cartoon (ribbon) helix inside-out problems

[Elaine Meng]

In the current ChimeraX it is fairly common to see places where the helix cartoon (ribbon) turns inside out. Or to describe this another way, one edge of the ribbon should consistently track the carbonyls, but instead there is a twist so that the carbonyl edge in one part of the helix is not the carbonyl edge in another part.

The attached ChimeraX script shows this in a couple of examples: 2mnr (see residue ranges 88-93,259-261,286-290 highlighted with color) and 2gbp (56-58,223-225,272-274). It is not hard to find examples. These are just some proteins I was looking at in more detail and for which I'd noted the residue numbers of the problem areas.

[Conrad Huang]

The problem is "fixed". I think the issue is that the orientation of the last residue in those helices are not consistent with the rest of the helix. Essentially, the ribbon has to twist almost 90 degrees between the next-to-last and last residues. Previously, the ribbon twisted in such a way that the "carbonyl edge" did not line up with the carbonyl in the last residue. The current code keeps the same edge toward the carbonyls for the last residue. Unforunately, it still doesn't look very good since there is still severe twisting, but at least it's in the correct direction.

[Elaine Meng]

Perhaps the orientation (C=O) of the C-terminal residue in a helix should be ignored since its C=O is beyond the SSE anyway, i.e. its participation in helix H-bonding is from its N-H.

Examples
2gbp :58,225,274
3fx2 :147,148

Analogous situations can occur at the end of a strand or at a bulge within a strand, where the C=O (actually the CONH unit forming the subsequent peptide bond) is not participating in the sheet H-bonding.

Examples
2gbp :9,61,176,147,210,234,251
3fx2 :120-122