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.

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

More images...