Introduction to MarvinSketch

Introduction

MarvinSketch is a Java based chemical drawing tool. MarvinSketch allows you to create and edit molecules in various file formats including MDL mol, Compressed mol, unique SMILES, SMARTS, Sybyl mol, PDB, CML, XYZ, POV-Ray.
MarvinSketch includes many advanced features, such as recent structures (i.e. structure history), visual fragment placement, ambiguity reduction, and multi-level undo/redo.
The Marvin Applets are unique in the sense that they support all Java platforms, ranging from the ancient Java 1.0 to Swing. They work in older web browsers, but if they find themselves in a modern browser, they automatically utilize newer Java features.

MarvinSketch GUI Reference

Below is an image of the MarvinSketch GUI, followed by descriptions of each of the components

MarvinSketch Main Window

Canvas

The canvas is the drawing area for graphically creating and editing structures. You can easily draw atoms, bonds, rings, arrows, and much more on the canvas using your mouse.

Toolbar

The toolbar contains a collection of buttons and icons to quickly aid you in drawing molecular structures. The toolbar contains two types of buttons: click and toggle. Click buttons act as normal buttons - performing an action when you click them. Toggle buttons have multiple states that are alternated between with each mouse click. The toolbar contains several toggle buttons, most relating to drawable elements such as bonds, templates (predefined structures), and arrows. When one of these buttons is selected, it sets the drawing item associated with the mouse within the canvas.
The image below shows the different parts of the toolbar

parts of the toolbar

Toolbar Elements
Little Periodic Table	The most important (frequently used) atoms have buttons on the toolbar. This part of the toolbar is referred to as the Little periodic table. It also includes charge buttons ("-" and "+"). See How To Draw Structures
Periodic Table (More) button	MarvinSketch contains a full periodic table to allow you to add any chemical element to your molecule. Clicking the More button will open the Periodic table pop-up menu.
Bond Button	The Bond button allows you to select the bond type you wish to draw. Press and hold the bond button for a pop-up list of bond choices. See How To Draw Structures
Templates	MarvinSketch provides several predefined chemical structures, called templates (e.g., cyclopenthane, cyclohexan, benzene). See How to Draw Templates.
Reaction Button	Clicking on the Reaction button allows you to draw a Reaction arrow within the molecule. See How to Draw Reactions.
Edit Buttons	MarvinSketch provides the following familiar editing functionality in the Toolbar: Select, Cut, Copy, Paste, Erase, Undo, and Redo. To use the cut or copy functionality, you must first select part of the molecule. To paste cut/copied structures, click on Paste, then click the canvas where you would like to place the structure. For more information on these functions, see following sections: How to select a structure and How to delete a structure.
Zoom Buttons	The Zoom buttons allow you to zoom in and out, and to fit the molecule to the current size of the window.
Help Button	Opens the Help document.

AWT-Only Buttons

The AWT applet functions a little differently than the Swing applet and application. Its toolbar contains three AWT-specific buttons to manipulate the toolbar and access the Menu.
AWT Only Toolbar Buttons

The Window Mode button allows you to launch the Sketcher in a new window, allowing access to the Menu Bar. If the Sketcher is already in a separate window, this button returns it to the original location.
The Rearrange Toolbar button moves the Toolbar to the left of the canvas and orients it vertically.
The Hide Toolbar button toggles the visibility of the Toolbar.

Menu Bar

In addition to the features available through the toolbar, MarvinSketch has several features that can be accessed via the Menu bar.
N.B. In the AWT version of Marvin, the Menu bar is not initially visible. To access the Menu bar, click the Window Mode button (labeled with an arrow pointing upward and located to the left of the toolbar), which will launch the Sketcher in a new window with a visible Menu bar.

Menus and Major Submenus
File Menu	The File menu contains the available file operations, such as New, Open, Save, Print, and Close. The (unsigned) Swing and AWT applets contain only a subset of these functions. See Basic MarvinSketch Functions for more information on this functionality.
Edit Menu	The Edit menu contains general editing functionality (i.e. Copy and Paste) as well as Marvin-specific editing options. See the following sections for more information: Implicit/Explicit Hydrogens How to Work With Structures
Groups Submenu	The Groups submenu contains the tools for creating and working with abbreviated groups (S-groups). See Working With S-groups
Edit Source	Choosing Source from the Edit menu opens the Edit Source window. The Edit Source window opens the file for the current molecule as text. You can view and edit the molecule file in any of the supported formats (SMILES, molfile, XYZ, etc). See How to Work With Structures.
Preferences	The Preferences dialog allows you to change many of the MarvinSketch display settings, including look & feel, error highlighting, and object visibility. Your chosen settings will be saved and used when you open MarvinSketch in the future. See Saving Display Options.
View Menu	The View menu allows you to alter the way the molecule is displayed without altering the molecule itself. You can change the molecule display type, background color, color scheme, error highlighting, etc. See Structure Display Options
Hydrogens Submenu	The Hydrogens submenu controls the display of implicit and explicit hydrogen atoms in the molecule. See Implicit/Explicit Hydrogens
Templates Menu	The Templates menu contains a list of available template groups. By default, the Generic template list is displayed in the Templates panel of the toolbar. The Ring templates group contains a collection of different types of rings. It can also be displayed in the toolbar by selecting the Rings choice. The Amino Acids and Polycyclic template list includes too many templates to fit in the toolbar, so they are displayed in a pop-up window when you choose them. See How to Draw Templates.
Tools	See Calculator Plug-ins
Help	Select the Help menu item to access this help document. About Marvin displays information about Marvin. About JVM displays information about your software environment (JVM version, Operating system, Marvin's version).

