[Chimera-users] Helix Display Artefact

Elaine Meng meng at cgl.ucsf.edu
Tue Dec 28 09:21:24 PST 2021

Hi Sebastian,
This may not be easy to circumvent, i.e. may simply be a pathological case for how the ribbon orientation is calculated.   As you said, the problem is not of secondary structure assignment, since it's defined as helix, just drawn strangely.   

Without actually seeing the atomic coordinates, my guess is that the carbonyl is tipped outward.  You could move the carbonyl O to a more "canonical" location and see if that helps.  Or (equivalently) replace that stretch of residues with another for which the ribbon is drawn nicely.

In the Ribbon Style Editor (in menu under Tools... Depiction) in the Residue Class tab you can see that the orientation atom for amino acids is O.  I don't think there are any other good choices for standard amino acids... editing the Class settings is more for when you have different polymers e.g. beta-amino acids.  The documentation says a bit more about how the atoms are used in drawing the ribbon:

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Dec 28, 2021, at 8:44 AM, Sebastian Guettler via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Dear Chimera users,
> I have a problem with what I think is some sort of a helix display artefact is UCSF Chimera (including the latest release, 1.16). I attach an image. In cartoon display, the helix appears turned inside out for the last turn. It is displayed normally in ChimeraX and PyMol, and the display problem is independent of the secondary structure assignment algorithm (dssp, ksdssp, Stride). Any suggestions on how to solve this issue are welcome.
> Thank you,
> Sebastian
> ---------------------------------------------
> Sebastian Guettler, PhD
> Team Leader
> The Institute of Cancer Research (ICR)
> Divisions of Structural Biology and Cancer Biology
> London, UK
> ---------------------------------------------
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