Hi Alexis,
In the "morph" help page, the "Atoms in Common" section explains all about which atoms are included in the morph.  They have to be present in all of the input structures to be included:

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing>

You may want to read that whole section but here is the summary at the bottom:

"To summarize, HET residues such as ligands and ions are only included if at least one of the following applies:

        • the entire atomic models have identical sets of atoms with the same atom names, residue numbers, and chain IDs
        • the "same" option is true and the HET residues in question are present in all of the input structures with the same atom names, residue names, residue numbers, and chain IDs (even if other atoms are different)
        • the HET residues are bonded to the paired chains either directly or indirectly through other paired HET residues"

However, if some atoms are not present in all of the morph input models, you can of course simply display them from the original (input) model at the same time as playing back the morph trajectory, as in this movie tutorial:

<https://www.rbvi.ucsf.edu/chimerax/data/movies-may2019/moviemaking.html>

You could even do something fancier like make it "fly" into the binding site, although that requires more setup and saving views. This old Chimera movie tutorial that did something similar, but the ChimeraX commands would be different ("view name" instead of "savepos" etc.)
<https://www.rbvi.ucsf.edu/chimera/data/tutorials/movies08/moviemaking.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 Sep 1, 2023, at 2:00 PM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hello,
> The documentation for morph reads very protein-centric, and testing it with default options certainly makes it look like ligands are removed.
>
> Is there a way to have ligands included in a morph (assuming the same atoms are present in both models)?
> Cheers,
> Alexis