If you mean that the ligands are different chemical compounds:

As it explains in the help, the morph trajectory only includes the atoms from the input structures that are the same or that can be paired up easily.  Thus, it will not include the ligands and will not interpolate their positions.  Please read the help for details:

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

To display the ligand(s) in your movie, you have to display the original model(s) that were input to the morph - you can undisplay all their other parts, of course, and just hide and show the ligand atoms at the appropriate time in your movie script.  I.e. you may need to use "coordset" several times to play different parts of the morph, with show/hide commands between to show and hide the specific ligands.  Again, this just makes them appear and disappear but does not interpolate their positions.

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


> On Jun 3, 2024, at 7:26 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear ChimeraX users!
>
> I have a question about recording movie with the transitions between different conformations using morph command.  Having five conformations for the same protein, after its supermpostiion using
> mm #2-5 to #1
>
> I generated a trajectory with the transition using:
>
> morph #2,3,4,5,6 core 0.1 frames 100 wrap f rate linear
>
> And then recorded movie using:
>
> # start recording
> movie record size 3840,2160 supersample 1
> coordset #7 1,400,1 computeSs true
> wait 400
>
> My question is about morph command. Assuming that all 5 models are very well superimposed and the difference is only the bound ligand (which is different in every model!), would it be possible to include these different ligands in the final morphed trajectory, thus making a smooth transition between different binding poses ?
>
> Many thanks in advance !
>
> Enrico