[phenixbb] Unwanted LINK records

Pavel Afonine pafonine at lbl.gov
Fri Jul 26 12:08:08 PDT 2019

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.


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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