The aniso command 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.
The command ~aniso or aniso hide removes the depictions.
See also: define, measure inertia, nucleotides, Render by Attribute, 3D object formats
Tip: Since the ellipsoids may be obscured when atoms are shown as balls or spheres, using a thin stick representation is recommended (see style and size).
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.
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 (default true).
color color-spec | none
Color to use for ellipsoids, where none (default) means to match the corresponding atoms.
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 color 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 color-spec | none
Color to use for principal axis depictions, where none (default) means to match the corresponding atoms.
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 color-spec | none
Color to use for principal ellipse depictions, where none (default) means to match the corresponding atoms.