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. 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 bold, topology, reacting center, etc.
Structure Menu
Provides chemical functions relating to structures like molecule cleaning, aromatization, reaction-handling, naming and more.
Calculations Menu
Contains the available Calculator Plugins.
Tools Menu
Contains the available Services.
Help Menu
Provides information about using the program, technical details and license management.

Full Menu Reference

File Menu

New > Clear Desk Removes the structure being on the canvas including all fragments and graphical objects.
New > 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.
Insert File Inserts your saved molecule file into the canvas whitout erasing its former content.
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 Saves the molecule in a different location or with a different file name or format.
Import Name Opens the Source window in IUPAC Name format, and enables you to enter directly a IUPAC Name and convert it to structure.
Import Image Tries to convert an image file to a structure using OSRA.
Export to Image Exports the molecule to the required location in the required image format.
Find Structure Online > Find Structure in ChemSpider If ChemSpider contains the structure, it opens the records in your default browser.
Find Structure Online > Find Structure in Chemicalize If Chemicalize.org contains the structure, it opens the records in your default browser.
Find Structure Online > Find Structure in PubChem If PubChem contains the structure, it opens the records in your default browser.
Print Prints an image of the current molecule.
Document Style Changes atom and bond drawing properties in the document.
Multipage Settings Creates a multipage molecular document that helps to work with large drawings by dividing them into pages.
Recent Lists of recently used file names.
Close Finishes working with the currently open 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.
Select All Selects the structure being on the canvas including all fragments and graphical objects.
Delete Removes the selection from the canvas.
Transform These transformations affect the molecular coordinates. Note: The structure will be saved with the altered coordinates.
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 > Around arbitrary axis Rotates selection in 3D around an axis defined by two atoms selected by the user.
Transform > Rotate in 3D > Around X axis Rotates selection in 3D around a horizontal axis placed in the canvas.
Transform > Rotate in 3D > Around Y axis Rotates selection in 3D around a vertical axis placed in the canvas.
Transform > Rotate in 3D > Around Z axis Rotates the selection in 3D around an axis perpendicular to the canvas.
Transform > Rotate in 3D > Free 3D rotation Rotates selection in 3D with changing coordinates. Compare it to the Rotate in 3D transformation of View Menu, which affects only the position of observation.
Transform > Rotate in 3D > Group rotation The selected group rotates around the bond that connects it to the molecule.
Transform > Flip > Flip Horizontally Flips the selected object(s) horizontally, preserving the configuration of all enantiomers.
Transform > Flip > Flip Vertically Flips the selected object(s) vertically, preserving the configuration of all enantiomers.
Transform > Flip > Rotate 180° in Canvas Rotates the selected object(s) on the canvas plane, preserving the configuration of all enantiomers.
Transform > Flip > 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 > Mirror > Mirror Horizontally Mirrors the selected object(s) horizontally, inverting the configuration of all enantiomers.
Transform > Mirror > Mirror Vertically Mirrors the selected object(s) vertically, inverting the configuration of all enantiomers.
Transform > Mirror > Mirror to Canvas Plane Mirrors the selected object(s) to the canvas plane, inverting the configuration of all enantiomers.
Transform > Mirror > Group Mirror Mirrors the selected group if it has only one connecting bond to the structure.
Transform > Invert > Invert to geometric center Reflects the selected fragment(s) through the geometric center point.
Transform > Invert > Invert to an arbitrary center Reflects the selected fragment(s) through the chosen point in any fragment (an atom).
Transform > 3D plane Rotates the molecule to place the selected 3 atoms into the plane of the canvas.
Object > Bring to Front Brings the selected object in front of all others.
Object > Send to Back Places the selected object behind all others.
Object > Align Aligns the centers of the selected objects horizontally or vertically on the canvas.
Object > Distribute Distributes the selected objects horizontally or vertically in the space defined by the furthermost objects.
Object > Align and Distribute Performs alignment and distribution horizontally or vertically.
Template Library Organized collection of template molecules can be edited.
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.
Preferences The Preferences dialog window allows you to change many of the MarvinSketch display settings, including error highlighting and object visibility.

