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 ----- 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