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, and can only be shown for atoms that are also displayed. 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. See also: Axes/Planes/Centroids, Render by Attribute, measure inertia, 3D object formats, the ChimeraX thermal ellipsoids highlight
The Thermal Ellipsoids tool can be started from the Structure Analysis section of the Tools menu and can be manipulated like other panels (more...). It is also implemented as the aniso command. Anisotropic B-factor depictions are saved in sessions.
Atomic models with anisotropic B-factors are listed in the menu near the top right of the dialog. If more than one such model is open, the model to act on should be chosen from the menu.
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. Display tip: Since the ellipsoids may be obscured when atoms are shown as balls or spheres, using a thin stick representation is recommended (see style and size).
Clicking Show after entering a value creates or updates the depictions; clicking Hide removes them. When the Restrict Show/Hide... option is on and atoms are selected, only the depictions of the selected atoms in the chosen model will be shown or hidden. Otherwise (Restrict... option not used or no atoms selected), clicking Show removes any pre-existing depictions and generates new ones for the chosen model. Regardless of whether the Restrict... option is on, however, the settings are applied to all atoms of the chosen model even if their depictions are not displayed. Atoms can be displayed without their anisotropic depictions, but the anisotropic depiction for an atom cannot be displayed unless its atom is displayed.
The Presets menu in Thermal Ellipsoids includes several predefined combinations of style settings. Those listed below are built-in, and more can be defined by the user. Presets do not include scaling and smoothing settings, which are specified independently. Choosing a preset from the menu applies its settings immediately. See also: aniso preset