### Thermal Ellipsoids

**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**.

Options:

**Ellipsoid color**
(a color well,
default **No Color**, meaning to match the corresponding atoms)
**Smoothing factor** (default **1**)
- controls how many planar facets are used to draw each ellipsoid; higher
values give smaller facets and smoother ellipsoids
**Scaling factor** (default **1.0**, no scaling)
- controls ellipsoid size, where the unscaled ellipsoid radii
equal the atomic RMSDs along the ellipsoid axes
**Set scaling factor for probability (%)** [*P*]
- automatically fills in the **Scaling factor** field
for a specified % probability *P*
(press return after typing in a value;
*P* must be ≥ 0% and < 100%)

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.

### Limitations

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

UCSF Computer Graphics Laboratory / August 2009