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