Once more I skimmed the documentation too fast... thank you! 😊

From: Elaine Meng <meng@cgl.ucsf.edu>
Sent: Wednesday, September 30, 2026 5:37:55 PM
To: Guillaume Gaullier
Cc: ChimeraX Users Help
Subject: Re: [chimerax-users] morph command ignores ions in metalloproteins?
 
Hi Guillame,
It's covered in the "atoms in common" section of the morph documentation. Namely, you need to use "same true":

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

The zinc is in the morph when I have these structures open as #1 and #2 and use command

morph #1,2 same true

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 Sep 30, 2026, at 2:23 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hello,
>
> I am trying to make a morph between PDB entries 9SKS and 9SKT. The protein does what I want, but I can't find out how to include the active site :ZN in the interpolation. This ion is consistently numbered between both structures, and I give model numbers to the morph command, which should select the entire models including their ions. Nothing about this in the documentation. What am I missing?
>
> If interpolating ions with morph is impossible to do for some reason, then it would be helpful to list it in the "limitations" section of the command's documentation.
>
> Thank you in advance,
>
> Guillaume
>
> ---
> Guillaume Gaullier, PhD
> Researcher, Blikstad group
> Molecular Biomimetics / Microbial Chemistry
> Department of Chemistry - Ångström
> Uppsala University
> RegementsvÀgen 10
> 752 37 Uppsala
> Sweden
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