This page provides an overview of the GaussView user interface: the toolbars, windows, controls, and menu. For an introduction to using GaussView to build molecules, prepare Gaussian input files, and view Gaussian results, see:
- How To: Build Molecules
- How To: Set up a Gaussian Calculation
- How To: Run Gaussian Calculations
- How To: Visualize Gaussian Results
- How Do I …?
The GaussView Interface
The main GaussView interface consists of several windows in addition to other dialogs which appear in the course of working. The following figure illustrates a simple session in which the user has just started to build a molecule:
GaussView on the Desktop
Several GaussView features are visible here. At the top, we see the main GaussView control panel, containing the menu bar, a variety of toolbars, and the Current Fragment area. Below this, on the right, are the palettes used to select functional groups and individual atoms for addition to a molecule (note that these can function in a modal or amodal mode, according to user preference). At the bottom left is the active View window containing the molecule being built.
The GaussView interface consists of these main components:
- The control panel containing the menu bar and display area (grey background).
- Various toolbars. By default, these are placed below the menu bar in the control panel, but they may also be detached if desired (see below). They may also be rearranged within the control panel as desired. This is why your toolbar may differ from the illustration above.
- One or more molecule View window(s) (blue background by default).
- Dialogs corresponding to the various GaussView features.
- Preferences which control various aspects of the program’s functioning.
Molecules appear and can be modified in View windows. Do not confuse the View window; it shows what item will be added to the current molecule at the next mouse click.display area below the main toolbar for a
The toolbars that appear by default under the menu bar in the GaussView control panel are illustrated individually below. Descriptions of the various icons are provided here.
GaussView Toolbars in Standalone Mode (left) and the Builder Palette (right)
You can detach an individual toolbar from the main toolbar by grabbing its handle and dragging it out of the toolbar area. To reattach a standalone toolbar, either drag it back into the main toolbar or double click it.
The Builder toolbar can also appear as a standalone palette (as illustrated on the right above). You can open it with .
Molecules, Molecule Groups, and Views
GaussView uses these constructs to organize the many molecules which are being utilized at any given time:
- A molecule is most often a single molecule being worked on in isolation from other ones that may also be open. A molecule generally corresponds to a single file stored on disk. These are also sometimes referred to as models. Note that a molecule in this sense may contain more than one chemical species (i.e., “molecules” in the usual chemical sense).
- If there is more than one window open for the same molecule, the various different ones are referred to as views. Accordingly, a View window displays a molecule, and different views—and View windows—can display different orientations and properties of the same molecule.
- A molecule group is a collection of one or more molecules that are worked on as a unit. Molecule groups containing more than one molecule display each one in a separate subwindow of a combination View window (see Figure 4). Molecule groups are also referred to as model groups.
View window title bars display information about the current molecule group, molecule, and view: each distinct molecule group is identified by an icon whose color is uniquely associated with it. The figure below shows the color icons from two different View windows (each corresponding to a different molecule group). All dialogs that are directly associated with that molecule group will use the same color icon to visually associate themselves with their parent molecule group (including new views created using ). This color icon is also used to identify the molecule group in the menu.
The icon on the left corresponds to the 4th molecule in the 1st molecule group (red), while the one on the right is the 2nd view of the 1st molecule in the second molecule group (green). This same color icon will appear in all dialogs associated with that molecule. For some operating systems, the color icon is located in the status bar.
In addition to its color icon, each View window is uniquely identified by its group/molecule/view identifier. This identifier consists of the molecule group ( ), the molecule number ( ), and the view number ( ). Each of the molecules in a molecule group are numbered sequentially, starting at 1. If a molecule in the group is deleted, the molecules are renumbered to maintain a continuous sequence.
Note that dialogs corresponding to molecule-editing function are molecule-specific. If you activate a different View window with, say, the Atom List Editor open, its context does not follow. Examine the header label of a dialog in order to determine the corresponding View window.
Right clicking anywhere within a molecule window will bring up a context menu. The contents of the context menu duplicates much of the Builder, the menu bars, and the toolbars. This is provided as a convenience for the user.
View Window Context Menu
Working with MultiView Windows
For molecule groups containing more than one molecule, there are two display modes. Single-view mode displays a single molecule at a time (on the left in the figure below). The current molecule number appears in the toolbar.
In a single-view window, clicking the multiview icon brings up multiview mode, in which several molecules can be viewed at one time (on the right below). Be aware that the multiview fields and controls in the toolbar appear only when there is >1 molecule in the molecule group. The icon toggles between two forms, depending on the current view mode.
A Molecule Group Containing 12 Molecules
Individual molecule views are contained within the larger multiview window. The molecule number is shown in the title bar of each frame. The currently active molecule is shown with a slightly lighter background to distinguish it from the other molecules and is the one involved in atom selections or in the dialogs. Clicking on one of the individual molecule windows that is not the active molecule window will cause it to become the active molecule. In the event that not all of the individual molecules can fit in the View window, a scroll bar allows you to move between the different molecules.
Clicking on the small triangle to the right of the multiview icon reveals thecontext menu:
The Multiview Mode Content Menu
You can also open this menu by right clicking within the multiview display area. This menu controls the layout and behavior of multiview display mode:
- : Modify the background color of the current window.
- MultiView Options dialog (see below). : Open the
- : Resize all individual molecule frames so all are visible in the window.
- : Link all frames so that mouse actions in one affect all of them (e.g., rotations). By default, each view is independent.
- : Allow the resizing the SubWindows manually by clicking and dragging on the triangle in the lower right corner.
- : Allow for the moving of the SubWindows manually by clicking and dragging on the upper portion of the SubWindow.
