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.
Unless restricted to certain atoms with the spec option, the command aniso removes any pre-existing anisotropic B-factor depictions and generates new ones for just the currently displayed atoms. The command ~aniso removes the depictions.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.
spec atom-spec
Create/remove anisotropic B-factor depictions for just the specified atoms. Depictions will be created only for atoms that are also displayed.
scale factor
Adjust the size of the depictions 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 1.53818. The Thermal Ellipsoids interface can be used to calculate the scaling factor for any probability ≥ 0% and < 100%.
smoothing level
The level (default 3) controls how many planar facets are used to draw ellipsoids and ellipses. Higher values give smaller facets and a smoother appearance.
showEllipsoid true|false
Whether to display ellipsoids.
color colorname
Color to use for ellipsoids, where the colorname can be none (default, meaning to match the corresponding atoms) or any color name that specifies a single color.
transparency percent
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.
axisFactor factor
Length of principal axis depictions, specified as a multiplicative factor relative to ellipsoid size. If axisFactor is not specified, principal axes will not be depicted.
axisThickness d
Principal axes are depicted as rods with square cross-sections, where d is the side length of the square (default 0.01 Å).
axisColor colorname
Color to use for principal axis depictions, where the colorname can be none (default, meaning to match the corresponding atoms) or any color name that specifies a single color.
ellipseFactor factor
Size of principal ellipse depictions, specified as a multiplicative factor relative to ellipsoid size. If ellipseFactor is not specified, principal ellipses will not be depicted.
ellipseThickness d
Thickness of principal ellipse depictions (default 0.02 Å).
ellipseColor colorname
Color to use for principal ellipse depictions, where the colorname can be none (default, meaning to match the corresponding atoms) or any color name that specifies a single color.