[chimerax-users] Colouring submodels using a palette

[Lorena Zuzic]

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 at cgl.ucsf.edu>
Sent: 23 May 2022 18:19
To: Lorena Zuzic <lorena.zuzic at chem.au.dk>
Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at 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 at 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

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