Getting Started with GaussView

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:

 

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 Builder Fragment 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 Builder Fragment display area below the main toolbar for a View window; it shows what item will be added to the current molecule at the next mouse click.

GaussView Toolbars

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.

toolbars      
GaussView Toolbars in Standalone Mode (left) and the Builder Palette (right)
The Builder palette on the right is revealed with the View=>Builder menu path.

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 View=>Builder.

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 View=>Add View). This color icon is also used to identify the molecule group in the Windows menu.

mg_labels.tif
Color Icons from 2 Different Views

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 (G), the molecule number (M), and the view number (V). 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.

context_menu.tif
View Window Context Menu
Each of the options on the context menu brings up a submenu containing related items.

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.

multiview
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 the Multiview Display Mode context 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:

  • Workspace Background Color: Modify the background color of the current window.
  • Options: Open the MultiView Options dialog (see below).
  • Fit: Resize all individual molecule frames so all are visible in the window.
  • Synchronize: Link all frames so that mouse actions in one affect all of them (e.g., rotations). By default, each view is independent.
  • Manually Resizable SubWindows: Allow the resizing the SubWindows manually by clicking and dragging on the triangle in the lower right corner.
  • Manually Movable SubWindows: Allow for the moving of the SubWindows manually by clicking and dragging on the upper portion of the SubWindow.

Customizing MultiView Windows


The Multiview Options Dialog
The button labeled Less above closes the bottom part of the
dialog,
and its label is
More when the lower display is hidden.

The various controls in the MultiView Options dialog have the following uses:

  • Visible Rows and Visible Columns: Number of rows and columns of individual frames initially appearing in a multiview window.
  • Scrolling: Placement of scroll bars.
  • Auto Fit SubWindows: 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 the More button has been pressed:

  • Workspace Margin, Horizontal Spacing, and Vertical Spacing: Padding around the block of individual view subwindows and between the individual columns and rows (respectively).
  • Borders, Titles, Captions, and Numbers: When checked, Borders displays border on individual view frames. Titles and Numbers control whether the job title and structure number appear in each frame title bar. Captions 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 Edit=>Delete menu path will delete the current molecule and its View. The Delete 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.

If you want to remove all of the atoms but keep the empty view within the molecule group, click on the Select All Atoms button on the toolbar and then navigate to one of the two delete functions. This will clear the View window.

The Cut button and the Edit=>Cut offer the same functionality as the Delete function, except that it puts the molecule (or atoms) on the clipboard for future use.

Animating Multiple Structures

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. The Repeats button allows the user to specify how often the animation will play for. The Sequence button allows the user to specify how the animation will play. The Frame Delay (msec) button indicates, in miliseconds, how long the delay is between each frame. The Endpoint Delay (msec) 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:

Mouse Button
   
3-Button 1,2-Button Equiv. Action Function
Left
Left
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.
Center
Shift-Left
Drag Translate molecule.
Right
Ctrl-Left
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 the Alt key and moving the cursor. When you use the Alt key, only the fragment closest to the cursor is affected. Thus, Alt-Shift or Alt-Center mouse button will allow you to drag only the closest fragment.

Inquire Mode

The Inquire button 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: inqsm_h.tif.
  • 1 atom: Atom type and number: inqsm_1.tif.
  • 2 atoms: Bond length (distance): inqsm_2.tif.
  • 3 atoms: Interatomic angle: inqsm_3.tif.
  • 4 atoms: The 4-3-2-1 dihedral angle: inqsm_4.tif.

inq_3.tif
Inquire Mode Display
This display shows the value of the selected bond angle in the window’s lower left corner.

GaussView Menus

GaussView contains the following menus, which have the indicated general purposes:

  • File: Creating, opening, printing, and saving structures and movies, as well as setting GaussView preferences.
  • Edit: Performing configuration tasks on a structure as a whole.
  • Tools: Specialized features for specific building tasks and calculation types.
  • Builder: Creating and modifying molecular structures and structural parameters.
  • View: Managing and interacting with the display of molecules.
  • Calculate: Setting up and submitting Gaussian calculations and viewing current GaussView-initiated jobs.
  • Results: Examining calculation results, including surfaces, spectra, plots, and animations.
  • Windows: Managing the various GaussView windows.
  • Help: 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.

GaussView Preferences

Default settings for many GaussView features can be customized via the preferences, which are reached with the File=>Preferences menu 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: Ok (save current settings and exit), Cancel (exit and discard unsaved changes), Default (restore GaussView’s installation settings), and Help (obtain online help). When you use the Default button, a dialog similar to the one below will appear:

pref_restore.tif
Restoring Default Preferences
When you click the Default button in the Preferences, you are given the choice of restoring all default
preferences or only the ones pertaining to the current dialog (here, the default preferences for
Vibrations).

Displaying GaussView Tips

The Help=>GaussView Tips menu path opens 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).

d_tips.tif
GaussView Tips

Click Show tips at startup to view a tip each time you start GaussView.