Thermal Ellipsoids Thermal Ellipsoids icon

1a6m ellipsoids

Thermal Ellipsoids shows atomic anisotropic B-factors as ellipsoids, their principal axes, and/or their principal ellipses. These special depictions are created only for atoms with anisotropic B-factor information. Anisotropic B-factors are read from the input coordinate file (from ANISOU records in a PDB file or the analogous in CIF/mmCIF) and are included with only certain high-resolution structures. Ellipsoid axes and radii correspond to the eigenvectors and eigenvalues of the atomic mean-square displacement matrix. The radii are proportional to the root-mean-square displacements (RMSDs), the square roots of the eigenvalues.

Anisotropic B-factor depictions are surface models and are included in saved sessions. See also: Render by Attribute, Axes/Planes/Centroids, geometric objects

There are several ways to start Thermal Ellipsoids, a tool in the Structure Analysis category. It is also implemented as the command aniso.

The Presets menu in Thermal Ellipsoids provides quick access to several predefined combinations of the following options: Clicking Show Ellipsoids or pressing return after entering a value creates the depictions; clicking Hide Ellipsoids removes them. When the Restrict Show/Hide... option is on and atoms are selected, showing and hiding will affect only the depictions of the selected atoms. Otherwise, clicking Show Ellipsoids removes any pre-existing depictions and generates new ones for just the currently displayed atoms.

Close dismisses the dialog, and Help opens this manual page in a browser window.

Thermal Ellipsoid Presets

The Presets menu in Thermal Ellipsoids includes several predefined combinations of style settings:

Presets do not include scaling and smoothing settings, which are specified independently. Choosing a preset from the menu applies its settings immediately. Users can apply a built-in preset and then make further adjustments, or define and use their own custom presets:

Display Tip

Since the ellipsoids may be obscured when atoms are shown as balls or spheres, using a wire or thin stick representation is recommended. Sticks can be made thinner by decreasing the molecule stick scale attribute, for example with the command:
setattr m stickScale 0.5

UCSF Computer Graphics Laboratory / March 2010