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<p>Hi Nicole,</p>
<p>you could note the pdb name of the old structure and use the
homology modelling tool provided in Chimera (it is based on
Modeller then you need a password to access the server) to model
the new sequence, using the old one as a template. Check that the
alignment is correct (identical alignment except the new region)
and let the server prepare your structure.</p>
<p>Hope it helps,</p>
<p>Regards,</p>
<p>Marco<br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">Il 26/07/2021 21:19, Nicole Ostrovsky
via Chimera-users ha scritto:<br>
</div>
<blockquote type="cite"
cite="mid:CAMiWtumxDne_gNY5GCO+WR9bYOrj=_rgB4Lt7R80y_4ENkX_3g@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Hello,
<div><br>
</div>
<div>I have a structure which I've cut a section out of and I am
working on connecting the two loose ends together. I wanted to
connect them with two glycine residues - since they are
easiest to work with and have no side chains. I am doing this
using the Modify Structure option under the Build structure
tool and adding one atom at a time. However, when I try to
minimize my newly created glycine, I get the error message "No
MMTK name for atom "H1" in standard residue "GLY"" (I've
attached a picture of my reply log). I'm not sure how to
troubleshoot this.</div>
<div><br>
</div>
<div>Is there a better way to connect two ends of a peptide, or
should I change the way I am using the modify structure tool?</div>
<div><br>
</div>
<div>Thank you.</div>
<div><br>
</div>
<div>Nicole Ostrovsky</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
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</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>
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