Menus of MarvinSketch

The Menu Bar contains almost all commands that are available in MarvinSketch.
The main menus are groups of functionally similar commands shown in the following picture:

File Menu
The File menu contains the available file operations, such as New, Open, Save, Print, and Close. (Note that the unsigned Swing applets contain only a subset of these functions.)
Edit Menu
The Edit menu contains general clipboard operations like Copy and Paste, structure selecting and deleting commands, as well as Marvin-specific editing options.
View Menu
The View menu allows you to alter the way the molecule is displayed without modifying the structure file itself. You can change the molecule display type, background color, color scheme, error highlighting, etc.
See also: Structure Display Options.
The view menu also contains operations to change the graphical user interface.
Insert Menu
The Insert menu allows drawing structure templates, bonds, reaction arrows, graphics, text boxes, and more on the canvas. It is also possible to add a special text box containing the IUPAC Name of the structure.
See also: How To Draw Graphic Objects and Text Boxes.
Atom Menu
Contains all atom related properties such as charge, atom radicals, maps, and many more.
Bond Menu
Allows changing the type of a bond, and makes bond properties available like topology, reacting center, etc.
Structure Menu
Provides chemical functions relating to structures like molecule cleaning, aromatization, reaction-handling, and more.
Tools Menu
Contains the available Calculator Plugins.
Help Menu
Provides information about using the program, technical details and license management.

Full Menu Reference

File Menu

Clear Desk Removes the structure being on the canvas including all fragments and graphical objects.
New Window Opens another MarvinSketch window.
Open Loads your saved molecule file into Marvin and discard any unsaved changes to the molecule you were previously working with.
Recent Files List of recently used file names.
Close Finishes working with the currently open molecule.
Save Saves the molecule to the same file it was opened from and in the same format. If you are working with a new molecule, Save will function as Save As.
Save As Save the molecule in a different location or with a different file name or format.
Save As Image Save an image of the molecule in the required location in required format. A saved image cannot be opened for later editing in Marvin.
Document Settings Create a multipage molecular document that helps to work with large drawings by dividing them into pages.
Print Prints an image of the current molecule.
Exit Saves GUI settings, preferences and My Templates before exiting the application.

Edit Menu

Undo Reverses the last command or the last entry you typed.
Redo Reverses the action of the last Undo command.
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.
Copy As Smiles Copies the selection to the clipboard in SMILES format.
Paste Inserts the contents of the clipboard at the location of the cursor, without replacing selection.
Delete Removes the selection from the canvas.
Select All Selects the structure being on the canvas including all fragments and graphical objects.
Transform > Drag Selection Moves selection on the canvas with changing coordinates.
Transform > Rotate in 2D Rotates selection in the plane of the canvas with changing coordinates.
Transform > Rotate in 3D Rotates selection in 3D with changing coordinates.
Transform > Switch Transformation Changes transformation mode from Drag to Rotate in 2D, Rotate in 2D to Rotate in 3D, while Rotate in 3D to Drag.
Transform > Group Flip Rotates the selected structure group by 180° around an axis set on the bond connecting the selection to the rest of the molecule. Stereocenters in the molecules are retained, the wedge bond styles change to keep the stereo information.
Transform > Horizontal Flip Flips the selected object(s) horizontally, preserving the configuration of all enantiomers.
Transform > Vertical Flip Flips the selected object(s) vertically, preserving the configuration of all enantiomers.
Transform > Mirror Horizontally Mirrors the selected object(s) horizontally, inverting the configuration of all enantiomers.
Transform > Mirror Vertically Mirrors the selected object(s) vertically, inverting the configuration of all enantiomers.
Object > Bring to Front Brings the selected object in front of all others.
Object > Send to Back Places the selected object behind all others.
Format properties Changes atom and bond drawing properties.
Source You can alter a molecule by directly editing its source in the Edit Source Window. You can view and edit the source in any of the supported file formats.
Enter IUPAC Name Opens the Source window in IUPAC Name format, and enables you to enter directly a IUPAC Name and convert it to structure.
Preferences The Preferences dialog window allows you to change many of the MarvinSketch display settings, including look & feel, error highlighting, and object visibility.

