Hi Tristan,

That worked perfectly - many thanks for your help!

Phenix.metal_coordination didn’t like for_phenix.cif file created by Isolde write phenixRsrInput, but I was able to create the edits file by saving the model file as a PDB from ChimeraX directly.

Cheers and happy Easter,

Taha

On 25 Mar 2024, at 16:15, Tristan Croll tcroll@altoslabs.com wrote:

You don't often get email from tcroll@altoslabs.com. Learn why this is importanthttps://aka.ms/LearnAboutSenderIdentification ***CAUTION:*** This email was sent from an EXTERNAL source. Think before clicking links or opening attachments. 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.edumailto: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 restrainPositions 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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