Introduction to MarvinView

Table of Contents


MarvinView is a Java-based program for displaying molecular structures in 2- and 3-D. Though MarvinView is not intended as an editing tool, it can easily open the current molecule in a MarvinSketch window and retrieve the changes made there. MarvinView allows the user to quickly and easily control many aspects of the display, such as molecule display format, color scheme, dimension, and point of view.

MarvinView GUI Reference


The Canvas is the viewing area for display and manipulation of molecules. You can also change a number of display options from within the canvas, using your mouse.

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.

Edit Menu

The Edit menu contains general editing functionality (i.e. Copy and Paste) as well as Marvin-specific editing options.

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).

View Menu

The View Menu allows you to alter the display options for the structure. You can change the molecule display type and color scheme, hydrogen display options, display of atomic symbols, etc.

Hydrogens Submenu

The Hydrogens Submenu controls the display of implicit and explicit hydrogen atoms in the molecule.
See Hydrogen Display for more information.



See Calculator Plug-ins


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 Menu

The pop-up menu appears when you right-click on open canvas space . Pop-up menu items include:

Menu Item


Move The Move submenu contains a group of movement options. These options consist of Translate or Drag,Zoom, Rotate, and Rotate in 3D. Selecting one of these items will make that type of motion the result of mouse dragging on the canvas.
Animation The Animation submenu contains options for 3D animation of the displayed molecule.
Display The Display submenu contains options for changing the display format, display of atom labels, and resolution. Available display formats are Wireframe, Wireframe with Knobs, Sticks, Ball and Stick, and Spacefill. You can set the resolution to low or high via the Quality submenu.
Colors The Colors submenu allows you to specify the color scheme of the molecules. The available options are: Monochrome , CPK, Shapely, Group, and Atom Set

Hydrogens Submenu

The Hydrogens submenu controls the display of implicit and explicit hydrogen atoms in the molecule.
See Implicit/Explicit Hydrogens

Edit The Edit submenu contains a copy of the Edit menu from the Menu Bar.
Print Sends the molecule to the printer.
Window Pops up a separate MarvinView Window. This can be especially useful when the applet is embedded in an HTML page and the user wishes to have a separate window to work in.

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