Hi Yan Zhang, The file from Coot may not have had an explicit bond or link between those two atoms, but you can certainly add it in ChimeraX. One way is to just select the two atoms, Ctrl-click and Shift-Ctrl-click, then use command: bond sel reasonable false ... the "reasonable false" may or may not be necessary, but you would need it if the distance is longer than normal for that kind of bond. See <https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html> ... or you can use the graphical interface, menu: Tools... Structure Editing... Build Structure, change from "Start Structure" to "Adjust Bonds" section, use the "Add" bonds button to add a bond between the two selected atoms. Similar to the command, you may need to change from "reasonable" to "all possible" if the distance is long. See <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds> 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 2, 2024, at 7:36 PM, Yan ZHANG 张艳 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX Team, I am writing this letter due to an issue I have encountered. I have adjusted the phosphodiester bonds of the RNA chain using Coot for structure correction. However, when I opened it in ChimeraX, it appears to be in a broken state, even though the distance between the two atoms is 1.6 angstroms. I am unsure what the reason for this could be. I have attached an image below. The dashed line should originally be a P-O bond. Could you please suggest any solutions to this problem? I look forward to receiving your reply as soon as possible.<image001.png>