Hi Taha, I'm very glad you find ISOLDE useful! Regarding magnesium (and metal ions in general): ISOLDE itself doesn't currently try to write extra Phenix restraints for these, but you can use the program phenix.metal_coordination to generate an edits file that you can add to the phenix.real_space_refine input. That should automatically create a set of bond and angle restraints for all metals in the model. Best, Tristan On Mon, Mar 25, 2024 at 3:46 PM Shahid, Taha (Dr.) via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

Dear Tristan,

I find ISOLDE invaluable for my work. Not only has it enabled me to build models of the highest quality, but been hugely instructive in giving me an instinctive ‘feel' for protein structure.

I am having a minor problem with magnesium ions moving out of density when I run phenix.real_space_refine with settings output by *isolde write phenixRsrInput*. I typically specify r*estrainPositions true* and *includeHydrogens true *as well.

Is there a way to restrain these ions as well (perhaps an edit I could make to the real_space_refine.eff file)?

Many thanks,

Taha

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