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Hi Aaron,<br>
<br>
could you please send two model files: before and after refinement,
and indicate problematic residues?<br>
<br>
Thanks,<br>
Pavel<br>
<br>
<blockquote type="cite"
cite="mid:ACC17CD4-6640-4333-92FB-93133B3FC5FA@uow.edu.au">
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I'm trying to refine a structure containing ZN bound to four
cysteine residues.
<div class="">I have had trouble with Real-space refinement
mangling the residues around this ZN.</div>
<div class="">
<div class=""><br class="">
</div>
<div class="">At first, Real-space refinement tried to turn the
cysteine into disulfides.</div>
<div class="">I tried switching this off with…</div>
<div class=""><br class="">
</div>
<div class=""><font class="" face="Menlo">resname CYS and name
SG</font></div>
<div class=""><br class="">
</div>
<div class="">…in the <b class="">disulphide bond exclusion
selection string</b> under the
<b class="">Model interpretation</b> menu (there are no
disulfides in the protein).</div>
<div class=""><br class="">
</div>
<div class="">But the cysteine-zinc cluster continued to be
mangled. Inspection of the
<b class="">.geo file</b> shows that the SG-ZN distance is
being restrained, but the CB–SG–ZN angle is not.</div>
</div>
<div class="">I checked the relevant dictionary file...</div>
<div class=""><br class="">
</div>
<div class="">
<div style="margin: 0px; font-stretch: normal; font-size: 11px;
line-height: normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures: no-common-ligatures"
class="">phenix-1.17.1-3660/modules/chem_data/mon_lib/list/mon_lib_list.cif</span></div>
</div>
<div class=""><br class="">
</div>
<div class="">And the correct bond and angle restraints do seem to
be present:</div>
<div class=""><br class="">
</div>
<div class="">
<div style="margin: 0px; font-stretch: normal; font-size: 11px;
line-height: normal; font-family: Menlo;" class="">
.</div>
</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px;
line-height: normal; font-family: Menlo;" class="">
.</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px;
line-height: normal; font-family: Menlo;" class="">
.</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px;
line-height: normal; font-family: Menlo;" class="">
<div style="margin: 0px; font-stretch: normal; line-height:
normal;" class=""><span style="font-variant-ligatures:
no-common-ligatures" class=""> ZN-CYS 1 ZN 2 SG
single 2.340 0.020</span></div>
<div class=""><span style="font-variant-ligatures:
no-common-ligatures" class="">.</span></div>
<div class=""><span style="font-variant-ligatures:
no-common-ligatures" class="">.</span></div>
<div class=""><span style="font-variant-ligatures:
no-common-ligatures" class="">.</span></div>
<div class=""><span style="font-variant-ligatures:
no-common-ligatures" class=""> ZN-CYS 1 ZN 2 SG
2 CB 109.000 3.000</span></div>
<div class=""><span style="font-variant-ligatures:
no-common-ligatures" class="">.</span></div>
<div class=""><span style="font-variant-ligatures:
no-common-ligatures" class="">.</span></div>
<div class=""><span style="font-variant-ligatures:
no-common-ligatures" class="">.</span></div>
</div>
<div class=""><br class="">
</div>
<div class="">Suggestions on how to fix this welcome.</div>
<br>
</blockquote>
<br>
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