[chimerax-users] Building ions using ISOLDE

Hello, I am currently encountering an issue while trying to build Na ions with ISOLDE. Despite various attempts, the ions consistently move outside the density as soon as the simulation begins. The ion site is clearly defined by previous crystallography maps. I have also downloaded several EM maps that include modeled Na ions, such as PDB 6VWX (see below). In these cases, the ion still moves up or down the channel once the simulation starts. The only method I've found to keep the ion in place is by pinning it. I would greatly appreciate any advice or tips. [image: Screenshot 2025-10-21 at 10.33.05 PM.png] Best, Przemek