[chimerax-users] equivalent command for coloring elements specific colors?

[Elaine Meng]

Hi Liz,
The “at” symbol is for atom names (in both Chimera and ChimeraX), so the commands you gave would work only to color the atoms actually named O and N in the backbone, which are usually hidden when ribbon is shown (in both Chimera and ChimeraX).

You’re almost there — all you have to do to get the element in either program is to omit the “at” symbol.  In ChimeraX:

color O red targ a
color N blue targ a

Also command “color byelement” colors all atoms by element, “color byhet” all atoms except carbons, both using the stereotyped element colors:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/colortables.html#element>

Atom specification (by element or other things…)
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>

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

> On May 30, 2019, at 4:17 PM, Liz Kellogg <lizkellogg at gmail.com> wrote:
> 
> Oh, I get it now. O and N refer to backbone atoms only, so to color sidechains I would have to refer to each sidechain nitrogen and oxygen group specifically. Any shortcut for this in ChimeraX? Do I have to define a named selection?
> 
> On Thu, May 30, 2019 at 7:06 PM Liz Kellogg <lizkellogg at gmail.com> wrote:
> Hi, 
> 
> There used to be this handy command in Chimera to color oxygen atoms and nitrogen atoms specific colors:
> 
> color @O red,a 
> color @N blue,a
> 
> but I can't find the corresponding command in ChimeraX. Is there a way to color all nitrogen atoms blue and all oxygen atoms red?
> When I try what I think the equivalent command should be (I'm displaying cartoon backbone with stick side chains):
> color @O red target a
> color @N blue target a
> 
> it says 'Colored 1120 atoms' but none of the sidechains are colored differently.
> 
> Thanks for the help
> 
> Liz
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