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 images/download/thumbnails/1805497/clean2D24.png Calculates new 2D coordinates for the molecule.
    Clean 2D > Clean and Arrange in 2D images/download/thumbnails/1805322/Marvin_new_clean_2D_24.png 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 images/download/attachments/1805322/clean_3d24.png Calculates 3D coordinates for the molecule base on the method set in the Preferences > 3D Options dialog.
    Directed Merge > Assign Atoms images/download/thumbnails/1805322/merge_mapper_tool24.png Chooses the atoms of the fragments to be merged.
    Directed Merge > Merge images/download/thumbnails/1805322/merge_directed_3d24.png Merges the fragments at the atoms set.
    Add > Add Explicit Hydrogens images/download/thumbnails/1805322/hydrogenize24.png 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 images/download/thumbnails/1805322/attach_data24.png Attaches data such as the stoichiometry coefficient to the molecule.
    Add > Absolute Stereo (CHIRAL) images/download/thumbnails/1805322/absolute_stereo24.png 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 images/download/thumbnails/1805634/markushbond24.png 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 images/download/thumbnails/1805322/dehydrogenize24.png 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) images/download/thumbnails/1805322/remove_absolute_stereo24.png 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 images/download/thumbnails/1805322/aromatize24.png 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 images/download/thumbnails/1805322/dearomatize24.png Transforms the molecule to non-aromatic representation.
    Group > Group images/download/thumbnails/1805520/group24.png Creates a custom Substructure Group (S-group).
    Group > Frequency Variation images/download/thumbnails/1805634/groupr24.png 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 images/download/thumbnails/1805322/map_reaction24.png Inserts map numbers of the selected atoms.
    Mapping > Manual Atom Map images/download/thumbnails/1805683/map4b.png 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 images/download/thumbnails/1805322/unmap_reaction24.png 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 images/download/thumbnails/1805322/check-structure24.png Checks and corrects chemical structures. See Structure Checker for more information.
    Auto Check N/A Toggles auto checking of structures while drawing.