How To Use MarvinView Features

Table Of Contents

Loading Molecules into MarvinView

Marvin can open molecule files saved in any of the supported formats for viewing. You can also take advantage of the Cut/Copy/Paste and Drag & Drop Functionality of Marvin to move a molecule from another chemical drawing application into MarvinView.

Saving Molecules

MarvinView allows you to save an image of the molecule in the Viewer. You can select from JPEG, PNG, PPM, POVRay, and SVG file types.
Because MarvinView is designed for viewing and not editing, you cannot save into molecule format files from MarvinView. If you would like to edit and save the molecule, you should launch a MarvinSketch window.

Printing Molecules

You can print the molecule using the Print item in either the File Menu or the Pop-up Menu.

Editing Molecules

MarvinView is intended to be used mainly to display molecules. However, there is a limited set of functionality available to edit the molecule while you view it. To make major changes to the molecule, it can be opened in either a MarvinSketch window or a Source window. In either case, the alterations made can be imported back to the Viewer.

Editing Options in MarvinView

Marvin allows you to Clean your molecule in either 2D or 3D. This will recalculate the coordinates of the atoms and bonds to the most appropriate location, based on the type of cleaning you select. You can set cleaning options via the Edit > Clean submenu or from the Pop-up Menu.
You can toggle the display of rings as aromatic using the Edit > Bonds submenu.
Using the Misc submenu from the Edit Menu or from the Pop-up Menu, you can toggle the display of options such as Atomic Symbols, Map Numbers, and E/Z steroconfiguration labels.

Editing in MarvinSketch

MarvinView allows you to launch a MarvinSketch window for editing the current molecule. By selecting, Edit > Structure, the molecule will be opened in MarvinSketch. While you are editing the molecule in the sketcher, you will be unable to use the viewer. When you close the sketcher, you will be able to use the viewer again and all changes you have made in the sketcher will appear in the viewer.

Editing Source

Choosing Source from the Edit menu (in the Menubar or Pop-up Menu) opens the Edit Source window. The 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).
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. To change format, simply select the desired one from the Format Menu. To reload the molecule described by the text in this window into the MarvinSketch canvas (including any changes you may have made), select File > Import. This will close the Edit Source Window.

Structure Display Options

Saving Display Options

Manipulating the Molecule

You can translate, rotate, or resize the molecule on the canvas with a simple mouse drag. The View Menu and Pop-up Menu both contain a Move submenu that allows you set the type of motion to apply to the molecule.
By Selecting Translate or Drag, dragging the mouse across the canvas will result in a similar translation of the molecule.
Selecting Zoom allows you to resize the molecule. Dragging the mouse upward will zoom out, dragging downward will zoom in.
Selecting Rotate allows you to rotate the molecule in 2D. The center of the molecule becomes the center of rotation and the molecule will rotate around this point in the direction of the mouse drag.
Selecting Rotate in 3D allows you to rotate the molecule in 3D around a point at the 3D center of the molecule.

The View Menu and Pop-up Menu also contain the choice Animation, which allows you to start and stop an automatic 3D rotation of the molecule.

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