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<p>Dear Edmund,</p>
<p>to my knowledge the SwissPDB Viewer, now Deep View, perform this
task. When you open a pdb file lacking some residues it directly
fills the gaps and gives a message that the build residues are in
a different color (pink or purple, I guess).</p>
<p>Best</p>
<p>Marco</p>
<p><br>
</p>
<div class="moz-cite-prefix">Il 14/10/2020 04:19, Edmund Marinelli
ha scritto:<br>
</div>
<blockquote type="cite"
cite="mid:CAHiGUJiWN1_aoGSy_+un+aWH_a30bccijQyefsNhyt9SEgn1uQ@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Hello Elaine:
<div><br>
</div>
<div>So far I find no service that does what Modeller does,
believe it or not. As an example Swiss-Model failed to fill in
the missing residues, to my surprise. A couple of web
services that I ran across rely on Modeller and one has to buy
a license for Modeller or at least convince the Modeler lab
that you are not commercial and qualify as academic, which is
harder to do than one might think. There does exist the
French server Pepfold3 and related versions but those don't
handle the entire protein; instead one might get a 30-mer
modeled 'on its own'. Then comes the question of : how would
one mate that piece , which might have a different
coordinate frame of reference , to the protein which lacks
those residues in the PDB. This is a question, which on its
own, is important. If you have any insight to that issue I
would appreciate it. </div>
<div><br>
</div>
<div>If you know of any service that actually models the protein
and rebuilds the missing residues (note that the missing
residues are listed in the PDB file , but of course no
coordinates); I would be appreciative to know what they are. </div>
<div><br>
</div>
<div>Best regards, </div>
<div><br>
</div>
<div>Edmund R Marinelli (Ed) </div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, Oct 13, 2020 at 4:52
PM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu"
moz-do-not-send="true">meng@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">Hello
Edmund,<br>
No. However, there are probably dozens (hundreds?) of web
services that will model proteins and write out PDB files that
you can then open in any molecular graphics program.<br>
<br>
Within Chimera, besides the Modeller interface, you can
"manually" build peptides of specified sequence and phi/psi
angles and join them together (see Build Structure tool), or
add amino acid residues one by one at the terminus ("addaa"
command) or virtually mutate residues ("swapaa" command or
Rotamers tool).<br>
<br>
Build Structure<br>
<<a
href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html"
rel="noreferrer" target="_blank" moz-do-not-send="true">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html</a>><br>
Rotamers<br>
<<a
href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html"
rel="noreferrer" target="_blank" moz-do-not-send="true">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html</a>><br>
addaa<br>
<<a
href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addaa.html"
rel="noreferrer" target="_blank" moz-do-not-send="true">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addaa.html</a>><br>
swapaa<br>
<<a
href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html"
rel="noreferrer" target="_blank" moz-do-not-send="true">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Oct 13, 2020, at 4:22 PM, Edmund Marinelli <<a
href="mailto:edmundmarinelli@gmail.com" target="_blank"
moz-do-not-send="true">edmundmarinelli@gmail.com</a>>
wrote:<br>
> <br>
> Hello:<br>
> I see that Chimera uses Modeller for modeling missing
residues . Does Chimera have access to any other web based
services that would perform similar function? <br>
> Thanks,<br>
> Edmund R Marinelli, PhD <br>
> <br>
<br>
</blockquote>
</div>
<br>
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<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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