How To Use Basic MarvinSketch Functions

Table Of Contents

Throughout this section, icons appear next to features whose functionality that is not available in every version of MarvinSketch. The green check mark indicates that this feature is avalaible in the:

application
signed (Swing) applet
AWT applet

If no icons appear, this feature is available in all versions of MarvinSketch.

Create New Molecule

A new, blank molecule is created when you first launch MarvinSketch. You can immediately begin working with this molecule. A MarvinSketch window can hold only one molecule at a time, so all work you do within the canvas is considered part of the same molecule. You can create new, blank molecule at any time during your session by choosing File > New from the menu bar. This will open a new molecule and discard any unsaved changes to the molecule you were previously working with.
The application allows you to work with multiple molecules in multiple windows by choosing File > New > New Window .

You can open existing molecule files by choosing File > Open on the menu bar. This will load your saved molecule file into Marvin and discard any unsaved changes to the molecule you were previously working with.

You can also Paste existing structures from other windows to the open molecule. This will add the new structure to the currently open molecule, it does not create a new molecule.

Save Molecule File

You can save the molecule to any of the supported file formats. This will allow you to open and work with this molecule later. The default behavior of the Save button is to save the molecule to the same file it was opened from, in the same format. If you want to change the file name or format, choose Save As. If you are working with a new molecule, Save will function the same as Save As.

Save Image

The Save Image choice in the File menu allows you to save an image of the molecule in the sketcher. Marvin supports the following image formats: JPEG, PNG, PPM, POVRay, and SVG. A saved image cannot be opened for later editing in Marvin.

  You can print an image of the current molecule by choosing File > Print.

How to Draw Structures

You can create structures using atoms, bonds, and templates.

Atoms

1. Select an atom from the little periodic table, the Periodic Table pop-up window, or by shortcut.

2. Move the mouse into the molecule canvas. You will see the symbol of the selected item at the tip of your cursor. It can be placed in the molecule by left-clicking on the desired location.

   • Marvin is chemically intelligent. It will account for implicit hydrogens and set the charge according to valence rules.

3. You can replace any atom in the molecule by placing a new atom on top of it.

Bonds

1. Select a bond type using the Bond toolbar button or by shortcut.

2. To link two existing atoms, click on one then drag the cursor to the other.

   • Marvin will allow you to draw a bond between any two atoms in the molecule. Valence errors will be highlighted (if that option is enabled).

3. To draw a bond from a single atom, simply click the atom. A carbon atom will be added at the other end of the bond.

4. If you add a bond to empty canvas space, a carbon atom will be added to each end of the bond.

5. You can replace any bond in the molecule by placing a new bond type on top of it.

6. Bond types can also be changed using the Bond pop-up menu. Single bonds can be changed to Double or Triple by left-clicking on them.

Templates

MarvinSketch provides several predefined chemical structures, called templates (e.g., cyclopenthane, cyclohexan, benzene). Some templates are accessible directly from the toolbar. The remainder can be accessed via separate pop-up windows. The full list of MarvinSketch templates is available through the Templates menu.

1. Select a template using the Templates Menu or Templates toolbar area.

2. Place the template in the molecule by left-clicking on the desired location.

How to Draw Reactions

You can place a reaction arrow on the canvas at any time, even on a blank canvas. Reaction errors are indicated by a red box around the reaction arrow. Only one reaction is allowed per molecule.

1. Select the React button. You will see the reaction arrow on the tip of the cursor when you move the mouse into the canvas area.

2. Click the location of the tail of the arrow.

3. Drag the mouse and release at the location of the head.

Once you have placed a reaction arrow on the canvas, MarvinSketch considers each part of the molecule in relation to the reaction. All parts of the molecule that are behind the arrow are considered reactants. Everything in front of the arrow is a product. Anything placed along the arrow is considered an agent. The validity of the drawn reaction will automatically be checked by Marvin. See Reactions for more information on using and disabling this feature.

How to Select a Structure

1. Set Selection mode on by clicking the Select button.

   1. To select a single atom, click on it.

   2. To select two joined atoms, click on the bond that links them.

   3. To select a rectangular region, click at one corner of the desired region and drag the mouse to the opposite corner. While the mouse button is pressed down, a guide will be displayed to aid you.

   4. To select a non-rectangular region, use the lasso select function.

      1. Click anywhere on the canvas and release the mouse button.

      2. Draw the region with your mouse (leaving all mouse buttons unpressed). A blue guide line will appear where you have drawn. A pink line will connect the start and end points.

      3. When you have finished drawing the region, click the mouse. In the event that you have not closed the region, the pink line will be used to close it for you.

You can unselect all by clicking an empty area of the canvas.

How to Delete a Structure

Using the Erase button:

1. Set Erase mode on by clicking the Erase button.

   1. To erase a single atom or bond, click on it.

   2. To erase a rectangular region, click at one corner of the desired region and drag the mouse to the opposite corner. While the mouse button is pressed down, a guide will be displayed to aid you.

   3. To select a non-rectangular region, use the lasso erase function.

      1. Click anywhere on the canvas and release the mouse button.

      2. Draw the region with your mouse (leaving all mouse buttons unpressed). A blue guide line will appear where you have drawn. A pink line will connect the start and end points.

      3. When you have finished drawing the region, click the mouse. In the event that you have not closed the region, the pink line will be used to close it for you.

Using Selection mode:

1. Select a portion of the structure.

2. Click the Cut button or use the DELETE button on your keyboard.

Using pop-up menus:

1. Right click on an atom or bond.

2. Select Remove from the pop-up menu.

How to Work with Structures

Visually Editing the Structure

You can edit a molecule using the methods described in How to draw structures and How to delete a structure.

Editing the 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. 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.

Cleaning

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.

Aromatic Rings

You can toggle the display of rings as aromatic using the Edit > Bonds submenu.

Structure Display Options

There are wide range of functions related to the display of the molecules. These settings can be found in the View menu and the Preferences dialog. Additionally, you can move, rotate, and zoom in/out on the structure.

Moving and Rotating

You can move or rotate a selected structure.

1. Select the part of the structure you wish to move.

   1. Moving the selection:

      1. Move the mouse pointer toward the center of the selected structure until a blue rectangle appears.

      2. Translate the selection by dragging the mouse.

   2. Rotating the selection:

      1. Move the mouse pointer toward the "edge" until a blue gear appears.

      2. Rotate the selection by dragging the mouse.

Scaling

You can set the magnification of the molecule on the Canvas by the Zoom buttons. When a molecule is loaded into the sketcher it is scaled automatically to fit the window.

For more information, see Structure Display Options common to MarvinSketch and MarvinView.

Saving Display Options

Launching Other Windows

2D and 3D Viewer Windows

Choosing View >Open 2D Viewer or Open 3D Viewer launches a MarvinView window containing the current molecule from the Sketcher.

Copying Files Between Programs
(Cut/Copy/Paste and Drag & Drop)

MarvinSketch supports transfer of data between Marvin and other chemical drawing applications, between multiple Marvin windows, and to/from the desktop and file manager.
See Cut/Copy/Paste and Drag & Drop Functionality for more information.

Shortcuts

The table below contains a list of available shortcuts in MarvinSketch.

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