<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Meinan,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>The problem is that your file lacks CONECT records. In the absence of CONECT records it adds incorrect (in this case) distance-based bonds. If you look at the normal 2WDQ entry, which does have CONECT records, the F3S moiety is correct.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>So you need to add CONECT records. You could do it by hand, which would be tedious. Perhaps PyMOL can write out a PDB file with CONECT records?</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>You can also delete just the Fe-Fe pseudobonds with this command:</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>sel Fe ; del pb sel</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>UCSF Computer Graphics Lab</div></div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 21, 2020, at 7:17 PM, Meinan Lyu <<a href="mailto:mxl1032@case.edu" class="">mxl1032@case.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""> Dear <a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>，<br class=""><div class=""><br class=""></div><div class="">There is a 4 Fe-S in my structure, it shows a little bit funny when I open it with chimerax. It should only have links between Fe and S, but between 2Fe shows a link line two. Do you know how to show it normally like in pymol, or remove the links between 2Fe? I really want to draw some figures in chimerax. The attached are 4 Fe-S shown in chimrax,also shown in pymol. PDB id 2WDQ is also attached, which
4 Fe-S is in /B,F,J:303.</div><div class="">Thanks very much.</div><div class=""><br class=""></div><div class="">Be safe and Best,</div><div class="">Meinan</div><div class="">Postdoc from CWRU</div></div>
<span id="cid:f_k9ap8om70"><fe-s_chimerax.tif></span><span id="cid:f_k9ap8vcy1"><Fe-S_pymol.png></span><span id="cid:f_k9ap95e02"><2WDQ.pdb></span>_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class="">http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br class=""></div></blockquote></div><br class=""></div></body></html>