes part in the reaction.
    Reacting Center > Make or Break The assigned bond can form or disappear in the reaction.
    Reacting Center > Change The assigned bond remains and can alter during the reaction.
    Reacting Center > Make and Change The assigned bond can form, break, or change its type during the reaction.
    Reacting Center > Not Center The assigned bond can not be the reaction center.
    Stereo Search Uses stereo configuration of the specified double bond when the molecule is used as a query.
    Arrange > Bring to Front Brings the selected bond in front of the others.
    Arrange > Send to Back Sends the selected bond to the back of the others.
    Align > Horizontally Orients the selected bond horizontally.
    Align > Vertically Orients the bond vertically.
    Group Creates a custom Substructure Group (S-group)
    Add > Explicit Hydrogens Adds explicit H atoms.
    Add > Map Atoms Maps atoms.
    Add > Data Attaches data
    Add > Multi-Center Adds a multi-center attachment point representing a group of atoms.
    Add> Position Variation Bond Create a variable point of attachment to represent a connection point to a group of atoms.
    Remove > Explicit Hydrogens Removes explicit H atoms.
    Remove > Unmap Atoms Unmaps atoms.
    Transformation > Drag selection Enables you to drag the selected bond.
    Transformation > Rotate in 3D Options for rotation
    Format Formats color, thickness, and length of the selected bond.
    Add to My templates Adds the bond to the Advanced Template Toolbar
    Edit properties Adds bond properties.

    Edit Context Menu

    The edit context menu appears when you right-click on open canvas space. In case there is an atom, bond, or graphic object under the cursor, the appearing context menu contains the elements of the edit context menu merged with the context menu of the selected element.

    Menu item Description
    Cut Removes and copies the selection to the clipboard.
    Copy Copies the selection to the clipboard.
    Copy As Copies the selection to the clipboard in the specified format.
    Paste Inserts the contents of the clipboard at the location of the cursor, without replacing selection.
    Select All Selects the structure being on the canvas including all fragments and graphical objects.
    Group Creates an abbreviated Group from the selected substructure. For more information about creating and using groups, see S-groups.

    Object Context Menu

    This menu appears when a context is a graphical object like text, bracket, electron flow arrow, or other graphics.

    Menu item Description
    Bring to Front Brings the selected object in front of all others.
    Send to Back Places the selected object behind all others.
    Transformation Main menu for Flip, Mirror, and Invert submenus.
    Format Brings up the Graphics Object Properties dialog where you can select from several formatting options.
    Add to My Templates Adds the object to the advanced toolbar.