View Menu

Mouse Mode > Sketch The Sketch mode allows drawing into the canvas.
Mouse Mode > Zoom Zoom the content of the canvas by dragging the mouse without modifying atom coordinates.
Mouse Mode > Rotate in 3D Spin the structure around its central point in 3 dimension with the help of the mouse without modifying atom coordinates. Compare it to the Free 3D rotation of Edit Menu, which affects the molecular coordinates.
Mouse Mode > Reset View Restores the starting view as modified by rotation and zoom.
Zoom Level Allows you to select a magnification percentage from the list or to type a custom percentage.
Structure 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.
Structure Display > Wireframe Displays bonds as thin lines, and atoms (except Carbon) as symbols.
Structure Display > Wireframe with Knobs Displays bonds as thin lines, Carbon atoms as knobs, and other atoms as symbols.
Structure Display > Stick Displays bonds as thick lines, and atoms (except Carbon) as symbols.
Structure Display > Ball and Stick Displays bonds as thick lines, atoms as shaded balls, and atoms (except Carbon and Hydrogen) as symbols on balls.
Structure Display > Spacefill Displays atoms as large shaded balls, and atoms (except Carbon and Hydrogen) as symbols on the balls.
Structure Display > Quality > Low Quality Disables line anti-aliasing.
Structure 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 > Peptide Bridges Colors with different colors the new Peptide Bridge bonds which are crosslinking the peptide chains.
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 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 > None 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.
Peptide Display > 1-letter View peptide sequence with 1-letter aminoacid codes.
Peptide Display > 3-letter View peptide sequence with 3-letter aminoacid codes.
Advanced > Atom Numbering > Off Disable the visibility of atom indices.
Advanced > Atom Numbering > Atom Number Enable the visibility of unique internal atom indices. The indices are continuous starting from 1.
Advanced > Atom Numbering > IUPAC Numbering Enable the visibility of IUPAC numbering of atoms in a molecule. It is synchronized with the numbering of "Structure to name" option.
Advanced > Atom Properties Toggles the visibility of atom properties.
Advanced > Atom Mapping Toggles the visibility of atom mapping labels.
Advanced > Bond Lengths Toggles the display of bond lengths in Angstroms on the middle of the bonds.
Advanced > Lone Pairs Toggles the display of lone pairs.
Advanced > R-groups Toggles the display of R-group definitions.
Advanced > R-logic Toggles the display of R-logic definitions.
Advanced > Valence Toggles the display of valence numbers. Default setting is On.
Advanced > Ligand Error Toggles the display of ligand errors. Default setting is On.
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.
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.
Editor Style > Configurations Lists the available configurations, and allows quick switch.
Editor Style > 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.
Editor Style > Reset Current Configuration Removes all local modifications made on the active GUI configuration. Note that this action cannot be undone.
Editor Style > 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.
New Structure Opens a new MarvinSketch window to add new fragments to tha canvas without having to change e.g. the 3D view mode.
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.
Chain > Chain Places a carbon chain on the canvas. The number of carbon atoms can be increased or decreased by dragging the mouse. The chain drawing direction is mirrored based on the direction of the mouse movements.
Chain > Curved Chain Places a curved carbon chain on the canvas. The direction of the chain growth follows the mouse path. The number of carbon atoms can be increased or decreased by dragging the mouse. The chain drawing direction is mirrored based on the direction of the mouse movements.
Arrow > Single Reaction Arrow Places a Single Reaction Arrow object on the canvas.
Arrow > Retrosynthetic Arrow Places a Retrosynthetic Arrow object on the canvas.
Arrow > Equilibrium Arrow Places an Equilibirum Arrow object on the canvas.
Arrow > Two-headed Arrow Places a Two-headed Arrow object on the canvas.
Arrow > Single Arrow Places a Single Arrow graphical object on the canvas.
Arrow > Graph. Retrosynthetic Arrow Places a Retrosynthetic Arrow graphical object on the canvas.
Arrow > Graph. Equilibrium Arrow Places an Equilibrium Arrow graphical object on the canvas.
Arrow > Resonance Arrow Places a Resonance Arrow graphical object on the canvas.
Arrow > Curved Arrow Places a Curved Arrow graphical object on the canvas.
Arrow > Dashed Arrow Places a Dashed Arrow graphical object on the canvas.
Arrow > Crossed Arrow Places a Crossed 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 > Single Arrow Places a Single Arrow graphical object on the canvas.
Graphics > Graph. Retrosynthetic Arrow Places a Retrosynthetic Arrow graphical object on the canvas.
Graphics > Graph. Equilibrium Arrow Places an Equilibrium Arrow graphical object on the canvas.
Graphics > Resonance Arrow Places a Resonance Arrow graphical object on the canvas.
Graphics > Curved Arrow Places a Curved Arrow graphical object on the canvas.
Graphics > Dashed Arrow Places a Dashed Arrow graphical object on the canvas.
Graphics > Crossed Arrow Places a Crossed Arrow graphical object on the canvas.
Graphics > Polyline Places a Polyline object on the canvas.
Graphics > Rectangle Places a Rectangle object (Square object in case the Shift button is pressed) on the canvas.
Graphics > Rounded Rectangle Places a Rounded Rectangle object (Rounded Square object in case the Shift button is pressed) on the canvas.
Graphics > Ellipse Places an Ellipse object (Circle object in case the Shift button is pressed) on the canvas.
Text Places a Text object on the canvas. Allows changing text properties on the appearing toolbar.

