Spartan 5.1 User's Guide

Chapter 5: The Model Menu

This section reviews the features and functions available under the Model menu.

Selection of Model results in display of the following menu:

Wire
Ball and Wire
Tube
Ball and Spoke
Space Filling
Polyhedra
Hide

Hydrogens

Labels
Edit Labels

Annotate

Box

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

Available models include the wire model, the ball-and-wire model, the tube model, the ball-and-spoke model, and the space-filling (or CPK) model. This menu also provides for display and editing of atom labels, as well as for removal of the hydrogens from the model or of the entire model from view. Finally, the Model menu allows presentation of a "box", which may then be sized to define boundaries for graphical calculations.

All of the available structural models, as well as the graphical surfaces to be discussed later, may be displayed either in orthogonal or perspective projections. While orthogonal projections are generally easier to work with, perspective views are valuable in helping to visualize spatially large molecules. Selection of orthogonal or perspective projection is done by selecting Preferences under the Wavefunction Logo menu (see Section 3.3). The figures drawn in the text which follows correspond to orthogonal projections.


Section 5.1: Wire

Represents bonds as wires and atoms as vertices.

The bonds are drawn in two colors, one for each of the two atoms making up the bond, the colors being chosen to denote the type of atom. A listing of default atom colors (stored in a file colors in the .spartanrc directory; see Appendix B) is provided below.

These colors may be changed if desired using Colors from the Wavefunction Logo menu (see Section 3.2). All models use the same color scheme.

Main Group

Main Group (cont'd)

Hydrogen white Bromine orange
Lithium tan Rubidium red
Berylium green Strontium red
Boron tan Indium tan
Carbon grey Tin grey
Nitrogen blue-grey Antimony tan
Oxygen red Tellurium tan
Flurine green Iodine tan
Sodium yellow
Magnesum blue Transition Metals
Aluminum purple
Silicon grey First Row green
Phosphorous tan Second Row green
Sulfer sky blue Third Row green
Chlorine tan
Potassium red Noble Gases
Gallium orange
Germanium gray Helium orange
Arsenic orange Neon orange
Selenium orange Argon orange
Krypton orange
Xenon

yellow


Section 5.2: Ball and Wire

Represents atoms by small balls and bonds by wires.

The balls and wires are color coded to the atom types. These may be changed from default values using Colors from the Wavefunction Logo menu (see Section 3.2).


Section 5.3: Tube

Represents bonds as solid cylinders (tubes) and atoms as vertices.

As in the wire frame representations, the bonds are drawn in two colors, one for each of the two atoms making up the bond. These (atom) colors may be changed using Colors under the Wavefunction Logo menu (see Section 3.2).


Section 5.4: Ball and Spoke

Represents atoms by small spheres (the size and color of which depends on atom type), and bonds by tubes.

Both atom and bond colors may be changed using Colors under the Wavefunction Logo menu (see Section 3.2).


Section 5.5: Space Filling

Represents a molecule as a composite of spheres, the size and color of which depend on the atom type. Also known as CPK models, space-filling models are intended to portray overall molecular size, the sphere radii being chosen as approximating van der Waals contact distances.

Sphere (atom) colors may be changed using Colors under the Wavefunction Logo menu (see Section 3.2).

The volume and surface area of space-filling models may be obtained from Volume and Surface Area under the Geometry menu (see Sections 6.10 and 6.11; also Section 11.2.3).


Section 5.5.5: Polyhedra

Draws shaded polyhedra around atomic centers surrounded by O, F, Cl, Br, or I (or any combination of these elements).

Elements may be added to or subtracted from the above list by editing Polyhedra: Vertex Elements under the Preferences menu (see Section 3.3).

Polyhedra colors may be changed using Colors under the Wavefunction Logo menu (see Section 3.2).

Repetitions of the Unit Cell are determined during Import via the File menu (see Section 4.9).


Section 5.6: Hide

Removes the current model from the screen. It is used to simplify displays of 3D solid surfaces and 2D slices, where structure models may lead to unnecessary crowding. A model may be restored by selecting it from the Model menu.

Caution: Selection of Hide when only a structural model is present on screen followed by selection of another molecule in a multi-molecule display will cause the "hidden" molecule to be "lost", i.e., the structural model is no longer a visible target. Note, however, that the Page Up and Page Down keys may be used to traverse the set of molecules currently displayed on screen, including any hidden molecules. As they are traversed, the name of the selected molecule appears in the window title bar, allowing the hidden molecule to be located. The Home and End keys may be used to go to the beginning and end of the set of molecules, respectively. See also Section 2.5.


Section 5.7: Hydrogens

Selects whether or not hydrogens are to be displayed. It is used to simplify the displays of large molecules, e.g., polypeptides and polynucleotides, where inclusion of hydrogens may lead to unnecessary crowding. If hydrogens are to be included in the model a check mark (3) appears to the left of Hydrogens. Hydrogens acts in a toggle manner, i.e., repeated selection turns the display of hydrogens "on" and "off".


Section 5.8: Labels

Selects whether or not atom labels are to be displayed. If labels are to be displayed with the model, a check mark (3) appears to the left of Labels. Labels may be used only with wire and ball-and-wire models; they disappear from view if other model types are requested. Labels acts in a toggle manner, i.e., repeated selection turns labels "on" and "off". Default labels, which consist of the atomic symbol followed by a number, e.g., "C6", may be changed by using Edit Labels (see below). User-defined points and planes (see Sections 6.8 and 6.9) are also labelled.


Section 5.9: Edit Labels

Allows atom labels (or labels associated with user-defined points or planes) to be changed from default settings. Among other reasons, this is important in order to provide a consistent set of labels for molecules in a group to facilitate geometric comparisons or to define centers for molecule alignment (see Sections 11.2.2). Selection of Edit Labels results in display of a message in the menu bar.

Clicking on an atom (or point or plane) results in a dialog.

The label may be changed by editing the contents of the Label box, following which another atom (or point or plane) may be selected and its label changed, and so forth. When all label editing has been completed, clicking on Done exits the dialog.

Acceptable labels do not need to conform to the default format, but may comprise any character string.


Section 5.9.5: Annotate

Allows the user to specify one or more alternative names (aliases), provide a heat of formation, or make comments. This information is added to the input file and is presently accessible only through Annotate. (Future developments will allow information to be entered into database.) Selection of Annotate results in a dialog.

Additional names are entered by typing in the upper text box followed by clicking on Add. Highlighted entries in the text box to the right of "Name(s)" may be replaced by the entry in the upper text box by clicking on Replace and deleted altogether by clicking on Delete.

A heat of formation may be added by typing the value into the text box to the right of "Experimental Heat of Formation:". Comments may be added by entering directly into the text box below "Comments:".


Section 5.10: Box

Displays either a simple wire frame or a transparent "box" (selection of which occurs in Preferences under the Wavefunction Logo menu, see Section 3.3) enclosing the molecule. The box will translate and rotate with the molecule. It may be sized by positioning the cursor on top of any corner, depressing the left mouse button and moving the mouse. Two of the box faces will expand and contract in response; one will be the most visible face and the other will be the analogous face at the back of the box. These faces will be demarked by red lines instead of white. Overall the box may be treated as a 3-dimensional window with only two dimensions able to be manipulated at a time. Box acts in a toggle manner, i.e., repeated selection turns the box "on" and "off".

The box is used by Spartan's graphics module to define the limits for the calculation. The default box comfortably encloses a space-filling model.


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