Tool: Thermal 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, 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.

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Display Settings

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).

• Scale factor (default 1, no scaling) – controls ellipsoid size, where the unscaled ellipsoid radii equal the atomic RMSDs along the ellipsoid axes
• Smoothing level (default 3) – controls how many planar facets are used to draw ellipsoids and ellipses; higher values give smaller facets and a smoother appearance
• Set scale factor for probability (%) [P] – automatically fills in the Scale factor field for a specified % probability P (press return after typing in a value; P must be ≥ 0% and < 100%)

• Depict ellipsoids – whether to show ellipsoids
  • Color – whether to use atom color or that in the color well (click to change the color interactively)
  • Transparency (a menu including same as color and several percentage transparency options)
• Depict principal axes – whether to show ellipsoid principal axes
  • Color – whether to use atom color or that in the color well (click to change the color interactively)
  • Length factor (default 1.5) – length of principal axis depictions relative to ellipsoid size
  • Thickness (default 0.01 Å) – thickness of principal axis depictions (dimensions perpendicular to length)
• Depict principal ellipses – whether to show ellipsoid principal ellipses
  • Color – whether to use atom color or that in the color well (click to change the color interactively)
  • Size factor (default 1.0) – size of principal ellipse depictions relative to ellipsoid size
  • Thickness (default 0.02 Å) – thickness of principal ellipse depictions

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Thermal Ellipsoid Presets

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

• axes – axes only (length factor 1.0)
• ellipses – ellipses only (size factor 1.0)
• octant – ellipsoids with black ellipses (size factor 1.01)
• simple – ellipsoids only, color from atoms
• simple-axes – ellipsoids with axes (length factor 1.5)
• snowglobe-axes – white half-transparent ellipsoids with axes (length factor 0.99)
• snowglobe-ellipses – white half-transparent ellipsoids with ellipses (size factor 0.99)

Presets do not include scaling and smoothing settings, which are specified independently. Choosing a preset from the menu applies its settings immediately.

Users can create their own custom presets by saving the current settings with the command aniso preset save, and such user-defined (not built-in) presets can be removed with aniso preset delete.