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://rbvi.ucsf.edu/chimerax/docs/user/tools/colorzone.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> 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

Hi Andrew, That is still not clear, since there is no surface shown in your image, and I don't know what commands/data were used to show a surface. Also if ChimeraX worked before, but not today, it doesn't really make sense to me, and I would guess that something about the data or how you displayed it must be different. Again, we would need more details like ALL of the commands you used, what it looked like, and (at least in words) what you expected it to look like. You could even attach a session file if you are willing to share your data publicly. To see what color the atoms are, display them. E.g. command show atoms You can hide them again, e.g. command hide atoms If you have a map isosurface, you would use color zone. Maybe your zone distance is too small if your isosurface is not very close to the atoms, and you could try using a larger value, or you are not specifying correctly which atoms to use. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> If you have a molecular surface (not a map surface) you can make it match the atomic colors by using "fromatoms" as the color name: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Aug 21, 2025, at 2:41 PM, Andrew Mugo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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, AndrewFrom: 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 [You don't often get email from meng@cgl.ucsf.edu. Learn why this is important athttps://aka.ms/LearnAboutSenderIdentification ]

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....> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....>

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

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