Hello Alicia,
You can try using the Matchmaker tool.  ChimeraX menu: Tools... Structure Analysis... Matchmaker.  To see the help page, you can click the Help button on the tool, or you view the copy at our website:

<https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html>

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

> On Jul 31, 2022, at 12:48 PM, Alicia Gardiol via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> We have experimental protein structures in PDB, and Alpha Fold predicted structures.  Which is the best software to superpose these structures using a MAC computer.
>
> - Two different predicted proteins (predicted 1 to predicted 2) and
> - Same protein predicted and experimental (predicted 1 to experimental 1)
>
> Thank you and best wishes.
>
> Alicia Gardiol, PhD