thanks for the answer. I am not really sure about how to modify the input file. Is there an example file for creating residues (what headers should be included and what form is necessary)? Is it possible to export selected parts of the molecule to get an idea what atoms in the input file should be part of a residue?

Hi Michael,
You can definitely have different fill colors for different residues in the same atomic model. However, I believe there is one color per residue. So you wouldn't necessarily need to cut the molecule, but to rename/renumber parts of it as different residues, and then specify them by residue name or number, e.g.

color blue :1 targ f
color yellow :2 targ f

etc. where "targ f" means to color just the fill of residues 1,2, ... Or you could select the residue and then click the green magnifying glass icon in the top bar and use the "Selection Inspector" dialog to inspect the residue and then change the "Ring fill color":

However, I don't know of any easy way to do such renaming/renumbering parts of one big residue into multiple smaller residues... only somewhat tedious text-editing of the input file.

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 Apr 10, 2026, at 1:43 AM, Michael Moos via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hello,
>
> I try to color different parts of a molecular chain and am stuck with the problem that I can not define the fill color individually for the selected parts. The color is valid for the selected sticks but fill color changes for the whole molecule. Is there a solution for this problem? It works if I cut the molecule in different parts but I would like to keep it as whole.
>
> The program itself is very nice and I prefer to use it for displaying long molecules. A color code would be necessary for marking the different parts of the molecule for better visualization (see attached file).
>
> Kind regards,
>
> Michael
>
> --
> Dipl. Chem. Michael Moos
> Universität Würzburg
> Institut für Organische Chemie
> Lehrstuhl für Physikalische Organische Chemie
> AK Prof. Lambert
> Am Hubland C1
> 97074 Würzburg
>
> Phone: +49931 31 88764
> Fax: +49931 31 88764-0
> Web: https://www.chemie.uni-wuerzburg.de/oc/lambert-group/

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