View Menu

Transform > Sketch The Sketch mode allows drawing into the canvas.
Transform > Zoom Zoom the content of the canvas by dragging the mouse without modifying atom coordinates.
Transform > Rotate in 3D Spin the structure around its central point in 3 dimension with the help of the mouse without modifying atom coordinates.
Transform > Reset View Restores the starting view as modified by rotation and zoom.
Zoom Allows you to select a magnification percentage from the list or to type a custom percentage.
Display > Atom Symbols in 3D Sets atom symbol visibility in 3D mode. Note that in 3D mode, atoms may become invisible in Wireframe and Stick mode by hiding atom symbols.
Display > Wireframe Displays bonds as thin lines, and atoms (except Carbon) as symbols.
Display > Wireframe with Knobs Displays bonds as thin lines, Carbon atoms as knobs, and other atoms as symbols.
Display > Stick Displays bonds as thick lines, and atoms (except Carbon) as symbols.
Display > Ball and Stick Displays bonds as thick lines, atoms as shaded balls, and atoms (except Carbon and Hydrogen) as symbols on balls.
Display > Spacefill Displays atoms as large shaded balls, and atoms (except Carbon and Hydrogen) as symbols on the balls.
Display > Quality > Low Quality Disables line anti-aliasing.
Display > Quality > High Quality Enables line anti-aliasing.
Colors > Monochrome Displays all atoms with default drawing color.
Colors > CPK Displays all atoms with Corey-Pauling-Kultun colors.
Colors > Shapely This color scheme is based on RasMol's shapely color scheme for nucleic and amino acids.
Colors > Group Coloring atoms based on PDB residue numbers.
Colors > Atom/Bond Sets Colors atoms and bonds according to the color of the pre-defined set they belong to.
Colors > Background Sets custom background color with adjusted default drawing color.
Colors > White Background Sets the background color to white and the default drawing color to black.
Colors > Black Background Sets the background color to black and the default drawing color to white.
Stereo > R/S Labels > All R/S Labels Always show atom chirality (R/S).
Stereo > R/S Labels > Absolute Stereo Show atom chirality if chiral flag is set for the molecule or the atom's enhanced stereo type is absolute.
Stereo > R/S Labels > No R/S Labels Do not show atom chirality (R/S).
Stereo > E/Z Labels Toggles the display of absolute double bond stereo configuration labels. Bonds known to have an (E) or (Z) configuration will be marked as such.
Stereo > Absolute Labels Toggles the display of the Absolute label if the chiral flag is set on the molecule.
Implicit Hydrogens > On All View hydrogens by symbol on all atoms. This option is disabled in Spacefill and Ball & Stick display modes.
Implicit Hydrogens > On Hetero and Terminal View hydrogens by symbol on hetero and terminal carbon atoms. This option is disabled in Spacefill and Ball & Stick display modes.
Implicit Hydrogens > On Hetero View hydrogens by symbol on hetero atoms only. This option is disabled in Spacefill and Ball & Stick display modes.
Implicit Hydrogens > Off Disable hydrogens by symbol on all atoms.
Misc > Atom Numbers Toggles the visibility of unique internal atom indices. The indices are continuous starting from 1.
Misc > Atom Mapping Toggles the visibility of atom mapping labels.
Misc > Graph Invariants Toggles the display of graph invariants (canonical labels).
Misc > Bond Lengths Toggles the display of bond lengths in Angstroms on the middle of the bonds.
Misc > Lone Pairs Toggles the display of lone pairs.
Misc > R-groups Toggles the display of R-group definitions.
Pages > Fit Page Width Adjusts the width of the current page to the width of the canvas.
Pages > Fit Page Height Adjusts the height of the current page to the height of the canvas.
Pages > Fit Page Adjusts the current page so that the whole current page will be placed centralized within the canvas.
Pages > Previous Page Goes to the previous page of multipage molecular document.
Pages > Next Page Goes to the next page of multipage molecular document.
Pages > First Page Goes to the first page of multipage molecular document.
Pages > Last Page Goes to the last page of multipage molecular document.
Pages > Goto Page Goes directly to a specific page by entering a number in the appearing dialog window.
Periodic System Shows periodic system and query/atom property drawing window.
Open MarvinView2D Launches a MarvinView window in 2D mode containing the current molecule from the Sketcher.
Open MarvinView3D Launches a MarvinView window in 3D mode containing the current molecule from the Sketcher.
Open MarvinSpace Launches a MarvinSpace window containing the current molecule from the Sketcher.
Toolbars > Toolbars Sets the visibility of individual toolbars.
Menubar Sets the visibility of the main menubar.
Status Bar Sets the visibility of the status bar.
Configurations > Configurations Lists the available configurations, and allows quick switch.
Configurations > Reset current configuration Removes all local modifications made on the active GUI configuration. Note that this action cannot be undone.
Configurations > Configuration Settings Configurations are GUI alternatives storing whole menu, toolbar and popup personalizations. This makes easy to define and quickly change the GUI for various purposes like sketching, publishing, teaching, etc.
Customize Customization allows you to personalize the GUI of MarvinSketch including menus, toolbars and keyboard shortcuts.

