[chimerax-users] remove the lines between C-alpha atoms in a helix

[Elaine Meng]

Hi Steve,
(1) there are multiple ways to hide these, but one way is to look in Model panel, use the disclosure triangle on the top-level model to list the "chain trace" submodel.  You can uncheck its "Shown" box, or you can close it.  After you do whichever one you want, look in the Log to see the equivalent command in case you prefer to use a command in the future.

(2) yes you can rainbow a subset of the chain, exactly as you said.  Did you try that command?  If it didn't work how you wanted, get a newer ChimeraX version.  This capability was added in November 2020.
<https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog>

(3) sorry no, there is no separate helix inside color for ribbons in ChimeraX currently... there is a ticket to add it:
<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/1719>

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

> On Apr 12, 2022, at 9:14 AM, Steve Chou via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear ChimeraX users,
> 
> Question 1:
> When I display the C-alpha atoms in a helix as spheres, I always get lines connecting these atoms. Is there a way to remove/hide the lines?
> show /A:1-15 at CA target a
> 
> Question 2:
> Is it possible to just color a helix, not a whole chain, in a rainbow?
> rainbow /A:1-15 at CA
> By default, the rainbow spans the whole chain (residues 1-200), and residues 1-15 are colored from red to orange. Is it possible to color residues 1-15 from red to blue?
> 
> Question 3:
> Is it possible to color a helix in two colors - the outside (e.g., red) and inside (e.g., white) in different colors?
> 
> Many thanks in advance!
> Steve