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<p>Dear Laura,</p>
<p>maybe you can have a look at your pdb file by using a text editor
to check if the pdb contains some unusual portion (like missing
residues). As far I know Chimera tries to reconstruct missing
residues but sometimes there could be something wrong.</p>
<p>Best regards</p>
<p>Marco</p>
<p><br>
</p>
<div class="moz-cite-prefix">Il 24/03/2020 10:05, Laura Rotilio ha
scritto:<br>
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<div dir="ltr">Goodmorning,
<div>I'm writing because I'm trying to open my pdb file
but this error came out "Attempt to form loop bond". </div>
<div>I tried to have a look at the _init_.py file in the
line 1109 and I found this message: </div>
<div>molList = pdbio.readPDBfile(file, errOut=errLog)<br>
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<div><br>
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<div>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>
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<div>Thanks in advance for helping me, </div>
<div>Laura Rotilio</div>
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-- <br>
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<p style="margin:0px 0px
13px;font-size:10px;font-family:Verdana;color:rgb(35,35,35)"><span
style="letter-spacing:0px">Laura Rotilio, Ph.D.
Student</span></p>
<p style="margin:0px 0px
13px;font-size:10px;font-family:Verdana;color:rgb(35,35,35)"><span
style="letter-spacing:0px"><b>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)"><span
style="letter-spacing:0px">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)"><span
style="letter-spacing:0px">University of Pavia</span></p>
<p style="margin:0px 0px
13px;font-size:10px;font-family:Verdana;color:rgb(35,35,35)"><span
style="letter-spacing:0px">Via Ferrata 9, 27100
Pavia</span></p>
<p style="margin:0px 0px
13px;font-size:10px;font-family:Verdana;color:rgb(35,35,35)"><span
style="letter-spacing:0px">Italy</span></p>
<p style="margin:0px 0px
13px;font-size:10px;font-family:Verdana;color:rgb(35,35,35)"><span
style="letter-spacing:0px">Tel. <a
href="tel:%2B39-0382-985525"
value="+390382985525"
style="color:rgb(17,85,204)" target="_blank"
moz-do-not-send="true">+39-0382-985525</a>/985534</span></p>
<p style="margin:0px 0px
13px;font-size:10px;font-family:Verdana;color:rgb(71,135,255)"><span
style="letter-spacing:0px;color:rgb(35,35,35)">Fax </span><span
style="letter-spacing:0px"><a
href="tel:%2B39-0382-528496"
value="+390382528496"
style="color:rgb(17,85,204)" target="_blank"
moz-do-not-send="true">+39-0382-528496</a></span></p>
<p style="margin:0px 0px
13px;font-size:10px;font-family:Verdana;color:rgb(2,30,170)"><span
style="letter-spacing:0px;color:rgb(35,35,35)">Web <a
href="http://www.unipv.it/biocry"
style="color:rgb(17,85,204)" target="_blank"
moz-do-not-send="true"><span
style="letter-spacing:0px;color:rgb(2,30,170)">www.unipv.it/biocry</span></a></span></p>
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<pre class="moz-quote-pre" wrap="">_______________________________________________
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</pre>
</blockquote>
<pre class="moz-signature" cols="72">--
Dr.Marco Sette, Ph.D.
Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail: <a class="moz-txt-link-abbreviated" href="mailto:sette@uniroma2.it">sette@uniroma2.it</a>
e-mail: <a class="moz-txt-link-abbreviated" href="mailto:m77it@yahoo.it">m77it@yahoo.it</a>
Tel.: +39-0672594424
Fax: +39-0672594328
<a class="moz-txt-link-freetext" href="http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette">http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette</a></pre>
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