Chimera Commands Index

aniso [ spec atom-spec ] [ color colorname ] [ scale factor ] [ smoothing level ]

~aniso [ spec atom-spec ]

Aniso is the command-line implementation of Thermal Ellipsoids, which 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.

Unless restricted to certain atoms with the spec option, the command aniso removes any pre-existing ellipsoids and generates new ones for just the currently displayed atoms. The command ~aniso removes ellipsoids.

Option keywords for aniso are case-independent and can be truncated to unique strings:

spec atom-spec
Create/remove ellipsoids for just the specified atoms. Ellipsoids will be created only for atoms that are also displayed.
color colorname
Color to use for the ellipsoids. The colorname can be none (default, meaning to match the corresponding atoms) or any color name that specifies a single color.
scale factor
Adjust the size of the ellipsoids by a constant factor (default 1.0, no scaling). The unscaled ellipsoid radii equal the atomic RMSDs along the ellipsoid axes. The scaling factor for 50% probability is 1.5382. The Thermal Ellipsoids interface can be used to calculate the scaling factor for any probability ≥ 0% and < 100%.
smoothing level
The level (default 1) controls how many planar facets are used to draw each ellipsoid. Higher values give smaller facets and smoother ellipsoids.

See also: measure inertia, Render by Attribute, Axes/Planes