Special Toolbars

    These toolbars are not visible by default. To make one visible select its checkbox in the View > Toolbars submenu. The following special toolbars are available in MarvinSketch:

    Chemical Toolbar

    This toolbar contains chemical functions and it is not visible by default. To make it visible, choose View > Toolbars > Chemical.

    The chemical toolbar of MarvinSketch

    Toolbar item Icon Description
    Clean and Arrange in 2D Clean and arrange in 2D icon Cleans structures and positions them to the center of the canvas.
    Clean 2D Clean 2D icon Calculates new 2D coordinates for the molecule.
    Clean 3D Clean 3D icon Calculates new 3D coordinates for the molecule. Clean3D builds up conformers of fragments from which the best, that is, the lowest energy conformer is given back. The quality of the structures is measured by a simple energy function (Dreiding-type molecular mechanics).
    Convert to Aromatic Form Convert to aromatic form icon Transforms the molecule to aromatic representation using the transformation method set.
    Convert to Kekulé Form Convert to Kekulé form icon Transforms the molecule to non-aromatic representation.

    Markush Toolbar

    This toolbar contains functions that help to work with Markush structures and it is not visible by default. To make it visible, choose View > Toolbars > Markush. The Markush toolbar of MarvinSketch

    Toolbar item Icon Description
    Position Variation Bond Position variation bond icon Creates a variable point of attachment to represent a connection point to a group of atoms.
    Frequency Variation Frequency variation icon Creates a repeating unit with repetition ranges.
    R-group Attachment R-group attachment icon Adds an attachment to the structure.

    3D Editing Toolbar

    This toolbar is not visible by default. It contains functions that can be useful in editing the structures in 3D. To make it visible, choose View > Toolbars > 3D editing.

    The 3D editing toolbar of MarvinSketch

    Toolbar item Icon Description
    Assign Atoms Assign atoms icon Maps atoms to merge.
    Merge Merge icon Merges assigned atoms.
    3D Plane 3D plane icon Alters the coordinates of the molecule to put the 3 selected atoms of the molecule onto the plane of the canvas.
    New Substituent New substituent icon Adds a new fragment to the canvas.