The Molecule Panel

The options in this panel control how atoms and bonds appear in the View window. The three popup menus specify how atoms in each of the three ONIOM layers will be displayed. If the ONIOM facility is not being used, then the setting for the High Layer is used. The layer display settings are also used by some other GaussView features unrelated to ONIOM (e.g., displaying atoms at the boundaries of PBC unit cells).

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The Display Format Molecule Panel

The various supported display types are:

The Use Bond Color checkbox controls whether bonds are partially or entirely colored by atom type in the tube display format. The two options are illustrated below:

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Tube Display Formats

These windows show pyrazine using the tube display format without (left) and with (right) the Use Bond Color item checked. The format on the right is the default.

The Atomic Radii popup menu and Scale Radii by field cause the atoms in the View window to be displayed at the indicated scaling of the standard or Atomic (the Standard and Covalent options on the popup menu, respectively). Using Covalent with a scaling value of 150%–200% will produce a space-filling-like molecular display, as in the following figure:

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A CPK-Like Display

The Z-Clip slider may be used to remove the frontmost portions of the image to allow views into the interior of the molecular display.