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
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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