<div dir="auto"><div>I do have the same problem with the latest version. I wonder how I can set the anti-link option in the GUI. </div><div dir="auto"><br></div><div dir="auto">Based on what does Phenix make those links? Distance? <br><br><div class="gmail_quote" dir="auto"><div dir="ltr" class="gmail_attr">On Fri, Jul 26, 2019, 3:09 PM Pavel Afonine &lt;<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>&gt; wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Luca,<br>
<br>
first off please try the latest version of Phenix and see if that helps. <br>
If it does not help, please send me the model (no data needed at this <br>
moment) and I will investigate.<br>
<br>
Pavel<br>
<br>
On 7/26/19 08:21, Luca Pellegrini wrote:<br>
&gt; Hello,<br>
&gt;<br>
&gt; 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>
&gt;<br>
&gt; 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 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>
&gt;<br>
&gt; Best wishes,<br>
&gt; Luca<br>
&gt;<br>
&gt; Luca Pellegrini, PhD<br>
&gt; Department of Biochemistry<br>
&gt; University of Cambridge<br>
&gt; Cambridge CB2 1GA<br>
&gt; United Kingdom<br>
&gt;<br>
&gt; <a href="mailto:lp212@cam.ac.uk" target="_blank" rel="noreferrer">lp212@cam.ac.uk</a><br>
&gt; tel.: 0044 1223 760469<br>
&gt; <a href="https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group" rel="noreferrer noreferrer" target="_blank">https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group</a><br>
&gt; @PellegriniLab<br>
&gt;<br>
&gt;<br>
&gt;<br>
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</blockquote></div></div></div>