Is the problem showing atoms only after using ISOLDE on the structure? Probably no one can help without the PDB/mmCIF file. You could save it to a file after the simulation and use ChimeraX menu entry Help / Report a Bug... and attach the saved structure. Any data in a ChimeraX bug report is public, so don't submit it if you don't want the structure publicly visible.

On Sep 24, 2026, at 8:51 AM, Barry Kesner via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

On windows 11 using chimera 1.12 I I had to modify an RNA structure by adding a 5’ G. Then I used Isolde to relax the region. However, after creating the new bond I was not able to see the atoms for the 2nd G. And after the simulation I was not able to display the atoms for almost all residues except for a select few!

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