<div dir="ltr">There is an option to control this, link_ligands, that defaults to True. You should be able to set it to false by search for it in the parameter list.<div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Jul 26, 2019 at 12:51 PM Ahmad Khalifa <<a href="mailto:underoath006@gmail.com">underoath006@gmail.com</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"><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 <<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</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">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>
> 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 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" rel="noreferrer" 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 noreferrer" target="_blank">https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group</a><br>
> @PellegriniLab<br>
><br>
><br>
><br>
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