[Chimera-users] Re: Trouble in Creating Peptide bond

Dear Vignesh, In Join Models, the "C-N peptide backbone" is only for backbone peptide bonds. You have to choose the "other bond" option instead and include more information like the bond length, torsion angle, etc. as described in the help page: https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h... If you can't apply, it is probably because you did not select exactly two atoms, the C atom to be bonded in one model and the N atom to be bonded in the other model, or you did not enter all the needed information. Also if one side is -CO2 you probably also need to delete one of the oxygens (O) beforehand so that the carbon (C) can have another bond. 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 Feb 6, 2024, at 2:38 AM, Vignesh Nandhagopal via Chimera-users wrote:

Dear Dr. Elanie C. Meng, Thank you for your valuable reply. It's very useful I need to make a peptide bond between the side chain amino group of an amino acid and a carboxylic group of amino acid in another protein. In Join models I have tried to make the other bonds I can't able to apply. Looking forward to hearing from you.

On Fri, 2 Feb 2024 at 21:50, Elaine Meng wrote: Dear Vignesh, You are using the wrong part of the tool. Where the dialog says "Start Structure" you chould change that to "Join Models" instead.

Then you need to hide ribbons and show atoms so that you can see the N and C atoms you want to connect with a peptide bond, e.g. commands

~ribbon disp

Then you need to select the two atoms for this bond, Ctrl-click and Shift-Ctrl-click on them in the 3D view. Then proceed as described for the peptide bond option of Join Models here:

https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h...

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

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On Feb 2, 2024, at 12:03 AM, Vignesh Nandhagopal via Chimera-users wrote:

Dear Chimera Help Team, I want to create a peptide bond. I followed this manuscript which I have attached along with this mail. I followed the steps of the manual I have used and I have seen a slight change in build structure. Kindly help me with this I am getting an error in the unrecognized protein code. Kindly help me with the steps.

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