**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.
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.

Anisotropic B-factor depictions are
surface models
and are included in saved sessions.
See also:
**Render by Attribute**,
**Axes/Planes/Centroids**,
geometric objects

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

**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**(a color well, default**No Color**, meaning to match the corresponding atoms)**Transparency**(a menu including**same as color**and several percentage transparency options)

**Depict principal axes**- whether to show ellipsoid principal axes**Color**(a color well, default**No Color**, meaning to match the corresponding atoms)**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**(a color well, default**No Color**, meaning to match the corresponding atoms)**Size factor**(default**1.0**) - size of principal ellipse depictions relative to ellipsoid size**Thickness**(default**0.02**Å) - thickness of principal ellipse depictions

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

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

**Simple ellipsoid**- ellipsoids only, color from atoms**Principal axes**- axes only (length factor 1.0)**Principal ellipses**- ellipses only (size factor 1.0)**Ellipsoid and principal axes**- ellipsoids with axes (length factor 1.5)**Octant lines**- ellipsoids with black ellipses (size factor 1.01)**Snow globe axes**- white half-transparent ellipsoids with axes (length factor 0.99)**Snow globe ellipses**- white half-transparent ellipsoids with ellipses (size factor 0.99)

**Preset from current settings...**save a custom preset with the current style settings to the**preferences**file**Delete user preset...**remove a previously user-defined preset

setattr m stickScale 0.5

UCSF Computer Graphics Laboratory / March 2010