<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 Laura,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>The “loop bond” message specifically means that your PDB file has a CONECT or LINK record that says that an atom is bonded to itself! So my advice would be to edit your PDB file and remove all CONECT and LINK records and let Chimera figure out the bonds on its own.</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 class=""><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Mar 24, 2020, at 2:05 AM, Laura Rotilio <<a href="mailto:laura.rotilio@iusspavia.it" class="">laura.rotilio@iusspavia.it</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class="">Goodmorning, <div class="">I'm writing because I'm trying to open my pdb file but this error came out "Attempt to form loop bond". </div><div class="">I tried to have a look at the _init_.py file in the line 1109 and I found this message: </div><div class="">molList = pdbio.readPDBfile(file, errOut=errLog)<br class=""></div><div class=""><br class=""></div><div class="">I can't understand this message and I don't know how to eventually modify my pdb file in order to be able to open it. </div><div class=""><br class=""></div><div class="">Thanks in advance for helping me, </div><div class="">Laura Rotilio</div><div class=""><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div dir="ltr" class="gmail_signature"><div dir="ltr" class=""><p style="margin:0px 0px 13px;font-size:10px;font-family:Verdana;color:rgb(35,35,35)" class=""><span style="letter-spacing:0px" class="">Laura Rotilio, Ph.D. Student</span></p><p style="margin:0px 0px 13px;font-size:10px;font-family:Verdana;color:rgb(35,35,35)" class=""><span style="letter-spacing:0px" class=""><b class="">Structural Biology Lab., Prof. A. Mattevi</b></span></p><p style="margin:0px 0px 13px;font-size:10px;font-family:Verdana;color:rgb(35,35,35)" class=""><span style="letter-spacing:0px" class="">Dept. Biology and Biotechnology "L. Spallanzani"</span></p><p style="margin:0px 0px 13px;font-size:10px;font-family:Verdana;color:rgb(35,35,35)" class=""><span style="letter-spacing:0px" class="">University of Pavia</span></p><p style="margin:0px 0px 13px;font-size:10px;font-family:Verdana;color:rgb(35,35,35)" class=""><span style="letter-spacing:0px" class="">Via Ferrata 9, 27100 Pavia</span></p><p style="margin:0px 0px 13px;font-size:10px;font-family:Verdana;color:rgb(35,35,35)" class=""><span style="letter-spacing:0px" class="">Italy</span></p><p style="margin:0px 0px 13px;font-size:10px;font-family:Verdana;color:rgb(35,35,35)" class=""><span style="letter-spacing:0px" class="">Tel. <a href="tel:%2B39-0382-985525" value="+390382985525" style="color:rgb(17,85,204)" target="_blank" class="">+39-0382-985525</a>/985534</span></p><p style="margin:0px 0px 13px;font-size:10px;font-family:Verdana;color:rgb(71,135,255)" class=""><span style="letter-spacing:0px;color:rgb(35,35,35)" class="">Fax </span><span style="letter-spacing:0px" class=""><a href="tel:%2B39-0382-528496" value="+390382528496" style="color:rgb(17,85,204)" target="_blank" class="">+39-0382-528496</a></span></p><p style="margin:0px 0px 13px;font-size:10px;font-family:Verdana;color:rgb(2,30,170)" class=""><span style="letter-spacing:0px;color:rgb(35,35,35)" class="">Web <a href="http://www.unipv.it/biocry" style="color:rgb(17,85,204)" target="_blank" class=""><span style="letter-spacing:0px;color:rgb(2,30,170)" class="">www.unipv.it/biocry</span></a></span></p></div></div></div></div></div></div></div>
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