Cerius2 Modeling Environment

4       The Cerius2 Interface

The Cerius² product line is a range of molecular modeling software, all based on the core control and presentation platform called the Cerius² Visualizer. The Visualizer is an integrated collection of tools whose functions include Cerius² session management, session logging, building and visualizing atomistic models, model management, saving and loading models, 3D graphical representation, data presentation, and environment customization.

The Visualizer supports numerous specialized Cerius² application modules. These plug into the Visualizer and are all controlled with a consistent mouse-driven graphical user interface (GUI). The GUI provides intuitive control of all functions, maintaining a consistent look and feel throughout the Cerius² environment.

This section explains

This section tells you how to run Cerius² and introduces basic features of the graphical interface. It includes:

Starting Cerius2

Initial layout of the Cerius2 screen

Using the mouse--the basics

Using the main control panel

Controls and control panels

Information sources

Other windows

The rest of this guide describes in detail how to use the Visualizer. Another guide, Cerius² Builders, describes the specialized builder modules you can add to the Visualizer to supplement its basic model-sketching capabilities. Each other optional application module or group of related modules includes its own documentation.

Starting Cerius2

Once you are correctly set up, you should make a working directory in which to run Cerius². You should have write access to such directories. (Write access is necessary because symbolic links and log files are created in the startup (run) directory during a Cerius² session.) You may want to create subdirectories in which to store related Cerius² files for each of your projects and use one of these as your run directory.

Start a regular Cerius² session by changing (cd) to the desired run directory and entering at the UNIX prompt:

>	cerius2

A specific example of starting Cerius² is presented under Starting Cerius2.

Initial layout of the Cerius2 screen

Main control panel

For details on using the main control panel, please see Using the main control panel.

Model window

Mouse and keyboard shortcuts

Summaries of mouse and keyboard shortcuts available in the model window are accessible from the Help pulldown menu on the main control panel menu bar (by selecting Help/Topics/Mouse Operations... or Help/Topics/Keyboard Operations...). Information on mouse and keyboard operations can also be found in Mouse and Keyboard Actions.

Text window

Caution

Using the mouse--the basics

• Left button = the action button. Used to click a control panel button, drag a slider, select an option from a pulldown menu or popup, and so on.

• Middle button. Used by your system's native window manager and also for certain model-manipulation activities.

• Right button = the help button. Used to obtain help text for GUI controls. For details, see On-screen help.

Note

Mouse activities

Definitions

• Click = move the mouse so as to place the cursor over the control or other item mentioned and then press and immediately release the left mouse button.

• Double click = place the cursor over the control or other item mentioned and then click the left mouse button twice in succession (relatively quickly).

• Click and drag = place the cursor over the control or other item mentioned and then press the left mouse button and, while keeping the button depressed, move the cursor to the item mentioned and then release the button when the cursor is over that item. For menus, popups, and similar controls, a list of items usually appears as soon as you click.

• Select, choose, set the popup to a value, etc., = click or click and drag. It will be clear from the context.

• Pick = click an item (usually an atom) in the model window.

• Check and uncheck = click a check box so that it contains or does not contain (respectively) a checkmark.

• Toggle = click an on/off control to change its state from on to off or vice versa.

Parts of the main control panel

The menu bar contains pulldown menus that provide access to all Visualizer tools. For descriptions of the menu bar entries, see The menu bar.

The toolbar provides a set of frequently used Visualizer tools, some of which are duplicated in control panels relating to model viewing and selection. For full details, see The toolbar.

The model manager enables you to control the selection, editing, and saving of models in the Cerius² modeling environment. The model manager is described fully under Handling multiple models.

Application modules are represented by menu cards grouped into card decks in the deck of cards menu. For more information, see Deck of cards menu.

Window manager controls, located in the window border, allow you to stow all open Cerius² windows to a single icon on your desktop.

The menu bar

The items on the menu bar provide click-and-drag access to related sets of controls:

• File--Access to session control, output, and file operations. These include working with Cerius² sessions, loading and saving structure files, and printing. See Managing Models and Sessions, Printing models and graphs.

• Edit--Access to atom selection and editing tools. See Selecting atoms and groups of atoms and Basic editing.

• Build--Access to the Visualizer's general model building (including the 3D-Sketcher) and attribute editing tools. See Building Models. Builder modules that provide additional, specialized model building functionality are accessed from the deck of cards menu and are described in Cerius² Builders.

• View--Access to tools that enable you to manipulate the view of models in the model window, as well as to produce high-quality displays and renderings of those models. See Viewing and Displaying Models and Enhancing Model Display.

• Move--Access to tools that enable you to alter the 3D geometry of models by moving atoms. See Translating and rotating atoms and Aligning and positioning atoms.

• Geometry--Access to geometry analysis tools, which enable you to examine the 3D structure of models. See Geometry Analysis.

• Utilities--Access to Visualizer utilities, which enable you to control, record, and play back Cerius² sessions, customize various aspects of the Cerius² modeling environment, and access and control external applications. See Customizing the Interface and Scripts and Licensing.

• Help--Access to on-screen help on the basics of the Cerius² modeling environment and to some prerecorded demonstrations. Simply select the topic that you are interested in. See also On-screen help.

The functions of several pulldown menu items can also be carried out by using keyboard shortcuts (generally <Alt>-key combinations) when the cursor is in the model window. Relevant key combination are shown beside the item on the pulldown menu itself. See also Keyboard shortcuts.

The toolbar

Some controls on the toolbar duplicate functions of control panels relating to model viewing and selection; others provide unique functionality.

Types of controls in the toolbar

• Model viewing controls--Use these controls to change the model's display style; add, change, or remove labels; and reset the position of the model. See Model display style, Labels, and Setting position and orientation.