Insert Menu

Template Library Organized collection of template molecules.
Groups The full list of Abbreviation Groups.
Custom Objects Collection of custom created graphical objects.
Bond > Single Places Single type bond on the canvas.
Bond > Double Places Double type bond on the canvas.
Bond > Triple Places Triple type bond on the canvas.
Bond > Aromatic Places Aromatic type bond on the canvas.
Bond > Single Up Places Single Up type wedge bond on the canvas.
Bond > Single Down Places Single Down type wedge bond on the canvas.
Bond > Single Up or Down Places Single Up or Down type wedge bond on the canvas.
Bond > Double Cis or Trans Places Double Cis or Trans query type double bond on the canvas.
Bond > Double C/T or Unspec Places Double C/T or Unspec query type double bond on the canvas.
Bond > Single or Double Places Single or Double type bond on the canvas.
Bond > Single or Aromatic Places Single or Aromatic type bond on the canvas.
Bond > Double or Aromatic Places Double or Aromatic type bond on the canvas.
Bond > Any Places Any type bond on the canvas.
Bond > Coordinate Places Coordinate type bond on the canvas.
Arrow > Single Reaction Arrow Places a Single Reaction Arrow object on the canvas.
Arrow > Double Reaction Arrow Places a Double Reaction Arrow object on the canvas.
Arrow > Resonance Arrow Places a Resonance Arrow object on the canvas.
Arrow > Equilibrium Arrow Places an Equilibirum Arrow object on the canvas.
Arrow > Single Arrow Places a Single Arrow graphical object on the canvas.
Bracket > Parentheses Places a Parentheses object on the canvas.
Bracket > Square Brackets Places a Square Brackets object on the canvas.
Bracket > Braces Places a Braces object on the canvas.
Bracket > Chevrons Places a Chevrons object on the canvas.
Electron Flow > 1 Electron Places an electron flow arrow object on the canvas representing one-electron transfer.
Electron Flow > 2 Electrons Places an electron flow arrow object on the canvas representing two-electron transfer.
Graphics > Line Places a Line object on the canvas.
Graphics > Regular Arrow Places a Regular Arrow object on the canvas.
Graphics > Two-headed Arrow Places a Two-headed Arrow object on the canvas.
Graphics > Polyline Places a Polyline object on the canvas.
Graphics > Rectangle Places a Rectangle object on the canvas.
Chain Places a carbon chain on the canvas. The number of carbon atoms can be increased or decreased by dragging the mouse.
Text Places a Text object on the canvas. Allows changing text properties on the appearing toolbar.
IUPAC Name Places a Text object containing the preferred IUPAC name of the molecule being drawn.

Atom Menu

Stereo > R/S > Off Removes the absolute stereo configuration from a chiral atom along with the marking wedge bond.
Stereo > R/S > R Sets the absolute stereo configuration on a chiral atom to R, marking it with wedge bond.
Stereo > R/S > S Sets the absolute stereo configuration on a chiral atom to S, marking it with wedge bond.
Stereo > Reaction > No Stereo Configuration Sets the stereo configuration of the atom not to be considered during the reaction.
Stereo > Reaction > Inversion Sets the stereo configuration of the atom to be inverted during the reaction.
Stereo > Reaction > Retention Sets the stereo configuration of the atom to be retained during the reaction.
Stereo > Enhanced See Stereo Documentation for details.
Charge Allows you to change the charge of any atom between [-128, 128]. The number of implicit hydrogens will be adjusted if possible to accommodate the new charge. Valence errors will be highlighted in red.
Radical > Not Radical Removes the radical designation from an atom.
Radical > Monovalent Sets Monovalent radical center.
Radical > Divalent Sets Divalent radical center.
Radical > Divalent Singlet Sets Divalent radical center with singlet electronic configuration.
Radical > Divalent Triplet Sets Divalent radical center with triplet electronic configuration.
Radical > Trivalent Sets Trivalent radical center.
Radical > Trivalent Doublet Sets Trivalent radical center with doublet electronic configuration.
Radical > Trivalent Quartet Sets Trivalent radical center with quartet electronic configuration.
Isotope Sets or changes the isotope number of the selected element, or resets the default atom (no isotope) when it is set to Off.
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.
Group > * Attachment Point If the selected atom is part of a group (R-group definition or abbreviated group), you can specify an attachment point.
Link Node Specifies query structures containing rings or chains of variable size.
Add Branch Adds a new bond with implicit hydrogens to the selected atom. This option is disabled for atoms that can have no more bonds.

