[phenixbb] Unwanted LINK records

[Ahmad Khalifa]

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 at 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 at cam.ac.uk
> > tel.: 0044 1223 760469
> > https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group
> > @PellegriniLab
> >
> >
> >
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