equivalent command for coloring elements specific colors?
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
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
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
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
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Liz Kellogg