GaussView Basics

The main GaussView interface consists of several windows, in addition to other dialogs which appear in the course of working. Figure 1 illustrates a simple session in which the user has just started to build a molecule.

Figure 1. GaussView on the Desktop
Several GaussView features are visible here: beginning at the upper left and moving clockwise, we see the main GaussView control panel, containing the menu bar, a variety toolbars, and the Current Fragment window. Next, we see the palettes used to select functional groups and rings for addition to a molecule (note that these can function in a modal or amodal mode, according to user preference). Finally, we see 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 Current Fragment display.

• Various toolbars. By default, these are placed below the menu bar in the control panel, but they may also be detached if desired (see Figure 2). They may also be rearranged within the control panel as desired (so your window may differ from the illustration in Figure 1).

• One or more model view windows.

• Dialogs corresponding to the various GaussView features.

• Preferences which control various aspects of the program's functioning.

Figure 2. GaussView Toolbars in Standalone Mode
These toolbars appear by default under the menu bar in the GaussView control panel. The Builder toolbar can also appear as it does on the right, when selected with View=>Builder.

Model Groups, Models and Views

GaussView uses these constructs to organize the many molecules which may be being worked with at any given time

• A model is most often a single molecule being worked on in isolation from other ones that may also be open. A model generally corresponds to a single file stored on disk.

• If there is more than one window open for the same model, the various different ones are referred to as views. Thus, a view window displays a model, and different views can show different orientations of and properties of the same model/molecule.

• A model group is a collection of one or more models that are worked on as unit. Model groups containing more than one model display each one in a separate subwindow of a combination view window (see Figure 3). Model groups are also referred to as molecule groups.

Figure 3. A Model Group Containing 20 Molecules (Models)
The controls in the toolbar appear only when there is >1 model in a model group. The icon on the right end of the toolbar toggles between single window (left) and multi-window view (right).

The title bar of each view window displays information about the current model group, model and view: . This window shows the 10th model in the first model group, and it is the first view as well.

The various models in a model group can be animated by pressing the green button in the toolbar. The animation can be stopped via the red X icon which replaces it. The animation speed is controlled by the Animation Delay setting in the General panel of the Display preferences.

Model groups are created automatically (on request) when results files for certain types of jobs are opened (e.g., geometry optimizations). They may also be created manually by adding additional models to an existing model group. They are required as input for certain sorts of Gaussian jobs (e.g., QST2 and QST3 transition structure optimizations).

Using the Mouse

Interaction with molecules is designed around the movements of a three mouse. The functions of the mouse buttons are described in the following table

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.