<div dir="ltr">Dear Elanie,<div><br></div><div>Thanks a lot for favorable reply. </div><div>My reference model is a map and has been moved separately. I will have it figured it out.</div><div><br></div><div>Thanks and best,</div><div>Yanhe</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> 于2022年9月23日周五 13:21写道:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Yanhe,<br>
If the reference model has *not* been moved separately from the scene, the following might work:<br>
<br>
view orient<br>
<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#initial" rel="noreferrer" target="_blank">https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#initial</a>><br>
<br>
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.)<br>
<br>
Eric points out there is a horrible way to do it if the reference model is an atomic structure:<br>
<br>
(1) open another copy of the same atomic model<br>
(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**<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html" rel="noreferrer" target="_blank">https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html</a>><br>
(3) use "view orient"<br>
(4) close the extra copy (if you want)<br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Sep 23, 2022, at 10:47 AM, Yanhe Zhao via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:<br>
> <br>
> Dear Developer,<br>
> <br>
> 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)<br>
> <br>
> Thanks and best,<br>
> Yanhe<br>
<br>
</blockquote></div>