• Atom selection controls--Use these tools to control atom selection. See Selecting atoms and groups of atoms.

• Cascade control panels--Click to reorganize all open control panels into an ordered cascade, which helps prevent screen clutter.

• Close all control panels--Click to close all open control panels.

• Menu card search--Click to access the Menu Card Search control panel, which enables you to search for words in the deck of cards menu hierarchy and in the menu bar menus (Menu card searching).

The model manager is described fully under Basic model management tasks.

Deck of cards menu

Access to application modules

The exact appearance of the deck of cards menu depends on which application modules you have purchased. Each module that is added to the Cerius² interface is represented by a menu card. Some menu card entries provide direct access to control panels; others (whose labels end with an arrow) give access to pullright menus, which each give access to a control panel. A Reset control (shown in red letters) appears on most cards and can be used to reset the controls for that module.

You can select a specific deck of cards from the deck selector popup (by clicking and dragging). Alternatively, you can cycle backwards or forwards through available card decks by clicking the left or right directional buttons next to the deck selector popup.

Menu cards are grouped into decks of 1-5 cards, which usually represent modules having related functionality. To bring any card in the current deck to the front, simply click the card's title.

Customization

You can customize the deck of cards menu by using controls in the Utilities pulldown menu on the main control panel's menu bar. You can make new decks, name them, change the card order, and so on. For details, see Customizing the Interface.

Controls and control panels

Control panels are windows that contain functionally grouped Cerius² controls. Many different control types are available, each designed to provide an intuitive method of invoking an action, providing a value, setting an option, or selecting an item. The control panel below illustrates many types of controls.

Types of controls

Different types of controls are distinguished by their appearance. For instance, popups are yellow, two-state controls (which can be on or off, checked or unchecked, etc.) are purple or green (respectively), and buttons that perform an immediate action when clicked are blue.

Labels and shape

A control's function is generally indicated by labels (words) on or next to the control and/or by a graphical icon. A control's function may also be suggested by its shape (e.g., a slider or a dial, which you manipulate by clicking and dragging).

Except for the deck of cards itself, all buttons and menu items that provide access to a control panel are followed by an ellipsis (...). For example, selecting a menu item or clicking a button labeled Preferences... brings up a control panel that enables you to set related preferences.

Functions of typical controls

The label on a labeled button indicates what action occurs if you click the button.

• Radio buttons are used to select only one of a group of options.

• An action button (or run button) performs the associated action (usually indicated by the label and/or some nearby text) when you click it.

• Popups and similar controls display a list of options when clicked, from which you can select one by dragging the cursor.

• Entry boxes are used to display current values and enter new ones.

Tip

Functions of specific controls

If you are unsure about the function of a particular control, click it with the right mouse button to obtain help (see On-screen help).

Buttons in the control panel window border

Clicking the close button in the upper right corner of the control panel border closes the control panel.

Clicking the button in the upper left corner gives access to some of your system's window-manager functions.

Managing control panels

To access a control panel, you select a menu item from the main Visualizer control panel (The menu bar), select an item from a card (Deck of cards menu), or click a pushbutton in an open control panel. Instructions for accessing particular control panels are given throughout this guide.

Tip

Closing control panels

To close a control panel, click the close button in the upper right corner of the control panel's border.

To close all open control panels, click the clear panels tool on the toolbar of the Visualizer main panel.

Cascading control panels

To group all open control panels into an orderly cascade, click the cascade panels tool on the toolbar of the Visualizer main panel.

Stowing all Cerius² windows to an icon

To stow all open Cerius² windows to a single icon on your desktop, click the stow button on the upper window border of the main control panel. To open the windows again, simply click the icon on your desktop.

Additional information

More advanced management of control panels, including customization so that certain control panels are opened whenever you start Cerius², is discussed under Control panel management.

Information sources

If you allow the cursor to rest over many controls, a small balloon help message appears, identifying the tool's function.

General information about Cerius² and basic GUI operations is available from the Help pulldown menu on the main control panel's menu bar.

Example

An example of using the Cerius² help facility is presented in Accessing on-screen help.

Menu card searching

Messages and status information

When you request that Cerius² perform some procedure with potentially important consequences (e.g., loss of data), a warning message window appears. These windows typically give you a chance to confirm or cancel your request or to make an alternative request, by clicking a push-button control.

Typical controls include:

• Ignore or Ignore request--Command processing continues from the point at which it was interrupted.

• Stop Current Process ASAP--The tool or application stops processing as soon as possible, that is, when Cerius² determines that it can do so cleanly.

• Exit Session Immediately--The Cerius² session is ended immediately.

When Cerius² is busy processing a command issued from the Visualizer or an application module, a Cerius² message window indicating the status of the job may be displayed. This window can take several forms, depending on the nature of the command in process. In some, a moving bar indicates progress. In others, where progress is less easily quantifiable, a diamond-shaped activity indicator appears.

During such periods of prolonged activity, you cannot perform any other Cerius² tasks except basic mouse-controlled model-viewing actions. If the command in process can be stopped cleanly before its scheduled conclusion, the message window contains an INTERRUPT button.

Click the INTERRUPT button (if present) to stop processing the command. A warning window (see Warnings) with several options appears, giving you the chance to confirm your choice or change your mind.

When Cerius² is iconified

If a process is running when you stow the main control panel to a desktop icon (see Managing control panels), the Cerius² icon displays a progress meter.

Other windows

• Graph window (Working with Graphs).

• Table window (Working with Tables).

• Rendering windows (Rendering and ray-tracing).

• Periodic table window (Building Models, e.g., Dummy atoms).