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.

Cyclodextrin Pore

The outer-membrane protein CymA admits bulky molecules into the periplasmic space of Klebsiella oxytoca. Here, CymA (PDB 4d5d chain A) is depicted in a style reminiscent of a diagnostic X-ray, with transparent molecular surface and β-strand “ribs” in white. The protein has ingested α-cyclodextrin (top) and β-cyclodextrin (bottom), bound at the entry site and near the exit, respectively. Cyclodextrin carbon atoms are shown in blue-gray and oxygen atoms in brick red. For image setup, see the command file xray.cxc.

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