Hello Nebojša,
There are some rules about whether the nonprotein atoms will be included in the morph trajectory, listed here:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing>

I will try to summarize here:

(1) Only atoms common to all of the input structures are included in the morph trajectory. This is probably the issue.  Maybe some of your structures don't have the glycosylations or they are shorter or different between the different structures.  It is OK for the proteins to have different sequences as long as they are similar enough to sequence-align, but where the sidechains are different only the backbone will be included in the final morph.

(2) 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
        • you use command option "same 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

#2 is probably satisfied because the glycosylations are covalently bonded to the proteins, but #1 is probably not satisfied.  You could try to add atoms to (or delete atoms from) the individual input structures to meet #1, but depending on how large the differences, this is likely to be difficult.

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

> On Dec 13, 2022, at 12:45 PM, Nebojsa Bogdanovic via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hello,
> I am looking into morphing several protein structures that contain glycans important form the function. The structures are all the same protein, in different states so the sequence info is good. Is there any function that retains the glycans visible once the command morph #1-5 same true produces a new model? I can just show them from origin structures but this does not look the best.
>
> Thank you and best regards
>
> Nebojša Bogdanović, Ph.D
> Department of Physiology and Biophysics,
> School of Medicine,
> Case Western Reserve University