6.4 Setting Ellipsoid Display Options

Displacement ellipsoids can be displayed for structures where the CIF or SHELX res file contains Atomic Displacement Parameter values (Uequiv and Uij values) (see Section 6.2.1):

Click on Display in the top level menu, then Styles and Ellipsoid Settings... from the resultant pull-down menus. This will open the Ellipsoid Display Options window which can be used to customise various settings.

Probability level (%): use this to alter the probability level (thus size) the ellipsoids are displayed at. For crystal structures determined from neutron diffraction data or at low temperature, you may want to increase the probability level; for structures determined at high temperature, you may want to reduce the probability levels.

Draw hydrogens as fixed-size spheres: use this tick box to control the display of H atoms.

The Draw principal ellipses and Draw Non-Positive-Definite atoms as cubes tick boxes can be switched on or off to enable or disable the specified functionality. A non-positive-definite atom is termed as such when the corresponding ellipsoid cannot be represented in real space, e.g. the ellipsoid may have a negative volume. Non-positive-definite atoms therefore highlight a problem with the data, e.g. a particular element may have been determined as a carbon atom but it is in fact a nitrogen atom.

Bonds can either be represented as Wireframe or Stick.

The settings are saved between Mercury sessions. Use the Defaults button to return to the standard settings.