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I tend to think to disable it globally in phenix.real_space_refine.
Anyone affected please vote YES/NO and I will start from there.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 7/26/19 12:49, Ahmad Khalifa wrote:<br>
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<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>
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<div dir="auto">Based on what does Phenix make those links?
Distance? <br>
<br>
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<div dir="ltr" class="gmail_attr">On Fri, Jul 26, 2019, 3:09
PM Pavel Afonine <<a href="mailto:pafonine@lbl.gov"
moz-do-not-send="true">pafonine@lbl.gov</a>> wrote:<br>
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<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>
> 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"
moz-do-not-send="true">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"
rel="noreferrer" moz-do-not-send="true">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"
moz-do-not-send="true">https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group</a><br>
> @PellegriniLab<br>
><br>
><br>
><br>
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