Good Morning. I have two more quick questions about using Isolde:

1) Can another model be used as a template for the 'isolde restrain basepairs' command?

2) is there a way to set restraints to coordinate the waters around a Mg ion, for example (i.e. so they have the correct geometry)?

On Tue, 17 Oct 2023 at 12:20, Tristan Croll <tcroll@altoslabs.com> wrote:

I'm afraid not. MD parameters are more difficult to transfer to the traditional crystallographic restraint schemes than you might first think. You'll need to use one of the dedicated restraint generation tools like phenix.elbow or CCP4's AceDRG. Using eLBOW, for more complicated ligands I've generally gotten best results in the past by using its optional plugin to ORCA (https://www.faccts.de/docs/orca/5.0/tutorials/).

-- Tritan

On Tue, Oct 17, 2023 at 11:04 AM Sean Connell via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,

Sorry If this has been asked recently and I missed it, but is there a way to convert the residues parameter XML file created by Isolde (for a ligand) into a restraints file that can be used in the phenix realspace refinement?

Sean
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