SPARTAN 5.1 User's Guide: Chapter 3

Spartan 5.1 User's Guide

Chapter 3: The Logo Menu

This section reviews the functions available under the Wavefunction Logo menu. These are used to change background color, to control various aspects of the graphics display, to setup printing and to monitor jobs in execution. The menu also provides a Periodic Table showing availability of different methods, and a useful calculator.

Selection of from the menu bar (or typing "Alt W") results in display of the following menu:

About SPARTAN

Colors

Preferences

Print Setup

Monitor

Periodic Table

Calculator

(Keystroke equivalents are given by the letter underlined in the menu entry.)

Section 3.1: About Spartan

This opens a dialog which provides the version number of the program, copyright information as well as the address, phone and FAX numbers for Wavefunction and the e-mail address for technical support.

Always refer to the version number of Spartan when reporting problems, as well as to the type of workstation and version of operating system.

Section 3.2: Colors

This may be used to alter the default colors of graphical objects, including atoms, bonds and isosurfaces (without mapped properties), as well as the background color of Spartan's screens and the background color of graphical slices (see Section 9.4 and in particular Section 9.4.4). Selection leads to a message in the menu bar.

This directs the user to pick on some graphical object on screen. This accomplished, a second message and a dialog appear.

The graphical object selected is identified at the top of the dialog. Further down are three buttons, clicking on which accesses predefined colors: Default (which depends on the graphical object selected), White and Black. Object color may also be set by adjusting the Red, Green, and Blue slider bars. Finally, the color of the previously selected graphical object may be matched to the color of any monochrome object on screen (atoms, bonds and surfaces without mapped properties) or to the screen background color, by moving the cursor anywhere on screen (except inside the colors dialog box) and clicking.

Graphical objects have a picking priority: atoms > bonds > surfaces > background. It may be necessary to orient the graphic on screen such that the object of interest does not overlap an object of higher priority. Selection of atom and bond colors is best performed using ball-and-spoke models (see Section 5.4).

Color selection options may be performed in any order and as many times as desired. Once completed, clicking on Another, sets the color and displays the first on-screen message requesting selection of another graphical object. Clicking on Done sets the color and exits the dialog. Clicking on Cancel exits the dialog without instituting the last (since the last click on Another) color change.

Changes to default colors result in changes to the local copy of the color file (colors under the directory .spartanrc; see Appendix C). They will be maintained for execution under the present user home directory.

Section 3.3: Preferences

This opens a dialog which controls aspects of the graphics display.

View: Orthogonal/Perspective
Controls the view of any structural models and/or graphics images on screen. See Section 5 for a discussion of viewing perspectives.
Tumble: On/Off
Controls automatic tumbling of any structural models and/or graphic images on screen. Tumbling is initiated by moving the mouse with the middle button depressed and then releasing the button. To tumble all objects (except plots) on screen, hold down the Control key in addition to the middle button while moving the mouse; after tumbling starts, release both keys. Tumbling is stopped by clicking the middle mouse button. Tumbling applies only to displays in the main window.
Box: Transparent/Wire
Switches between representation of the box drawn around a molecule (see Section 5.10) as a transparent solid (Transparent) and as a simple wire frame (Wire). The transparent solid representation is used to assess molecular size when the structure is portrayed with a space-filling model.
Global Rotate: Screen Centered/Molecule Centered
Controls rotation of a set of molecules on screen. Screen Centered provides a single center for rotation for all molecules, and is useful in forming intermolecular complexes (see discussion of Merge As in Section 4.6). Molecule Centered rotates each molecule about its individual center, and is useful in aligning molecules on screen.
Expert: On/Off
Controls access to "expert modes" associated with several of Spartan's dialogs. "On" permits access, "Off" forbids access. Setting to "Off" may be of value to beginning users. The default setting is "On".
Edit Modes

Controls whether Builder Editing tools (e.g., Delete) automatically turn-off after first use (thus reverting to Add mode), or persist to allow performance of the same function multiple times (e.g., Delete, Delete, etc.).
Toolbar: Under Menu Bar/Under Fragment Panel
Controls the position of the tool bar in Spartan's builders.
Minimizer: MMFF94/SYBYL
Selects the force field (MMFF94 or SYBYL ) used for structure refinement in Spartan's builders. Both force fields have been supplemented to include elements and bonding arrangements not provided in the orginal parameterizations.
Polyhedra: Vertex Elements

Certain structures, involving a central atom surrounded by a set of other atoms, may be displayed as simple polyhedra. This section controls which surrounding elements are permitted. The default elements (O, F, Cl, Br, I) may be changed.

The Color and Preferences dialogs are also available in Spartan's builders as well as in the Conformation Search, Transition Search, Vibration Sequence, Coordinate Driving and Combinatorial Study dialogs, although some features may not be available in these dialogs. Changes made in the main screen or in any one of these dialogs are global changes. Changes in default preferences result in changes to the local copy of the preferences file (preferences under the directory .spartanrc; see Appendix C). They will be maintained for execution under the present user directory.

Section 3.4: Print Setup

This enters a dialog which specifies both a printer and details of printing.

