Dear Billy and Nigel, Thank you. Phenix.refine GUI in the latest nightly/release candidate no longer has the master enable/disable button, and so the problem is resolved. Engin On 8/13/15 11:28 AM, Billy Poon wrote:

Hi Engin,

Thanks! We updated that part of the GUI so that it should be more intuitive. There is now a button that lets you apply automatic linking to all the components and a button that disables all automatic linking. You can, of course, still pick which components to enable by checking the specific boxes.

On Tue, Aug 11, 2015 at 7:40 AM, Engin Özkan mailto:[email protected]> wrote:

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

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