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.

Photosynthetic Reaction Center

The photosynthetic reaction center from a purple sulfur bacterium is shown as a cartoon with “tube” helices and membrane boundaries from the OPM database (Orientations of Proteins in Membranes, entry 1eys). Blue and red balls represent the cytoplasmic and periplasmic sides of the bacterial inner membrane, respectively. The title and other text labels were added with the 2dlabels command and repositioned interactively with the move label mouse mode . ChimeraX session file: prc.cxs

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