You’re not doing anything wrong - ISOLDE (more specifically, the AMBER force field with implicit solvent) simply doesn’t behave well with scenarios like ion channels where metal ions get very close to each other. Annoying, but non-trivial to improve on.

You have two general remedies to work with: (a) do what you’ve been doing and add nice strong position restraints to hold them in place (also consider including some metal-protein distance restraints); or (b) after placing and settling one, select (only) it and do “isolde ignore sel” to mark it for exclusion from future simulations.

On Tue, 21 Oct 2025 at 22:53, Przemyslaw Dutka via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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.

Best,
Przemek

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