[chimerax-users] Ribbon coloring

[Elaine Meng]

Hi Xavier,
In ChimeraX the ribbon shape changes at the CA atom, but the ribbon color changes at the peptide bond;  I believe some other programs also do it this way.  In Chimera, however, this is not an issue: the color changes at the same place that the ribbon shape changes, at the peptide bond.

See attached screenshot with Chimera image on top, ChimeraX below.

However, there is a partial solution.  There is a currently undocumented option in "cartoon style" ... it is "ssEnds long" (default "ssEnds short").  However, this only extends the shape to the peptide bond at the C-terminal end of each helix and strand. There were technical reasons that it did not work for the N-terminal ends, so the option is not very satisfying and that is one reason it is not described in the help page currently.  However, you can try

cartoon style ssEnds long

and see if that is good enough for you.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco




In ChimeraX after "cartoon style ssEnds long" the helix shape extends to the peptide bond on the right (C-term end of helix) but not the N-term peptide bond on teh left:

> On Nov 29, 2022, at 6:57 AM, F.Xavier Gomis-Rüth via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine,
> when coloring a helix differently from the attached coils, is there a means to prevent the first short segment of the coil
> to get the color of the helix? It seems to me there was some kind of "halfbond"-mode one...
> Best,
> Xavier
> -- 
> <fxgr_signanew.jpg>
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