Hi Elaine,

rainbow #1.5-23 structures palette blue:orange

This is exactly what I was looking for! Thank you very much for your help. The ligand positions are a part of a trajectory but were (for analysis reasons) saved in a .pdb file, which is why ChimeraX read it as submodels instead of trajectories. Cheers, Lorena ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 23 May 2022 18:19 To: Lorena Zuzic <lorena.zuzic@chem.au.dk> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Colouring submodels using a palette Hi Lorena, Atomic models, regardless of whether they are models, submodels, subsubmodels ... are "structures" -- you just need to specify which ones to color, if there are other models also present that you don't want to color. E.g. if you have models #1-3 but only want to color submodels of #1, something like: rainbow #1 structures palette blue:orange ...or to act on specific submodels #1.5 to #1.23 only, something like: rainbow #1.5-23 structures palette blue:orange See rainbow documentation: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sequential> I'm going from your description that these ligand positions are really submodels. If this was opened as a trajectory in ChimeraX, the commands above would not work since the time steps are not different models (or submodels). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On May 23, 2022, at 6:04 AM, Lorena Zuzic via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi all,

I have a model that contains 256 submodels of a ligand across trajectory frames. I would like to colour the individual models using a palette (e.g., blue:orange) so that the time progression across frames is depicted in colour. Is there a way to assign palette range to submodels?

Best wishes, Lorena