Type
Selection of either Grayscale PostScript, Color PostScript or SGI RGB Image is made by toggle switches.
Destination
To designate a printer, select Printer and choose from among the available printers. To designate a PostScript file, select File. This results in a file name appearing near the lower left of the dialog (overwriting Copies). The default "~/spartan.ps" may be changed if desired. Alternatively, selection of which printer among those available on the network is made by clicking on an entry inside the box.
Copies
Selection of the number of copies to be printed is made by changing the default value (1) in the box to the right of Copies.
Options
Selection of Page Layout leads to a dialog.
1. Orientation
  Selection of either Portrait or Landscape orientation is made by toggle switches.
2. Size
  Selection leads to a menu of available sizes:
  
  Letter
  Legal
  Custom(in)
  A4
  Custom(mm)
  
  The paper size corresponding to the selection appears to the right of the dialog. Two of the selections (Custom (in)) and Custom (mm)) require the user to enter the desired dimensions, in inches and millimeters, respectively.
3. Margins
  Selection of margins is made by changing the default values in the Left, Right, Top and Bottom boxes.
  The Page Layout dialog is exited with settings recorded by clicking on OK. Clicking on Cancel exits the dialog without the settings being recorded.
Selection of Printer Parameters leads to a dialog, the entries in which pertain to (and are maintained for) the selected printer (see Destination, above).
1. Grays/Colors (depending on the setting of Type)
  Selection leads to one of two menus depending whether Grayscale or Color PostScript printer was selected:
  
  Grays: 2
  4
  16
  256
  Colors: 8
  64
  4096
  16.7M
2. Lines of Resolution
  A box is provided into which the desired number of lines (per inch) may be entered.
3. Halftone Pattern
  Selection results in a menu:
  
  Halftone Pattern: Dot
  Line
4. Pattern Angle
  A box is provided into which the desired halftone pattern angle (in degrees) may be entered.
  The Printer Parameters dialog is exited with settings recorded by clicking on OK. Clicking on Cancel exits the dialog without the settings being recorded.

The Print Setup dialog is exited with all settings recorded by clicking on OK. Clicking on Cancel exits the dialog without the settings being recorded.

Section 3.5: Monitor

Monitor allows listing of all Spartan jobs which are presently executing as well as facilitates killing jobs. Selection results in display of a dialog.

This contains the status of all Spartan jobs running at present (subject to user filtering; see Section 3.5.1.3.1). Jobs owned by the present user may be highlighted for action (see Section 3.5.1.4) by clicking on the entry in the dialog.

Section 3.5.1: Menus in the Monitor Dialog

Selection of Monitor results in a dialog with a series of pull down menus.

Section 3.5.1.1: Logo

Selection of from the menu bar (or typing "Alt W") results in display of the following menu:

About Monitor

Preferences

About Monitor

Opens a dialog which provides the version number of the Spartan monitor program, copyright information, as well as the address and phone and FAX numbers for Wavefunction.

Preferences

Opens a dialog which provides slider bars which control the time interval for sampling (Sampling Interval) from 1 to 120 seconds, and the interval for timeout across a network (Timeout Interval) from 1 to 120 seconds.

Section 3.5.1.2: File

Selection of File results in display of the following menu:

Quit

Exits the monitor program.

Section 3.5.1.3: View

Selection of View results in display of the following menu:

Filters

Displays a dialog, which controls the extent of the display.

Users refers to accounts and Hosts to machines. Selection of Self under Users limits the display to the current account, whereas selection of All displays
all users. Selection of Local under Hosts limits the display to the current host (local host), whereas selection of All displays jobs running on all hosts listed in the host table.

Section 3.5.1.4: Actions

Selection of Actions results in display of the following menu:

Kill

Kill Now!!

Kill

Kills in an orderly fashion the job which is highlighted. The job is allowed to complete an optimization cycle before it is killed (or a "complete atom" in the case of a frequency calculation), after which all files and the displayed structure are updated. Only jobs owned by the user may be killed. Jobs run using Gaussian 94 do not have access to this feature.

Kill Now!!

Immediately kills the job which is highlighted. Files and the displayed structure are not updated. Only jobs owned by the user may be killed. Gaussian 94 jobs may be killed in this way.

Section 3.5.1.5: Help

Selection results in display of the following menu:

Monitor Overview

Overview

Provides an overview of the features and functions available in Spartan's monitor program.

Section 3.6: Periodic Table

Selection leads to a dialog containing a Periodic Table.

Elements for which a particular calculation method are available are highlighted in the Periodic Table, following selection from the Level menu:

Level:

STO-3G
3-21G/3-21G(*)
6-31G*/6-31G**
6-311G**

DN*/DN**

MNDO
AM1
PM3/PM3(tm)

Note that only quantum chemical methods are included. Molecular mechanics models depend not only on atom but also on "chemical environment". Additional information regarding the availability of methods may be found under Available Elements in the Help menu (see Section 10.10).

Section 3.7: Calculator

Selection opens a calculator.

This functions in the same way as a normal "pocket calculator", except that it is linked to Spartan's spreadsheet (see Section 11.2.1). Note, the inclusion of an Æ key. This is used to simplify calculation of reaction energies. For example, the sequence of key strokes: "A + B Æ C + D =" (A, B, C, D are numbers or entries from a spreadsheet) is interpreted as "C + D - (A + B)" (products - reactants).

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