**Aniso** is the command-line implementation of
**Thermal
Ellipsoids**, which shows atomic anisotropic B-factors
as ellipsoids, their principal axes, and/or their principal ellipses.
These special depictions will be 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.

Some predefined
combinations of settings are available from the **Presets** menu in the
**Thermal
Ellipsoids** graphical interface.

See also:
**define**,
**measure inertia**,
**Render by
Attribute**,
geometric objects

**Tip**: Since the ellipsoids may be obscured when atoms are shown as
balls or spheres, using a wire or thin stick
representation is recommended
(see **represent**,
**linewidth**).
Sticks can be made thinner by decreasing the molecule stick scale attribute,
for example with the command:

setattr m stickScale 0.5

Option keywords for **aniso** are case-independent
and can be truncated to unique strings.
A vertical bar "|" designates mutually exclusive options, and
default values are indicated with **bold**.
Synonyms for true: True, 1. Synonyms for false: False, 0.

specatom-spec

Create/remove anisotropic B-factor depictions for just the specified atoms. Depictions will be created only for atoms that are also displayed.

scalefactor

Adjust the size of the depictions by a constantfactor(default1.0, no scaling). The unscaled ellipsoid radii equal the atomic RMSDs along the ellipsoid axes. The scaling factor for 50% probability is 1.53818. TheThermal Ellipsoidsinterface can be used to calculate the scaling factor for any probability ≥ 0% and < 100%.

smoothinglevel

Thelevel(default3) controls how many planar facets are used to draw ellipsoids and ellipses. Higher values give smaller facets and a smoother appearance.

showEllipsoidtrue|false

Whether to display ellipsoids.

colorcolorname

Color to use for ellipsoids, where thecolornamecan benone(default, meaning to match the corresponding atoms) or any color name that specifies a single color.

transparencypercent

Ellipsoid transparency expressed as a percentage, where 0% is completely opaque and 100% is completely transparent. If not specified, the transparency (if any) of the ellipsoid color(s) will be used.

axisFactorfactor

Length of principal axis depictions, specified as a multiplicativefactorrelative to ellipsoid size. IfaxisFactoris not specified, principal axes will not be depicted.

axisThicknessd

Principal axes are depicted as rods with square cross-sections, wheredis the side length of the square (default0.01Å).

axisColorcolorname

Color to use for principal axis depictions, where thecolornamecan benone(default, meaning to match the corresponding atoms) or any color name that specifies a single color.

ellipseFactorfactor

Size of principal ellipse depictions, specified as a multiplicativefactorrelative to ellipsoid size. IfellipseFactoris not specified, principal ellipses will not be depicted.

ellipseThicknessd

Thickness of principal ellipse depictions (default0.02Å).

ellipseColorcolorname

Color to use for principal ellipse depictions, where thecolornamecan benone(default, meaning to match the corresponding atoms) or any color name that specifies a single color.