Bond Menu

Type > Single Changes the selected bond type to Single.
Type > Double Changes the selected bond type to Double.
Type > Triple Changes the selected bond type to Triple.
Type > Aromatic Changes the selected bond type to Aromatic.
Type > Single Up Changes the selected bond type to Single Up.
Type > Single Down Changes the selected bond type to Single Down.
Type > Single Up or Down Changes the selected bond type to Single Up or Down.
Type > Double Cis or Trans Changes the selected bond type to Double Cis or Trans.
Type > Double C/T or Unspec Changes the selected bond type to Double Cis/Trans or Unspec.
Type > Single or Double Changes the selected bond type to Single or Double.
Type > Single or Aromatic Changes the selected bond type to Single or Aromatic.
Type > Double or Aromatic Changes the selected bond type to Double or Aromatic.
Type > Any Changes the selected bond type to Any.
Type > Coordinate Changes the selected bond type to Coordinate.
Topology > No Topology Unsets the bond topology property.
Topology > In Ring Sets a bond property so that when the molecule is used as a query, the specified bond must be in a ring to score a hit.
Topology > In Chain Sets a bond property so that when the molecule is used as a query, the specified bond must be in a chain to score a hit.
Reacting Center > No Reacting Center Unsets reacting center query feature of the selected bond.
Reacting Center > Center Sets reacting center query feature on the selected bond: the bond takes part in the reaction.
Reacting Center > Make or Break Sets reacting center query feature on the selected bond: the bond is created or disappears in the reaction.
Reacting Center > Change Sets reacting center query feature on the selected bond: the bond remains in the reaction, but its bond type changes, for example from single to double.
Reacting Center > Make and Change Sets reacting center query feature on the selected bond: currently it works exactly as "Center".
Reacting Center > Not Center Sets reacting center query feature on the selected bond: the bond must not change in the reaction.
Stereo Search Uses stereo configuration of the specified double bond when this molecule is used as a query.
Regenerate Bonds Generate bonds for an XYZ structure with a different bond length cut-off.
Align > Horizontal Alters the molecule so that the selected bond is oriented horizontally.
Align > Vertical Alters the molecule so that the selected bond is oriented vertically.

Structure Menu

Clean 2D > Clean in 2D Calculates new 2D coordinates for the molecule.
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 > Clean in 3D Calculates new 3D coordinates for the molecule. Clean3D builds up conformers of fragments from which the best, i.e. the lowest energy conformer is given back. The quality of the structures is measured by a simple energy function (Dreiding type molecular mechanics).
Clean 3D > Cleaning Method > Fine Build Fine Clean3D builds up conformers of fragments to find low energy conformer. Leaves failed fragments intact.
Clean 3D > Cleaning Method > Fine with Hydrogenize The build process always adds explicit Hydrogens to the structures which are removed if not present in the original molecule. This option prevents the removal of extra Hydrogen atoms, otherwise gives the same results than Fine build.
Clean 3D > Cleaning Method > Fast Build Fast clean, which if fails, performs fine clean. It accepts any generated structure, and it is the default behavior of the Clean3D function.
Clean 3D > Cleaning Method > Build or Optimize Builds 3D structure for non-3D molecules and just optimizes the 3D molecules with the Dreiding force field.
Clean 3D > Cleaning Method > Gradient Optimize Optimizes with the Dreiding force field using the actual structure as starting geometry.
Clean 3D > Display Stored Conformers Allows you to choose one of the possible conformer structures which were calculated via the Conformers plugin.
Add > Add Explicit Hydrogens 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 Attaches data like stoichiometry coefficient to the molecule.
Add > Absolute Stereo (CHIRAL) Sets chiral flag for the molecule.
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 > Remove Explicit Hydrogens Removes explicit H atoms and increases the number of implicit hydrogens.
Remove > Data Removes attached data from the molecule.
Remove > Absolute Stereo (CHIRAL) Removes the chiral flag of the molecule.
Edit data Changes a previously attached data like stoichiometry coefficient of the molecule.
Aromatization > Aromatize Transforms the molecule to aromatic representation using the transformation method set.
Aromatization > Aromatization Method > Basic Basic aromatization method is described here.
Aromatization > Aromatization Method > General General aromatization method is described here.
Aromatization > Aromatization Method > Loose Loose aromatization method is described here.
Aromatization > Dearomatize Transforms the molecule to non-aromatic representation.
Aromatization > Rearomatize After transforming to non-aromatic representation, transforms the molecule to aromatic representation using the transformation method set.
Group > Create Group Creates a custom S-group, R-group or 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 (restricted to 4 types: generic, component, monomer, mer).
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 > Map Atoms Automatic assignment of map numbers to all selected atoms of a reaction by using the automapper tool.
Reaction > Mapping Method > Complete All atoms in the reaction are mapped.
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.
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.
Reaction > Unmap Atoms Removes map numbers of the selected atoms.
Reaction > Merge Reactants Merges the selected fragments to a reactant, product or agent.
Reaction > Split to Reactants Splits the previously merged reaction fragments.
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.

Help Menu

Help Contents Shows MarvinSketch User's Guide.
Licenses Starts ChemAxon License Manager where you can manage the licenses of all ChemAxon products.
About MarvinSketch Shows MarvinSketch product information and technical details.