[phenixbb] Unwanted LINK records

[Pavel Afonine]

I tend to think to disable it globally in phenix.real_space_refine. 
Anyone affected please vote YES/NO and I will start from there.

Pavel

On 7/26/19 12:49, Ahmad Khalifa wrote:
> 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 
> <mailto: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 <mailto:lp212 at cam.ac.uk>
>     > tel.: 0044 1223 760469
>     > https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group
>     > @PellegriniLab
>     >
>     >
>     >
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