<div dir="ltr"><div>Hi Luca,</div><div><br></div><div>Try running with the parameter:<br><br></div><div>refinement.pdb_interpretation.automatic_linking.link_ligands=False</div><div><br></div><div>Check if automatic linking is enabled with the All parameters button in the GUI. Looks like the default might be True?</div><div><br></div><div>-D<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Jul 26, 2019 at 11:21 AM Luca Pellegrini <<a href="mailto:lp212@cam.ac.uk">lp212@cam.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hello,<br>
<br>
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? <br>
<br>
I am aware of the anti-link option previously mentioned in the phenixbb: <a href="http://www.phenix-online.org/pipermail/phenixbb/2018-January/023677.html" rel="noreferrer" target="_blank">http://www.phenix-online.org/pipermail/phenixbb/2018-January/023677.html</a>, but I was wondering if there was another way of preventing this from happening. I am using Phenix 1.15.2-3472.<br>
<br>
Best wishes,<br>
Luca <br>
<br>
Luca Pellegrini, PhD<br>
Department of Biochemistry<br>
University of Cambridge<br>
Cambridge CB2 1GA<br>
United Kingdom<br>
<br>
<a href="mailto:lp212@cam.ac.uk" target="_blank">lp212@cam.ac.uk</a><br>
tel.: 0044 1223 760469<br>
<a href="https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group" rel="noreferrer" target="_blank">https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group</a><br>
@PellegriniLab<br>
<br>
<br>
<br>
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</blockquote></div><br clear="all"><br>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr">Dale Kreitler</div><div dir="ltr">Graduate Research Assistant<br><div><div>Gellman Lab</div><div>Department of Chemistry</div><div>University of Wisconsin-Madison</div></div></div></div></div></div>