Coloring by Sequence Conservation

Atomic structures, including cartoons and molecular surfaces, can be colored by the conservation in an associated multiple sequence alignment. The figure shows a structure of the β₂-adrenergic receptor signaling complex (PDB 3sn6) with receptor cartoon colored blue→white→red from least conserved to most conserved. The β₂-adrenergic receptor is a member of the class A G-protein-coupled receptor superfamily. Conservation was calculated from a superfamily alignment from PASS2 using the entropy-based measure from AL2CO (included with ChimeraX courtesy of Pei and Grishin). The sequence alignment and step-by-step instructions for making this image are given in the Coloring by Sequence Conservation tutorial.

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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