May 2015

SSE Bounds in Pymol cartoon

The segments Pymol draws as a broader ribbon are slightly shorter than the corresponding ranges of strand and helix given in the input file. They might be shorter by 1 residue on each end. This is more evident with color by SSE: the color boundaries extend beyond the ends of the broader segments in the cartoon.

Below are images for the same PDB file in Pymol and Chimera colored by SSE (helix red, coil green, strand yellow). This is PDB 4r0b, the same molecule as in example 2 in the main ribbon writeup. Cartoon style is Pymol default, Chimera default except edged strands. Images from left to right are Pymol, Chimera B spline, and Chimera cardinal spline with strand smoothing (Chimera b40577 12 May 2015). The cardinal spline helices look a bit sad. Cardinal spline helices improved in Chimera b40583 13 May 2015, fourth image.