How to move ions along with protein structure
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
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
Hu Elaine Meng, Thank you for your reply, I'll look forward to this solution. On Tue, 10 Sep, 2024, 9:24 pm Elaine Meng, <meng@cgl.ucsf.edu> wrote:
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/m...
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
participants (2)
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Amir Mehdi -
Elaine Meng