Pop-up Menus

There are four pop-up menus in MarvinSketch. When you right click on the canvas, a menu will appear based on the position of the mouse. The following table summarizes these menus:

Mouse Location	Associated Right-Click Menu
Atom	Atom Pop-up Menu
R-group	R-group Pop-up Menu (Modified Atom menu)
Bond	Bond Pop-up Menu
Open canvas space	Edit Pop-up Menu

Atom Pop-up Menu

The Atom pop-up menu appears when you right-click on an atom on the canvas. It contains options for atom-specific activities.

Menu Item	Description
Charge	Applies a charge between [-9,9] to the atom. This submenu is not dynamically generated, so Marvin will let you set any of these values on any atom, highlighting the Valence Errors in red upon completion. In other words, Marvin will allow you to set a charge of -5 on hydrogen, despite the fact that this is chemically impossible.
Radical	Sets the selected atom as a radical. You can select the type of radical - monovalent, divalent, divalent singlet, or divalent triplet. The Off option removes the radical designation.
Isotope	The Isotope submenu contains a list of the isotopes of the selected element, dynamically generated based on the selected atom. Select an isotope to set or change the isotope number or choose Off to remove the the isotope number.
Map	The Map submenu contains a list of available map identifiers that can be set on each atom. Map labels are useful because they remain constant, unlike atom indexes, which can change as the molecule is altered. Another common use is to mark atoms in reactions. An advantage of Map labels is that they can be saved into SMILES and MDL format.
R-Group	Gives a submenu of R-group labels to change the selected atom to an R-group label.
Branch	Adds a new bond with implicit hydrogen to the selected atom. This option is disabled for atoms that can have no more bonds.
Remove	Removes the selected atom from the molecule.

R-group Pop-up Menu

The R-group pop-up menu appears when you right-click on an atom labeled as an R-group.

Menu Item	Description
Map	Map numbers are user defined atom identifiers. They are commonly used in reaction equations marking atoms taking part in the reaction. Maps are also useful in complex chemical expressions referring to atoms of certain functional groups.
R-Group	Gives a submenu of R-group label choices, Build Markush structures or R-group queries using the R-group labels. R-groups symbolise alternative substituents.
Remove	Removes the selected atom from the molecule.

Bond Pop-up Menu

The bond pop-up menu appears when you right-click on a bond within the molecule. It allows you to make a number of changes to the selected bond.

Menu Item	Submenu Items	Description
Bond Type Radio Buttons	Single	Changes the selected bond type to Single
	Double	Changes the selected bond type to Double
	Triple	Changes the selected bond type to Triple
	Aromatic	Changes the selected bond type to Aromatic
More	Query bond types	Changes the selected bond to a bond type (Single Up, Single Down, Single Up or Down, Double Cis or Trans, Double C/T or Unspec, Single or Double, Single or Aromatic, Double or Aromatic, Any) for use in a query.
Attributes	Stereo Search	Uses stereoconfiguration of specified double bond when this molecule is used as a query.
	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.
	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.
Align	Vertical	Orients the bond vertically
Align	Horizontal	Orients the bond horizontally
Remove		Removes the selected bond from the molecule

Edit Pop-up Menu

The Edit pop-up menu appears when you right-click on open canvas space (i.e. not on an atom or bond). This menu has two different states, corresponding to selection mode being turned on or off. Edit pop-up menu items include:

	Enabled when Selection Mode is
Menu Item	Description	ON	OFF
Recent	The Recent submenu contains a list of atoms and templates previously placed on the canvas. It does not include recently used bonds. You can change the drawing object by selecting one of the items in this list.	X	X
Copy	Puts a copy of the selected object on the clipboard.	X
Copy as SMILES	Puts a copy of the selected object on the clipboard in SMILES format.	X
Cut	Puts the selected object on the clipboard and removes it from the canvas.	X
Paste	Sets the drawing object to the item on the clipboard.	X	X
Select All	Quickly selects the entire molecule.	X	X
Create Group	Creates an abbreviated Group from the selected substructure. See the S-Groups section for more information on creating and using Groups.	X
Map Atoms	Maps selected atoms with unique map numbers.	X
Flip	Flips the structure on the canvas. The submenu allows you to choose horizontally or vertically.	X	X
Attributes	Edits structure attributes.	X	X
Print	Sends the molecule to the printer.	X	X

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