Adjustable β-Strand Smoothing

Cartoon ribbons are drawn to pass through the exact positions of peptide α-carbons in helix and coil, but by default, strands are smoothed to appear less ripply. This means that α-carbons in strands may not fall on the ribbon. A tether is drawn wherever a sidechain is displayed but would otherwise be detached from the ribbon. (Tether appearance can be adjusted with cartoon tether.)

However, β-strand ribbon smoothing can be tuned continuously between zero (off) and 1.0 (default, fully on), and this can be done for all residues or for specific residues only. The image compares ribbon positions for residues 139 and 164 in the active site of mandelate racemase (PDB 2mnr) with and without smoothing. The unsmoothed position (transparent blue) can be obtained with:

cartoon :139,164 smooth 0

This leaves ribbon smoothing at other residues unchanged. Values between 0 and 1 would give intermediate positions.

Calmodulin and Target Peptide

Calmodulin (CaM) acts as a calcium sensor. When its four Ca++ sites are fully occupied, it binds and modulates the activity of various downstream proteins, including CaM-dependent protein kinase I (CaMKI). Here, a complex between CaM and its target peptide from CaMKI (PDB 1mxe) is shown with cartoons, a transparent molecular surface, silhouette outlines, and light soft ambient occlusion. (If you prefer a less smudgy/rustic appearance, try using light gentle instead.) For image setup other than positioning, see the command file cam.cxc.

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