The aniso command shows atomic anisotropic B-factors as ellipsoids, their principal axes, and/or their principal ellipses, according to options that can be adjusted with aniso style and aniso preset. These special depictions are created only for atoms with anisotropic B-factor information, and can only be shown for atoms that are also displayed.
The command ~aniso or aniso hide removes the depictions. Whereas aniso and ~aniso can show and hide the depictions for a subset of the displayed atoms in a model, settings applied with aniso style and aniso preset are per-model, in that they apply to all atoms in a model even if only part of the model is specified in the command. If given without options, aniso style reports in the Log the current anisotropic display settings of each applicable model in model-spec (where a blank specification indicates all, as per the usual convention).
Aniso presets are predefined sets of anisotropic style settings. Given without arguments, the aniso preset command lists the names of the existing presets in the Log. Given with a preset-name, aniso preset applies the preset to each applicable model in model-spec (where a blank specification indicates all, as per the usual convention). Several presets are built in, and the current anisotropic style settings of a model can be saved as a new preset with aniso preset save; if multiple models are specified with with this command, they must all have the same anisotropic style settings. A previously saved user-defined preset can be removed with aniso preset delete.
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.
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.