I do have the same problem with the latest version. I wonder how I can set the anti-link option in the GUI. 

Based on what does Phenix make those links? Distance? 

On Fri, Jul 26, 2019, 3:09 PM Pavel Afonine <pafonine@lbl.gov> wrote:

Hi Luca,

first off please try the latest version of Phenix and see if that helps.
If it does not help, please send me the model (no data needed at this
moment) and I will investigate.

Pavel

On 7/26/19 08:21, Luca Pellegrini wrote:
> Hello,
>
> Phenix.real_space_refine generates a few spurious covalent bonds between protein and ligand in my structure, which distort the local structure, and then adds the corresponding LINK records in the output file. Is there a way to avoid this?
>
> I am aware of the anti-link option previously mentioned in the phenixbb: http://www.phenix-online.org/pipermail/phenixbb/2018-January/023677.html, but I was wondering if there was another way of preventing this from happening. I am using Phenix 1.15.2-3472.
>
> Best wishes,
> Luca
>
> Luca Pellegrini, PhD
> Department of Biochemistry
> University of Cambridge
> Cambridge CB2 1GA
> United Kingdom
>
> lp212@cam.ac.uk
> tel.: 0044 1223 760469
> https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group
> @PellegriniLab
>
>
>
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