Hi Luca,

Try running with the parameter:

refinement.pdb_interpretation.automatic_linking.link_ligands=False

Check if automatic linking is enabled with the All parameters button in the GUI. Looks like the default might be True?

-D

On Fri, Jul 26, 2019 at 11:21 AM Luca Pellegrini <lp212@cam.ac.uk> 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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Dale Kreitler
Graduate Research Assistant
Gellman Lab
Department of Chemistry
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