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Style and View Menus
Style Menu
The Style menu enables you to display 3D models in various styles. To display the molecules in a workspace in a particular style, select the appropriate menu item in the Style menu. For example, to display a molecule in mesh style, select the Style/Mesh menu item.
Style menu items:
Wireframe
The Wireframe menu item displays molecules and hypotheses in the 3D workspace in a wireframe style:
Mesh
The Mesh menu item displays molecules and hypotheses in the 3D workspace in a mesh style:
Dots
The Dots menu item displays molecules and hypotheses in the 3D workspace in a tube style, with dots to represent the van der Waals radii of the atoms:
Tube
The Tube menu item displays molecules in the 3D workspace with bonds shown as tubes. The atoms are indicated by colored ends of the tubes:
Ball and Tube
The Ball and Tube menu item displays molecules in the 3D workspace in a ball-and-tube style, where the atoms appear as colored spheres and the bonds appear as tubes. It is easier to select atoms in this style than in the tube style.
Sphere and Rod
The Sphere and Rod menu item displays molecules in the 3D workspace in a sphere-and-rod style, where the atoms and bonds appear much the same as in the default ball-and-tube style, but both atoms and bonds have larger radii.
Spacefilling
The Spacefilling menu item displays molecules in the 3D workspace in a spacefilling style:
When you rotate, zoom, or move any molecular model, you may notice that the model is simplified while the movement is in progress. When movement has finished, the molecule returns to the proper representation. The simplified display speeds up the movement of the molecule.
3D Constraints
The 3D Constraints menu item allows you to choose a display style for constraints. Types of constraints include location, distance, angle, torsion, and excluded volume. When you select this menu item, the options Invisible, Mesh, Dots, Transparent, and Solid appear in a submenu.
To see the differences in the visible constraint display styles, bring a hypothesis with different constraints into the View Compound or View Hypothesis workbench. Select different display styles from the Style/3D Constraints menu item. Notice the different display styles for the constraints. Fragments, functions, and geometric objects in the hypothesis are not affected by the 3D Constraints menu item.
To turn off the display of constraints, select the Invisible option.
3D Geometric Objects
The 3D Geometric Objects menu item lets you choose a display style for 3D geometric objects (centroids, vectors, hydrogen-bond donors, hydrogen-bond acceptors, and best-fit planes). When you select this menu item, the options Invisible, Mesh, Dots, Transparent, and Solid appear in a submenu.
The Invisible option suppresses the display of 3D geometric objects:
The remaining options are illustrated below:
The 3D Geometric Objects menu item affects only 3D geometric objects.
View Menu
View menu items:
The View menu enables you to modify the appearance and labeling of molecules and hypotheses in workspaces. For example, you can view a molecule with or without atom labels or hydrogen atoms.
The Constraint Names, Constraint Tolerances, and Geometric Object Names menu items are applicable only to 3D workspaces. The 2D Monochrome menu item applies only to 2D workspaces.
You can select colors for displaying object names and labels in 2D and 3D workspaces with the Global Preferences control panel, which is accessible from the Preferences menu.
Atom Labels
The Atom Labels menu item allows you to choose whether atom labels for molecules and hypotheses and labels for hypothesis functions appear in the 2D and 3D workspaces. When you select the Atom Labels menu item, move the cursor through the arrow at the right until a submenu appears showing thet options 2D and 3D. These options act as toggles. For example, if atom labeling in the 2D workspace is switched off, selecting 2D switches it on. If atom labeling is already on in the 2D workspace, selecting 2D switches it off. The same thing happens for 3D. If a highlighted box is next to the 2D or 3D option, atom labeling is switched on for that workspace. If there is no highlight, atom labeling is off. For hypotheses, a list of chemical symbols for atoms appears in {} (braces) to indicate the elements allowed.
Chirality Labels
The Chirality Labels menu item allows you to display chirality labels on compounds. When you select the Chirality Labels menu item, a submenu appears showing the options 2D and 3D. These options act as toggles. For example, if chirality labels do not appear in the 2D workspace, selecting 2D displays the labels. If the chirality labels already appear in the 2D workspace, selecting 2D switches them off. Chirality display is the same for the 3D workspace. If a highlighted box is next to the 2D or 3D option, chirality labels appear in that workspace.
More information:
Hydrogens
The Hydrogens menu item allows you to choose whether or not "unimportant" hydrogen atoms in molecules appear in the 2D and 3D workspaces. Important hydrogens always displayed are those attached to non-carbons, as well as aldehydic and acetylenic hydrogens.
When you select the Hydrogens menu item, a submenu appears showing the options 2D and 3D. These options act as toggles. For example, if hydrogen atoms do not appear in the 2D workspace, then selecting 2D switches them on. If hydrogen atoms already appear in the 2D workspace, then selecting 2D switches them off. The same thing happens for 3D. If a highlighted box is next to the 2D or 3D option, hydrogen atoms appear in that workspace.
Constraint Names
The Constraint Names menu item allows you to determine whether the names of constraints appear in the 3D workspace. The Constraint Names menu item acts as a toggle: If the 3D workspace does not currently show constraint names, selecting this menu item switches them on, and vice versa. If a highlighted box appears next to the menu item, constraint names appear in that workspace.
Constraint Tolerances
The Constraint Tolerances menu item lets you display the values you have defined for constraints in the 3D workspace. The Constraint Tolerances menu item acts as a toggle: If the 3D workspace does not currently show constraint tolerances, selecting this menu item switches on their display. If a highlighted box appears next to the menu item, constraint tolerance values appear in that workspace.
Geometric Object Names
The Geometric Object Names menu item lets you suppress or display the labels associated with geometric objects (centroids, vectors, hydrogen-bond donors, hydrogen-bond acceptors, and best-fit planes) that you have defined.
The menu item acts as a toggle: If the 3D workspace does not currently show geometric object names, selecting this menu item switches them on. If a highlighted box appears next to the menu item in the menu, geometric object names appear in that workspace.
Catalyst assigns sequential numbers to individual components of a 3D geometric object. Thus, in the left-hand illustration below, the point associated with hydrogen bond donor-1 is point-2, because the hydrogen-bond acceptor geometric object was defined first.
2D Monochrome
The 2D Monochrome menu item allows you to choose whether the 2D workspace displays objects in monochrome or color. The 2D Monochrome menu item acts as a toggle: If the 2D workspace currently displays objects in color, selecting the menu item makes it display objects in monochrome. Conversely, if the 2D workspace currently displays objects in monochrome, selecting the menu item makes it display them in color. If a highlighted box is next to the 2D Monochrome menu item, the 2D workspace displays objects in monochrome.
Compound Names
The Compound Names menu item allows you to choose whether the name of compounds and hypotheses appear in 2D and 3D workspaces.
The Compound Names menu item acts as a toggle: If the workspaces do not currently show compound and hypothesis names, selecting the menu item makes the names appear. Conversely, if the workspaces currently show the names, then selecting the menu item makes the names disappear. If a highlighted box is next to the Compound Names menu item, the workspaces show compound and hypothesis names.
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Last updated April 2000.
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