The Multiview Options Dialog
The various controls in the MultiView Options dialog have the following uses:
- and : Number of rows and columns of individual frames initially appearing in a multiview window.
- : Placement of scroll bars.
- : When unchecked, resizing the multiview window does not affect the size of the individual frames, so more of them are typically visible when the window is made larger. When checked, individual frames are resized whenever the main window is so the same number of frames are always visible (based on the row and column values specified).
The following controls are visible when thebutton has been pressed:
- , , and : Padding around the block of individual view subwindows and between the individual columns and rows (respectively).
- , , , and : When checked, displays border on individual view frames. and control whether the job title and structure number appear in each frame title bar. controls all title-bar text as a whole, and unchecking it suppresses all text regardless of the settings of the other items.
Deleting Views from Molecule Groups
When you no longer need views within a molecule group, the View. The button on the toolbar can perform the same function. Notat that if any atoms are currently selected in the current View, then both of these delete functions will only delete those atoms, and leave the rest.menu path will delete the current molecule and its
If you want to remove all of the atoms but keep the empty view within the molecule group, click on thebutton on the toolbar and then navigate to one of the two delete functions. This will clear the View window.
Thebutton and the offer the same functionality as the function, except that it puts the molecule (or atoms) on the clipboard for future use.
Clicking on the green run button in the toolbar for a multiview molecule group will cause the View window to show each molecule in the group sequentially and continue to cycle through the full list until stopped. This has the effect of visually animating the sequence of molecules like a movie. This can be particularly useful for animating a series of related geometries, such as a Reaction Path plot. After the green run button has been pressed, it turns into a red stop button, which will stop the animation.
Animation Playback Controls
The small triangle next to the animation button contains a small menu. Thebutton allows the user to specify how often the animation will play for. The button allows the user to specify how the animation will play. The button indicates, in miliseconds, how long the delay is between each frame. The button indicates, in miliseconds, how long the delay is between the endpoint of the animation and the next loop.
Using the Mouse
Interaction with molecules is designed around the movements of a three-button mouse. The functions of the mouse buttons are described in the following table:
|Click||Insert atom/fragment, pick atom for modification, etc.|
|Click (C key pressed)||Select or deselect by atom.|
|Drag (R key pressed)||Select or deselect via marquee.|
|Drag Left/Right||Rotate about Y axis.|
|Drag Up/Down||Rotate about X axis.|
|Drag Left/Right||Rotate about Z axis.|
|Drag Up/Down||Zoom in and out.|
|Click in an open area||Display context menu.|
|Shift-Click on atom||Highlight corresponding row in Atom List Editor.|
Note that these mouse actions are active in any molecule display (including ones in GaussView dialogs).
Limiting Mouse Actions to One Fragment
If two items are not bonded to one another (not connected by visible chemical bonds on the screen), you can manipulate them individually on screen by holding down theand moving the cursor. When you use the , only the fragment closest to the cursor is affected. Thus, or will allow you to drag only the closest fragment.
Thebutton allows you to request geometric information directly from the View window when you click on the atoms of interest. Note that the selected atoms do not need to be bonded. The structural information appears in the View window’s status bar, as in the figure below. The number of atoms that you select affects the resulting display:
- Hover over atom: atom type and number: .
- 1 atom: Atom type and number: .
- 2 atoms: Bond length (distance): .
- 3 atoms: Interatomic angle: .
- 4 atoms: The 4-3-2-1 dihedral angle: .
Inquire Mode Display
GaussView contains the following menus, which have the indicated general purposes:
- : Creating, opening, printing, and saving structures and movies, as well as setting GaussView preferences.
- : Performing configuration tasks on a structure as a whole.
- : Specialized features for specific building tasks and calculation types.
- : Creating and modifying molecular structures and structural parameters.
- : Managing and interacting with the display of molecules.
- : Setting up and submitting Gaussian calculations and viewing current GaussView-initiated jobs.
- : Examining calculation results, including surfaces, spectra, plots, and animations.
- : Managing the various GaussView windows.
- : Viewing help files for GaussView and Gaussian, as well as GaussView tips.
A reference table listing all GaussView menu items and toolbar icons is available here.
Default settings for many GaussView features can be customized via the preferences, which are reached with themenu path. The following preferences are available:
- Building: Specify default settings for advanced fragment placement options.
- Charge Distribution: Specify desired settings for displaying atomic charge and dipole moment data.
- Clean Controls: Set the adjustable parameters and controls for the structure cleaning function.
- Colors: Customize the coloring of various GaussView displays.
- Desktop: Define file associations for extensions associated with Gaussian and GaussView files (Windows version only).
- Display Format: This category is broken down into four seperate categories: General, Molecule, Surface, and Text.
- File/Directory: Set preferred directory locations for various GaussView contexts.
- Gaussian Setup: Set the preferred Gaussian Calculation Setup dialog settings.
- Icons: Set default icon sizes in the user interface.
- Image: Set the preferred values for capturing images.
- Job Setup: Define execution procedures for Gaussian and related jobs.
- Movie: Specify preferences for animations created by GaussView.
- Print: Set the preferred values for printing images.
- Vibrations: Set the preferred Display Vibrations dialog settings.
- Window Behavior: Set the preferred behavior for dialogs.
All of the preferences dialogs contain several buttons:(save current settings and exit), (exit and discard unsaved changes), (restore GaussView’s installation settings), and (obtain online help). When you use the button, a dialog similar to the one below will appear:
Restoring Default Preferences
Displaying GaussView Tips
The GaussView Tips window, which displays various tips for using the program effectively. You can also choose to have a tip displayed each time GaussView starts up, using the checkbox at the bottom of the window (the default is unchecked).menu path opens the