Structure Menu in MarvinSketch

    This menu provides chemical functions relating to structures like molecule cleaning, aromatization, reaction-handling, naming, and more.

    Menu item Icon Description
    Clean 2D > Clean in 2D Clean in 2D icon Calculates new 2D coordinates for the molecule.
    Clean 2D > Clean and Arrange in 2D Clean and arrange in 2D icon Cleans structures and positions them to the center of the canvas.
    Clean 2D > Hydrogenize Chiral Center N/A Adds an explicit hydrogen atom to a chiral center having no terminal atoms when 2D cleaning is performed.
    Clean 3D Clean in 3D icon Calculates 3D coordinates for the molecule base on the method set in the Preferences > 3D Options dialog.
    Directed Merge > Assign Atoms Assign atoms icon Chooses the atoms of the fragments to be merged.
    Directed Merge > Merge Merge icon Merges the fragments at the atoms set.
    Add > Add Explicit Hydrogens Add explicit hydrogens icon Adds explicit H atoms instead of the current implicit ones. Explicit hydrogens are displayed with atoms joining their neighbor while implicit hydrogens are displayed by atom symbols only.
    Add > Data Data icon Attaches data such as the stoichiometry coefficient to the molecule.
    Add > Absolute Stereo (CHIRAL) Add absolute stereo chiral icon Sets chiral flag for the molecule.
    Add > Multi-Center N/A Adds a multi-center attachment point representing a group of atoms.
    Add > Position Variation Bond Position variation bond icon Create a variable point of attachment to represent a connection point to a group of atoms.
    Add > No Structure N/A Places a No Structure label on the canvas.
    Remove > Explicit Hydrogens Explicit hydrogens icon Removes explicit H atoms and increases the number of implicit hydrogens.
    Remove > Data N/A Removes the attached data from the molecule.
    Remove > Absolute Stereo (CHIRAL) Remove absolute stereo chiral icon Removes the chiral flag of the molecule.
    Edit data N/A Changes a previously attached data such as the stoichiometry coefficient of the molecule.
    Edit properties N/A Bond properties can be edited from this menu.
    Aromatic Form > Convert to Aromatic Form Convert to aromatic form icon Transforms the molecule to aromatic representation using the transformation method set.
    Aromatic Form > Conversion Method > Basic N/A The basic aromatization method is described here.
    Aromatic Form > Conversion Method > General N/A The general aromatization method is described here.
    Aromatic Form > Conversion Method > Loose N/A The loose aromatization method is described here.
    Aromatic Form > Convert to Kekulé Form Convert to Kekulé form icon Transforms the molecule to non-aromatic representation.
    Group > Group Group icon Creates a custom Substructure Group (S-group).
    Group > Frequency Variation Frequency variation icon Creates a Repeating Unit with Repetition Ranges.
    Group > Merge Brackets N/A Creates a bracket that crosses two bonds.
    Group > Edit Group N/A Modifies the properties of the selected group.
    Group > Contract Group N/A Contracts all groups to their abbreviations.
    Group > Expand Group N/A Displays the full structure instead of the abbreviations.
    Group > Ungroup N/A Removes all abbreviated group associations from the molecule.
    Reaction > Merge Reactants N/A Merges the selected fragments to a reactant, product, or agent.
    Reaction > Unmerge Reactants N/A Removes selected fragments from a previously merged reactant, product, or agent.
    Mapping > Map Atoms Map atoms icon Inserts map numbers of the selected atoms.
    Mapping > Manual Atom Map Manual atom map icon Inserts map numbers manually.
    Mapping > Reaction Mapping Method > Complete N/A All atoms in the reaction are mapped.
    Mapping > Reaction Mapping Method > Changing N/A Only those atoms are mapped that have changing bond. Either the bond order changes, a new bond is created, or the bond is deleted. Orphan and widow atoms are included.
    Mapping > Reaction Mapping Method > Matching N/A Maps all matching atoms in the reaction (Daylight style mapping). A reaction atom is called matching if it is not an orphan/widow atom: it exists on both sides of the reaction.
    Mapping > Unmap Atoms Unmap atoms icon Removes map numbers of the selected atoms.
    R-Logic N/A Allows setting additional R-group conditions such as occurrence, rest H, and if-then expressions to R-groups in the R-logic dialog window.
    Place Analysis Box N/A Places the Analysis Box containing the preset calculations.
    Structure to Name N/A Generates IUPAC and/or Traditional Name and/or displays CAS Registry Numbers®.
    Name to Structure N/A Opens the Source window in IUPAC Name format, and enables you to enter directly an IUPAC Name and convert it to structure.
    Markush Enumeration N/A Generates a whole or a subset of the library of a generic Markush Structure.
    Check Structure Check structure icon Checks and corrects chemical structures. See Structure Checker for more information.
    Auto Check N/A Toggles auto checking of structures while drawing.