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 important

***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.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

_______________________________________________
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu
To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu
Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

Altos Labs UK Limited | England | Company reg 13484917  

Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT