Dear Elaine, many thanks, with the information in your last email I was able to modify the pdb input. Now the colouring works separately for all residues. For a program update it would be nice to include an option to designate selected parts as residues in the program itself. Thanks again and best wishes, Michael Am 13.04.2026 um 17:59 schrieb Elaine Meng:
Hi Michael, I don't know what input file format you used, but if PDB we have a basic description of that format here: <https://rbvi.ucsf.edu/chimerax/docs/user/formats/pdbintro.html>
You would just edit the file in a text editor of your choice. You could display atom names as labels in ChimeraX (e.g. command: label #1 atoms), and from looking at that decide how to group them into residues. It might be as simple as just incrementing the residue number in the atom coordinates section (ATOM or HETATM rows). I guess you would need a residue for each different color of ring fill, and of course put atoms in the same ring in the same residue.
However, this might be a pain if you aren't familiar with editing PDB files. Another approach might be to split it up like you did and then also display an additional copy of the non-split one to get the appearance of bonds between the split parts.
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 13, 2026, at 1:08 AM, Michael Moos via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine, 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? best wishes, Michael Am 10.04.2026 um 17:57 schrieb Elaine Meng:
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": <Screenshot 2026-04-10 at 8.53.29 AM.png>
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/