<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">…rename your residues to CYS…<div><br></div><div>(doh!)</div><div><br><div><div>On Nov 10, 2014, at 10:18 AM, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.EDU">pett@cgl.ucsf.EDU</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi JD,<div><span class="Apple-tab-span" style="white-space:pre"> </span>Chimera 1.9 certainly minimizes disulfides okay if they're named CYS. Chimera 1.10 seems to have a bug in this regard. So try 1.9. If that doesn't work, rename your residues to 1.9 and try again (setattr r type CYS :CYM).</div><div><br></div><div>--Eric</div><div><br><div><div>On Nov 7, 2014, at 8:36 AM, Jean Didier Pie Marechal <<a href="mailto:JeanDidier.Marechal@uab.cat">JeanDidier.Marechal@uab.cat</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr" style="font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif; "><div style="margin-top: 0px; margin-bottom: 0px; ">Dear all,<br></div><div style="margin-top: 0px; margin-bottom: 0px; "><br></div><div style="margin-top: 0px; margin-bottom: 0px; ">I am trying to minimize a structure with a disulfide bond. My initial pdb has a CYM residue for amino acids involved in the bridge. Chimera correctly recognize the binding. But when entering the minimization run, chimera complains about the atoms of the cysteinate residues. Before sending you files I was just wondering if this is something that is not implemented in chimera or a problem on how I prepare my structure.<br></div><div style="margin-top: 0px; margin-bottom: 0px; "><br></div><div style="margin-top: 0px; margin-bottom: 0px; ">Best regards,<br></div><div style="margin-top: 0px; margin-bottom: 0px; ">JD<br><br></div></div>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></div></blockquote></div><br></div></div></blockquote></div><br></div></body></html>