[phenixbb] phenix.refine automatic linking options

Engin Özkan eozkan at uchicago.edu
Thu Aug 20 13:41:31 PDT 2015

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.


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 <eozkan at uchicago.edu 
> <mailto:eozkan at uchicago.edu>> 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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