Hi Yanhe,
If the reference model has *not* been moved separately from the scene, the following might work:

view orient

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#initial>

However, if the reference model has been moved separately from the scene, there isn't a simple way to do it.  As I understand it, we would need to enhance ChimeraX so that "view zalign" could take a vector specification as well as a coordinateSystem option to say that that vector is defined in the  coordinate system of the reference model.  Currently "view zalign" takes an axis-spec, but that is the model number of an axis object previously defined with "define axis."  (And although "define axis" can use two x,y,z points it does not have a coordinateSystem option, so the x,y,z points are always defined in scene coordinates, not the coordinates of a specific model.)

Eric points out there is a horrible way to do it if the reference model is an atomic structure:

(1) open another copy of the same atomic model
(2) matchmaker the original reference model onto the newly opened copy, **using the "bring"  option to also move all the other models at the same time**
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>
(3) use "view orient"
(4) close the extra copy (if you want)

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 23, 2022, at 10:47 AM, Yanhe Zhao via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear Developer,
>
> I have aligned all my models to one reference model, What is the right way to orient all models based on reference model's xyz axis? (They have different coordinate system)
>
> Thanks and best,
> Yanhe