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8. Viewing and Displaying Models
Displaying other atoms
Other atoms (non-cations) can be represented as crosses, small
spheres, or single pixels or not drawn at all. To change how other
atoms are displayed, click the Preferences… button in the Display
Attributes control panel to access the Style Preferences control
panel. Then set Non-Polyhedral Style to CROSS, BALL, POINT,
or NONE.
Thermal ellipsoids
Understanding the display Ellipsoid style represents a constant-probability surface for the
thermal motion of the atoms. Atoms described by anisotropic temperature factors are represented by ellipsoids. (Atoms described
by isotropic temperature factors are represented by spheres.) Lines
representing bonds are drawn by default but can be removed. The
orientation of the ellipsoid’s principal axis may be displayed.
Spheres and ellipsoids are drawn only if the temperature factors
describe a solid object. (In mathematical terms, the matrix must be
positive definite.) If this is not true or if no temperature factor has
been specified, atoms are represented by crosses.
Specifying ellipsoid style
To display atoms as thermal ellipsoids, you must first be sure that
anisotropic temperature factors (see Understanding the display and
Temperature factors) have been specified or loaded. Then you can:
♦ Set the display style popup on the toolbar to ELLIPSOID.
or:
♦ Select the View/Display Attributes… menu item to access the
Display Attributes control panel. Set the Style popup to ELLIPSOID.
Displaying bonds and
ellipsoid axes
To show or hide the principal ellipsoid axis, click the Preferences… pushbutton in the Display Attributes control panel to
access the Style Preferences control panel. Check or uncheck the
Show Principal Axes check box.
Similarly, to show or hide bonds, check or uncheck the Show
Bonding check box.
Size of ellipsoids
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You can define a scaling factor for the display size of thermal ellipsoids. A value of 1.0 corresponds to an ellipsoid whose radius at
any point on the surface is equal to the root mean square (rms)
atomic vibration in that direction. At a scaling factor of 1.0, the
Cerius2 Modeling Environment/April 1999