<div dir="ltr">Thanks a lot! I've tried both methods, they work very well. <br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Apr 22, 2020 at 12:37 PM Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.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"><div style="overflow-wrap: break-word;">Hi Meinan,<div><span style="white-space:pre-wrap"> </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><span style="white-space:pre-wrap"> </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><span style="white-space:pre-wrap"> </span>You can also delete just the Fe-Fe pseudobonds with this command:</div><div><br></div><div><span style="white-space:pre-wrap"> </span>sel Fe ; del pb sel</div><div><br></div><div><div>--Eric</div><div><br></div><div><span style="white-space:pre-wrap"> </span>Eric Pettersen</div><div><span style="white-space:pre-wrap"> </span>UCSF Computer Graphics Lab</div></div><div><br><div><br><blockquote type="cite"><div>On Apr 21, 2020, at 7:17 PM, Meinan Lyu <<a href="mailto:mxl1032@case.edu" target="_blank">mxl1032@case.edu</a>> wrote:</div><br><div><div dir="ltr"> Dear <a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>,<br><div><br></div><div>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>Thanks very much.</div><div><br></div><div>Be safe and Best,</div><div>Meinan</div><div>Postdoc from CWRU</div></div>
<span id="gmail-m_7323494871227167261cid:f_k9ap8om70"><fe-s_chimerax.tif></span><span id="gmail-m_7323494871227167261cid:f_k9ap8vcy1"><Fe-S_pymol.png></span><span id="gmail-m_7323494871227167261cid:f_k9ap95e02"><2WDQ.pdb></span>_______________________________________________<br>ChimeraX-users mailing list<br><a href="mailto:ChimeraX-users@cgl.ucsf.edu" target="_blank">ChimeraX-users@cgl.ucsf.edu</a><br>Manage subscription:<br><a href="http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" target="_blank">http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br></div></blockquote></div><br></div></div></blockquote></div>