[chimerax-users] Showing C-alphas

[Elaine Meng]

Hi Casey,
I assume you are also showing ribbons (cartoons).

By default, showing cartoons suppresses the display of the amino acid backbone atoms.  You can turn that off and allow showing both ribbon and backbone atoms at the same time with the "suppress false" option, for example:

cartoon suppress false

Then you can hide/show individual backbone atoms however you want regardless of the presence of ribbons.

However, the ribbon position in strands is smoothed so the CA may not be quite on the ribbon, and you will see a "tether"  drawn between its position and that of the ribbon.  Ways around it are to smooth strands less (also an option of the "cartoon" command) and/or to make the CA balls a little bigger so that they still overlap the ribbon.

These issues are explained in the "cartoon" (aka "ribbon") command help:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html>

... see options "smooth" and "suppressBackboneDisplay" ("suppress" for short).
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 30, 2021, at 10:57 AM, Casey via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> I am trying to show a single sphere at c-alpha carbons for some point mutants that i designed. When I use the command:
> show /a:473,476,477 atoms
> I can see all the atoms in chain A for residues 473, 476, 477.
> Using: show /a:473,476,477 at cb atoms
> I can show "two spheres" for the c-alpha and c-beta carbon.
> When I use:
> show /a:473,476,477 at ca atoms nothing happens and i don't see any spheres.
> 
> If I show the full atom and then do:
> hide /a:473,476,477 at ca* atoms
> 
> Just the c-alpha sphere gets hidden. 
> 
> Why is it that i can't just show the c-alpha spheres? Unfortunately for my figure i make silhouettes of my model and so i can't just hide the other atoms by making them fully transparent