Thermal Ellipsoids Thermal Ellipsoids icon

Thermal Ellipsoids generates ellipsoids to show atomic anisotropic B-factors. Anisotropic B-factors are read from the input coordinate file (for example, from ANISOU records in a PDB file) and are included with only certain high-resolution structures. Thermal ellipsoids will be created only for atoms with such information. 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. See also: Render by Attribute, Axes/Planes

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


Clicking Show Ellipsoids or pressing return after entering a smoothing or scaling factor creates ellipsoids; clicking Hide Ellipsoids removes them. When the Restrict... option is on and atoms are selected, showing and hiding will affect only the ellipsoids of the selected atoms. Otherwise, showing ellipsoids will remove any pre-existing ellipsoids and generate new ones for just the currently displayed atoms.

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


Not saved in sessions. The ellipsoids and dialog settings are not included in Chimera session files.

UCSF Computer Graphics Laboratory / August 2009