<div dir="ltr">Rhys<div><br></div><div>You can use the phil option</div><div><br></div><div>superpose_ideal_ligand = *None all SF4 F3S DVT</div><div><br></div><div>to superpose an ideal F3S to avoid the mess. I'm also happy to take a closer look.</div><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"><font face="arial, sans-serif">Cheers</font><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">Nigel</font><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">---</font></div><div><font face="arial, sans-serif">Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</font></div><div><font face="arial, sans-serif">Lawrence Berkeley National Laboratory</font><br><font face="arial, sans-serif">Berkeley, CA 94720-8235</font><br><font face="arial, sans-serif">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></font></div></div><div><font face="arial, sans-serif"><span style="color:rgb(73,74,76)">ORCID : </span><font color="#494a4c"><a href="https://orcid.org/0000-0001-8857-9464" target="_blank">orcid.org/0000-0001-8857-9464</a></font></font><br></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Apr 18, 2022 at 11:50 AM Edward Berry <<a href="mailto:berrye@upstate.edu">berrye@upstate.edu</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">Have you seen:<br>
Iron–sulfur clusters have no right angles<br>
Nigel W. Moriarty and Paul D. Adams, Acta Cryst. (2019). D75, 16–20<br>
<<a href="http://journals.iucr.org/d/issues/2019/01/00/rr5165/index.html" rel="noreferrer" target="_blank">http://journals.iucr.org/d/issues/2019/01/00/rr5165/index.html</a>><br>
<br>
The Phenix F3S library worked well for our Complex II structures a few years back. And those structures definitely confirm that the angles are not 90* for F3S. (FES Fe2S2 has close to right angles, I think)<br>
You have to be sure that the atoms are arranged in the same way as in the model or the restraints will try to invert your cluster;, and that the Cys ligands connect to the right irons.<br>
Ed<br>
<br>
Rhys Grinter wrote on 4/18/2022 12:24 AM:<br>
> Hi PHENIX BB,<br>
> <br>
> I'm currently refining a structure with 3Fe4S clusters into some high resolution cryoEM maps (1.57 Ang). However, refinement messes up the Fe4S cluster, by moving the existing Fe and S atoms into the wrong positions in the density.<br>
> <br>
> Is anyone aware of this issue and/or knows of a simple way to prevent this from happening?<br>
> <br>
> Cheers,<br>
> <br>
> Rhys<br>
> <br>
> -- <br>
> Dr Rhys Grinter<br>
> Lab Head<br>
> Molecular Physiology of Microbial Pathogens (MP2) Lab<br>
> Monash University<br>
> +61 (0)3 9902 9213<br>
> +61 (0)403 896 767<br>
> <br>
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