[phenixbb] phenix.refine automatic linking options

[Engin Özkan]

Dear Developers,

Using the latest phenix nightly, I observed something odd in the 
phenix.refine UI, and I thought I should report it. If one unchecks 
Automatic ligand linking, this seems to not override its options, as the 
instructions in the Options window suggest. Specifically, if "Automatic 
Ligand Linking" is unchecked, but the "Link metals" is checked within 
its Options window, metal link restraints are still created.

I checked the .geo file to confirm this.

Thanks,
Engin