Hi Mehdi,
I cannot reproduce this problem.  When I use join models, all the water and ions and ligands move together with the protein.  I can only guess that maybe your ions are in a different model than the protein that you are moving.  If so, you would need to combine the ions and protein into a single model before you join that single model with the other protein model.

How to combine models is discussed in this previous post:
<https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/message/WSE4LMA5YUK2U6KIPVXMHMAQL5KNPAKB/>

I hope this helps,
Elaine
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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 10, 2024, at 2:20 AM, Amir Mehdi via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
>
> Hi, I am MEHDI
> I am trying to make a fusion between two proteins but when I am joining them by using build structure->joint structure (C-N peptide bonds) it will only move the protein structure but not the ions attached with the structure, can you suggest me something what to do in this case?
> Thank you