Figure 1.

An example of the chain smoothing process. The protein is the chromophore-binding domain of bacterial phytochrome (1ZTU). The X-ray structure of 1ZTU (left) is shown in the cartoon representation and two progressively smoothed chains are shown (center and left). The color is ramped by residues from blue at the N-terminus (labeled by N) to red at the C-terminus (labeled by C). The crossover points are numbered sequentially from the N-terminus. The figure-eight knot is characterized by four crossover points, alternately under and over. The structural pictures are produced using Pymol (Delano Scientific, San Carlos, http://pymol.sourceforge.net/).