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The Visualization Toolbar provides access to some of the basic visualization aspects available in the 3D display. This toolbar controls how molecules are arranged in the 3D display, as well as in the 2D display (see chapter 6), and can also take a screen shot of the current main window regardless of what the actual main window is.
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The first button toggles the display between overlay and tiled mode. The icon displayed on the button indicates which mode it will switch to if clicked (overlapping boxes for overlay mode, a matrix for tiled mode). In overlay mode, all visible objects are drawn in the same coordinate space. In tiled mode, all objects are drawn in their own individual panes. By default, their are automatically centered in their respective panes. This option can be turned off in the preferences and each pane will use the same center coordinates for the display.
The second button, indicated by the letter ``H", toggles the display of hydrogens on molecules. When hydrogens are being hidden, an icon with a circle with a line through it will appear on top of the ``H".
The third button, indicated by inwardly pointing arrows, centers the viewed scene to selected atoms or, if no atoms are selected, to the center of mass of all the visible items on the scene. Centering does not fit the scene to the view, it only moves the scene to the calculated center.
The fourth button, indicated by outwardly pointing arrows, fits the entire scene to the display. All atoms in all visible molecules will be visible after pressing this button.
The fifth button, indicated by a camera, takes a screen shot of the displayed portion of the current main window. Clicking on this button opens a dialog to specify the name of the file to save the snapshot to.
The sixth button, indicated by the ``push pin" icon, toggles the display of text annotations of the currently Focused object. For more details on annotation see section 5.9.
n.b. When in overlay mode, there are times when Visible objects can't be seen due to the fact that they may exist in different points in space. To ensure that everything that is Visible is displayed, switch to tiled mode or use the ``fit to display" button described above.
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