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 > Off 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.
Valence Allows you to change the valence of any atom between [0, 8].
Radical > Off 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.
R-group Attachment The selected atom becomes the attachment point for the substituent.
R-group Attachment Order Changes the order (numbering) of the attachment points.
Link Node Specifies query structures containing rings or chains of variable size.
Periodic Table Shows Periodic Table and query/atom property drawing window.
Edit Properties Specifies the property of an atom.
Add S-group attachment If the selected atom is part of an S-group, you can specify an attachment point.
Remove S-group attachment Removes the highest-numbered attachment point from an atom of an S-group.

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. (Active only in 2D.)
Type > Single Down Changes the selected bond type to Single Down. (Active only in 2D.)
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.
Bold Changes the selected bond to Bold. See details on bold tool application.
Hashed Changes the selected bond to Hashed.
Topology > None 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 > None 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 > Horizontally Alters the molecule so that the selected bond is oriented horizontally.
Align > Vertically Alters the molecule so that the selected bond is oriented vertically.
Ligand order Changes the order of the attachment of R-group ligands.
Edit Properties Bond properties can be edited from this menu.

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.
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 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 > 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.
Edit properties Bond properties can be edited from this menu.
Aromatic Form > Convert to Aromatic Form 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 Transforms the molecule to non-aromatic representation.
Group > Group Creates a custom S-group, R-group or Repeating Unit with Repetition Ranges.
Group > Frequency Variation 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 (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 > 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 Inserts map numbers of the selected atoms.
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 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.
Structure to Name > Place IUPAC Name Inserts IUPAC Name onto the canvas.
Structure to Name > Generate Name Generates IUPAC and/or Traditional Name.
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 Checks and corrects chemical structures. See Structure Checker in MarvinSketch for more details.
Auto Check Toggles auto checking of structures while drawing.

Calculations Menu

Elemental Analysis Calculates the elemental composition of the molecule.
Protonation > pKa Calculates the pKa values of the molecule.
Protonation > Major Microspecies Draws molecular microspecies at given pH.
Protonation > Isoelectric Point Calculates gross charge distribution of a molecule as function of pH.
Partitioning > logP Calculates the octanol/water partition coefficient.
Partitioning > logD Calculates the octanol/water partition coefficient at any pH.
Solubility > Aqueous Solubility Calculates the solubility of the molecule in aqueous solution.
Charge > Charge Calculates the partial charge value of each atom.
Charge > Polarizability Calculates the polarizability of each atoms.
Charge > Orbital Electronegativity Calculates electronegativity of each atoms.
Charge > Dipole Moment Calculation Calculates the electric dipole moment of the molecule
NMR > CNMR Prediction Predicts 13C NMR chemical shifts of the molecule.
NMR > HNMR Prediction Predicts 1H NMR chemical shifts of the molecule.
NMR > NMR Spectrum Viewer Opens and displays JCAMP-DX NMR spectral file.
Isomers > Tautomers Generates two dimensional tautomers of the molecule.
Isomers > Stereoisomers Generates all possible stereoisomers of the molecule.
Conformation > Conformers Generates selected number of conformers or the lowest energy conformer of a molecule.
Conformaton > Molecular Dynamics Calculates the configurations of the system by integrating Newton's laws of motion.
Conformation > 3D Alignment Overlays drug sized molecules onto each other in the 3D space.
Geometry > Topology Analysis Provides characteristic values related to the topological structure of a molecule.
Geometry > Geometry Provides characteristic values related to the geometrical structure of a molecule. It can calculate steric hindrance and Dreiding energy.
Geometry > Polar Surface Area (2D) Provides estimation of topoligical polar surface area (TPSA).
Geometry > Molecular Surface Area (3D) Calculates van der Waals or solvent accessible molecular surface area.
Predictor Predicts molecular properties based on its structure. The method is based on QSAR algorithm using a multiple linear regression model and a least squares fitting.
Other > H Bond Donor/Acceptor Calculates atomic hydrogen bond donor and acceptor inclination.
Other > Huckel Analysis Calculates localization energies L(+) and L(-) for electrophilic and nucleophilic attack at an aromatic center.
Other > Refractivity Calculates molar refractivity of the molecule.
Other > Resonance Generates all resonance structures of the molecule.
Other > Structural Frameworks Calculates Bemis and Murcko frameworks and other structure based reduced representations of the input structures.

Tools Menu

Services Provides accessibility to previously integrated third-party calculations*.

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.