<div dir="ltr">What version of Phenix?<div><br></div><div>Can you share the model (directly) with me?<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></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Mar 2, 2020 at 3:23 PM Aaron Oakley <<a href="mailto:aarono@uow.edu.au">aarono@uow.edu.au</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">
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I'm trying to refine a structure containing ZN bound to four cysteine residues.
<div>I have had trouble with Real-space refinement mangling the residues around this ZN.</div>
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<div>At first, Real-space refinement tried to turn the cysteine into disulfides.</div>
<div>I tried switching this off with…</div>
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<div><font face="Menlo">resname CYS and name SG</font></div>
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<div>…in the <b>disulphide bond exclusion selection string</b> under the
<b>Model interpretation</b> menu (there are no disulfides in the protein).</div>
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<div>But the cysteine-zinc cluster continued to be mangled. Inspection of the
<b>.geo file</b> shows that the SG-ZN distance is being restrained, but the CB–SG–ZN angle is not.</div>
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<div>I checked the relevant dictionary file...</div>
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<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">phenix-1.17.1-3660/modules/chem_data/mon_lib/list/mon_lib_list.cif</span></div>
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<div>And the correct bond and angle restraints do seem to be present:</div>
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<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<div style="margin:0px;font-stretch:normal;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures"> ZN-CYS 1 ZN 2 SG single 2.340 0.020</span></div>
<div><span style="font-variant-ligatures:no-common-ligatures">.</span></div>
<div><span style="font-variant-ligatures:no-common-ligatures">.</span></div>
<div><span style="font-variant-ligatures:no-common-ligatures">.</span></div>
<div><span style="font-variant-ligatures:no-common-ligatures"> ZN-CYS 1 ZN 2 SG 2 CB 109.000 3.000</span></div>
<div><span style="font-variant-ligatures:no-common-ligatures">.</span></div>
<div><span style="font-variant-ligatures:no-common-ligatures">.</span></div>
<div><span style="font-variant-ligatures:no-common-ligatures">.</span></div>
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<div>Suggestions on how to fix this welcome.</div>
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<div>–å</div>
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