Hi Guillaume,
Some kinds of pseudobonds are tracked for each coordinate set (e.g. hydrogen bonds, metal-coordination bonds) and some are not (e.g. missing structure).  Your only real option here is to hide the coordination bonds.  I am working on porting the Metal Geometry tool from Chimera, and that will have an option to add coordination bonds throughout a trajectory/interpolation, but it’s still probably weeks before the tool will be finished.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Oct 1, 2026, at 2:46 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

And is there a way to display the ion coordination pseudo-bonds all the way through the interpolation? Now they are only displayed (even only seem to exist?) on the first frame, and the coordset documentation doesn't mention this (I read more carefully this time...). If not I will simply hide the pseudo-bonds.

Thank you,

Guillaume
From: Guillaume Gaullier
Sent: Thursday, October 1, 2026 9:57:42 AM
To: ChimeraX Users Help
Subject: Re: [chimerax-users] morph command ignores ions in metalloproteins?
 
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
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> Sweden
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