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