Hi Elaine,

Thank you for your quick reply.

I am sorry for not be very clear.

I colored my model as shown in the attached file using command line.

I want to color the corresponding isosurface map to match the model color: I use the color zone command or 'color map to match atoms' on the chimeraX (Map-appearance).

The isosurface map color changes to red/green or doesn't change.

How do I know if the undisplayed are actually colored by element?

My ChimeraX always works except today.

Best regards,

Andrew

From: Elaine Meng <meng@cgl.ucsf.edu>
Sent: Thursday, August 21, 2025 5:12 PM
To: Andrew Mugo <anmugo@buffalo.edu>
Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Model-Map coloring using the ChimeraX

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Hi Andrew,
I can't tell from your message exactly what you did or what you want.

Do you mean that you have atomic structure and you want to make a map isosurface have the same color(s) as the nearby atoms? If so you would use the Color Zone tool or "color zone" command.
<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fcolorzone.html&data=05%7C02%7Canmugo%40buffalo.edu%7Cfaad0f8e03674feaa6d908dde0f77323%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638914075589083367%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=%2F15dLolaT7KJQ9gZDlZUs3oxGtOuSu%2Fw6HZF1tQlXas%3D&reserved=0>
<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fcolor.html%23zone&data=05%7C02%7Canmugo%40buffalo.edu%7Cfaad0f8e03674feaa6d908dde0f77323%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638914075589104705%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=LfQo4tpPZJXg1HsApiv9NhStkD1S7HV595AmU0H6%2FRs%3D&reserved=0>

Maybe you are displaying ribbons for the atomic structure and you didn't realize that the atoms which might be undisplayed are actually colored by element, which would include red for oxygen, blue for nitrogen, etc. Color zone will match atomic colors (not ribbon color).

If this is not what you are asking about, please give more detailed information.

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

> On Aug 21, 2025, at 1:56 PM, Andrew Mugo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear ChimeraX user support team,
>
> I am having a problem of coloring map based on the model color.
> I uninstalled and re-installed ChimeraX 1.9/1.10 but when I try to color the map, the software gives electrostatic color like.
>
> Please let me know how I can solve this problem.
>
> Best regards,
> Andrew