Thermal Ellipsoids

Anisotropic B-factor data can be shown as thermal ellipsoids, axes, or ellipses with the aniso command or the Thermal Ellipsoids tool. The image shows myoglobin structure 1jw8 with thermal ellipsoid representations of the heme residue and protein sidechains that ligate or form H-bonds with the heme. Metal coordination bonds are shown as purple dashed lines and H-bonds as gold dashed lines.

For image setup other than position, see the command file myo-aniso.cxc (requires ChimeraX version 1.10 from February 2025 or newer).

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B-factor Coloring

Atomic B-factor values are read from PDB and mmCIF input files and assigned as attributes that can be shown with coloring and used in atom specification. This example shows B-factor variation within a structure of the HIV-1 protease bound to an inhibitor (PDB 4hvp). For complete image setup, including positioning, color key, and label, see the command file bfactor.cxc.

Additional color key examples can be found in tutorials: Coloring by Electrostatic Potential, Coloring by Sequence Conservation

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