oh yes! thanks so much! how neat! On Thu, May 30, 2019 at 7:19 PM Elaine Meng <meng@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@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@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users