Spartan 5.1 User's Guide

Chapter 2: General Operating Features

This section reviews the general operating features of Spartan's graphical user interface. It is intended to serve as a general reference.


Section 2.1: Starting Spartan

To start Spartan, bring up a "window" and type spartan. In a few seconds another "window" will appear. Move it into the desired screen location and click with any mouse button. This results in a clear screen except for a menu bar across the top.

The window may be moved about the screen by positioning the cursor in the area immediately above the menu bar, depressing either the left or the middle mouse button and moving the mouse. It may be scaled by grabbing one of the corners, depressing either the left or the middle mouse button and moving the mouse.


Section 2.2: Pull-Down Menus

Spartan's functions are, for the most part, controlled using pull-down menus under the headings in the menu bar. These can be reached by positioning the cursor on top of the appropriate item in the menu bar, and clicking with the left mouse button. The menu will appear below, e.g., clicking on Build:

Edit Structure

Conformer Search
Transition Search
Vibration Sequence
Coordinate Driving
Combinatorial Study

Isotopes

Clicking on the appropriate item in the menu selects it. An alternative mode is to slide the cursor while holding down on the left mouse button, first to the desired menu and then to the desired item under that menu, and only then release the button.


Section 2.3: Keystroke Equivalents

The functions available in Spartan's menus may also be easily accessed from the keyboard. Keystroke equivalents for each of the menus are designated by the underlined letter in each of the menu names, i.e., File, Model, Geometry, Build, Setup, Display and Help, and the menus are accessed by simultaneously depressing the Alt key and this letter (case insensitive). Alt W accesses the Wavefunction Logo menu. Each of the items in the individual menus also incorporates a letter which has been underlined, e.g., in the case of the Build menu:

Edit Structure

Conformer Search
Transition Search
Vibration Sequence
Coordinate Driving
Combinatorial Study

Isotopes

The item is accessed by pressing this key. For example, to enter the Conformer Search dialog, it is necessary first to simultaneously press the Alt and B keys to access the Build menu, and then to press the C key.


Section 2.4: Use of the Mouse

Enumerated below are functions associated with the three-button mouse.

Keyboard

Mouse Button

Left

Middle

Right

-
Shift
Control
Control + Shift

picking
-
-
-

X/Y rotate
Z rotate
global X/Y rotateb
global Z rotateb

X/Y translate
scalinga
global X/Y translate
global scaling

  1. Scaling is molecule centered when one molecule is open. When more than one molecule is open, scaling is screen centered. Scaling is always applied to all open molecules.

  2. lobal rotations can be either molecule or screen centered. Selection is made using Global Rotate in the Preferences dialog (see Section 3.3).

The left mouse button is reserved for picking (of graphical objects and/or of menu items), the middle button for rotation of objects, and the right button for translation or scaling of objects. Rotation and translation functions may be modified by holding down specific keys (Shift, space bar and Control) in addition to the appropriate mouse buttons.

With no keys depressed, the middle mouse button gives rise to rotation about the X and y (screen) axes and the right mouse button gives rise to translation in the x and y (screen) directions. Together with the Shift key, the middle mouse button gives rise to rotation about the z direction (perpendicular to the screen) and the right mouse button gives rise to scaling.

Spartan requires that all molecules on screen simultaneously be at the same scale. Scaling a single molecule in a multi-molecule display results in all molecules on screen being scaled together. New molecules brought onto the screen for the first time, either from the builders (see Section 7.1) or from Open (see Section 4.2) or Import (see Section 4.9) under the File menu will be brought on at the same scale as molecules already present.

The Control key (Ctrl) in conjunction with the middle or right mouse buttons and (optionally) the Shift key signifies that rotations or translations are to be carried out globally, i.e., on all molecules presently displayed, rather than only on the "selected" molecule.

In the builder, use of the space bar in addition to the middle mouse button allows for rotation about a "selected" bond. In conjunction with the right mouse button, the space bar allows for the extension (or contraction) of the selected bond. With the exception of bond rotation in the Combinatorial Study dialog (see Section 7.6.1), these functions are not available outside the builders.

Keyboard

Mouse Button

Left

Middle

Right

space bar

-

rotate (bond)

extend (bond)


Section 2.5: Keyboard Functions

Additional keys control various Spartan functions. These are enumerated below.

1. Pause

Renders graphics at higher resolution if possible.

2. Pause

Renders graphics in full scene anti-alias or full scene blur.

3. Pause

Shifts into 3D (stereo) mode using color filtration techniques. Pressing 3 again returns to normal mode. Additional discussion is provided in Section 2.8.

Page Up, Page Down, Home, End

Moves "up" (Page Up) and "down" (Down) the molecules displayed on screen. Moves to the "top" (Home) and to the "bottom" (End) of the molecules displayed on screen. The order of molecules on screen is the order in which they were built or brought onto screen.


Section 2.6: Molecule Selection

Two or more molecules may be simultaneously displayed in Spartan's main window. However, only one molecule may be selected. The selected molecule has access to all menu capabilities (molecule building, job setup and submission and text and graphical display and manipulation), while non-selected molecules may only be displayed as static or "animating" images. Exceptions involve scaling, and use of the Control key (see Section 2.4), both of which allow simultaneous manipulations of all objects on screen. Manipulations of any molecules displayed on screen which belong to the same group and have been "coupled" (see Section 11.2.2) are also simultaneous. Finally, job setup on any member of a list may pertain to all members of the list depending on whether or not Global status has been set in the individual setup dialogs (see Sections 8.2 to 8.8), and job submission pertains to the entire list.

Selection of one of the several sets of images currently on screen occurs by moving the cursor anywhere onto the image, i.e., onto the structure representation or onto any of the graphical surfaces, and clicking (with the left mouse button). This results in deselection of the prior set of images.


Section 2.7: Lists of Molecules and Spreadsheets

Spartan allows grouping of molecules into collections or lists. Some of these collections are very closely related and are automatically formed by Spartan as a result of conformation searching (see Section 7.2), vibration sequencing (see Section 7.4), coordinate driving (see Section 7.5) or combinatorial processing (see Section 7.6). Collections may also be user defined using Group As (Section 4.7). In either case, entire collections may be treated as single molecules insofar as job setup, and are treated as single molecules insofar as job submission. That is to say, operations performed on any member of a collection may (at the user's discretion) be automatically applied to all members of the collection.

Lists are presented as spreadsheets, and data may be graphed as well as fit to a variety of simple functional forms. Full discussion is provided in Section 11.


Section 2.8: 3-Dimensional Displays

Any graphical object displayed on Spartan's main screen may be rendered in 3D (stereo) using color filtration techniques. All that is required is for the viewer to wear "red/blue" glasses. While there is obviously loss of color in the resulting image, this simple technique works relatively well.

3D is turned "on" pressing the "3" key, and turned "off" by again pressing the "3" key (see Section 2.5).


Section 2.9: Iconifying Spartan

Spartan may be iconified by clicking on the " " box at the top right of the screen. This returns the user to the window from which Spartan was started, and places a small icon on screen.

Clicking on this icon returns to Spartan.


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