Structure Menu in MarvinSketch

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

    Clean 2D > Clean in 2D images/download/thumbnails/5317567/clean2D24.png Calculates new 2D coordinates for the molecule.
    Clean 2D > Clean and Arrange in 2D images/download/thumbnails/5317420/Marvin_new_clean_2D_24.png Cleans the structure(s) and places them in the center of the canvas.
    Clean 2D > Hydrogenize Chiral Center Adds an explicit hydrogen atom to a chiral center having no terminal atoms when 2D cleaning is performed.
    Clean 2D > Clean Wedge Bonds Arranges the wedge bonds of the molecule in 2D.
    Clean 3D images/download/thumbnails/5317496/clean3D24.png Calculates 3D coordinates for the molecule base on method set in the Preferences < 3D Options dialog.
    Directed Merge > Assign Atoms Chooses the atoms of the fragments to be merged.
    Directed Merge > Merge Merges the fragments at the atoms set.
    Add > Add Explicit Hydrogens images/download/thumbnails/5317420/hydrogenize24.png Adds explicit H atoms instead of the current implicit ones. Explicit hydrogens are displayed with atoms joining its neighbor while implicit hydrogens are displayed by atom symbols only.
    Add > Data images/download/thumbnails/5317420/attach_data24.png Attaches data like stoichiometry coefficient to the molecule.
    Add > Absolute Stereo (CHIRAL) images/download/thumbnails/5317420/absolute_stereo24.png Sets chiral flag for the molecule.
    Add > Multi-Center Adds a multi-center attachment point representing a group of atoms.
    Add > Position Variation Bond images/download/thumbnails/5317572/markushbond24.png Create a variable point of attachment to represent a connection point to a group of atoms.
    Add > No Structure Places a No Structure label on the canvas.
    Remove > Explicit Hydrogens images/download/thumbnails/5317420/dehydrogenize24.png Removes explicit H atoms and increases the number of implicit hydrogens.
    Remove > Data Removes attached data from the molecule.
    Remove > Absolute Stereo (CHIRAL) images/download/thumbnails/5317420/remove_absolute_stereo24.png Removes the chiral flag of the molecule.
    Edit data Changes a previously attached data like stoichiometry coefficient of the molecule.
    Edit properties Bond properties can be edited from this menu.
    Aromatic Form > Convert to Aromatic Form images/download/thumbnails/5317420/aromatize24.png Transforms the molecule to aromatic representation using the transformation method set.
    Aromatic Form > Conversion Method > Basic Basic aromatization method is described here.
    Aromatic Form > Conversion Method > General General aromatization method is described here.
    Aromatic Form > Conversion Method > Loose Loose aromatization method is described here.
    Aromatic Form > Convert to Kekulé Form images/download/thumbnails/5317420/dearomatize24.png Transforms the molecule to non-aromatic representation.
    Group > Group images/download/thumbnails/5317588/group24.png Creates a custom Substructure Group (S-group)
    Group > Frequency Variation images/download/thumbnails/5317572/groupr24.png Creates a Repeating Unit with Repetition Ranges.
    Group > Merge Brackets Creates a bracket that crosses two bonds.
    Group > Edit Group Modifies the properties of the selected group
    Group > Contract Group Contracts all groups to its abbreviations.
    Group > Expand Group Displays the full structure instead of the abbreviations.
    Group > Ungroup Removes all abbreviated group associations from the molecule.
    Reaction > Merge Reactants Merges the selected fragments to a reactant, product, or agent.
    Reaction > Unmerge Reactants Removes selected fragments from a previously merged reactant, product, or agent.
    Mapping > Map Atoms images/download/thumbnails/5317420/map_reaction24.png Inserts map numbers of the selected atoms.
    Mapping > Manual Atom Map images/download/thumbnails/5317748/map4b.png Inserts map numbers manually
    Mapping > Reaction Mapping Method > Complete All atoms in the reaction are mapped.
    Mapping > Reaction Mapping Method > Changing Only those atoms are mapped that have changing bond. Either the bond order changes, or new bond is created, or bond is deleted. Orphan and widow atoms are included.
    Mapping > Reaction Mapping Method > Matching 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/5317420/unmap_reaction24.png Removes map numbers of the selected atoms.
    Attribute > R-Logic 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 Places the Analysis Box containing the preset calculations.
    Structure to Name ... Generates IUPAC and/or Traditional Name and/or displays CAS Registry Numbers®
    Name to Structure Opens the Source window in IUPAC Name format, and enables you to enter directly a IUPAC Name and convert it to structure.
    Markush Enumeration Generates a whole or a subset of the library of a generic Markush structure.
    Check Structure images/download/thumbnails/5317420/check-structure24.png Checks and corrects chemical structures. See Structure Checker in MarvinSketch for more details.
    Auto Check Toggles auto checking of structures while drawing.