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

[Liz Kellogg]

oh yes! thanks so much! how neat!

On Thu, May 30, 2019 at 7:19 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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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>
>
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