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<p>Hi Rob</p>
<p>I was having exactly the same situation as you mention... Same
here if I save those mmCIFs in regular chimera as PDBs,
unstructured sequence is somehow lost. <br>
</p>
<p>The only think I could do was use <b>chimerax, where the
unstrucutred sequence is kept after saving it as a mmCIF format</b>.</p>
<ul>
<li> and then I open it and the whole sequence is kept. If I play
around with the mmCIF in chimerax everything is fine and kept
and can use it normally. <br>
</li>
<li>But If I would open it in traditional chimera, unstructured
sequence would be kept, but again, when saving it, the
unstructured sequence is lost....</li>
</ul>
<p>But this is NOT when saved in PDB format. Like if you would save
in PDB format in chimerax no unstructured sequence is neither
kept, as in traditional chimera...</p>
<p>I think ( and this is just a practical opinion, since I lack the
theory underneath) that this has something to do with the new
mmCIF files format. At least everything that I usually fetch
nowadays are mmCIF already (even if in the past they were
initially PDBs in the data base).</p>
<p>If there is an alternative way I would also be more than
interested :) <br>
</p>
<p>Regards<br>
</p>
<p>Marta <br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 23.03.20 15:02, Rob Blakemore wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAACY4a5jWvjHVA=pU4v=f9RTCdUze0MZ3iVVnUU+mhTynuuUuw@mail.gmail.com">
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<div dir="ltr"><br>
<div>Hi,</div>
<div><br>
</div>
<div>I'm encountering a problem wherein unstructured residues
are present in the sequence the first time I fetch it from
PDB, but are omitted after I save the file locally and
reopen it. Has anyone else encountered this and would you
happen to know a workaround?</div>
<div><br>
</div>
<div>
<div style="color:rgb(0,0,0);font-family:-webkit-standard">Details</div>
<div style="color:rgb(0,0,0);font-family:-webkit-standard">I'm
running Chimera 1.14 (build 42094) on MacOS Mojave
V10.14.6</div>
<div style="color:rgb(0,0,0);font-family:-webkit-standard">I'm
using 6VXX as the PDB file.</div>
</div>
<div><br>
</div>
<div>When I fetch a structure by ID: (PDB mmCIF) and open a
sequence (Tools --> Sequence --> Sequence), it shows
me a complete sequence containing both residues present in
the structure, as well as unresolved/unstructured residues.
The unresolved residues are outlined by a red border.</div>
<div><br>
</div>
<div>However, if I save this session to a file or save the
structure to PDB and then reopen it; if I then open the
sequence, it only shows me the sequence of residues present
in the structure, and omits all of the unresolved /
unstructured residues. (All the red outlined residues are
now gone)</div>
<div><br>
</div>
<div>Is there any way to preserve the unstructured residues
when saving these files? </div>
<div><br>
</div>
<div>Thank you,</div>
<div>Rob Blakemore</div>
<div><a href="mailto:robert.blakemore@tufts.edu"
moz-do-not-send="true">robert.blakemore@tufts.edu</a></div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
<br>
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<pre class="moz-quote-pre" wrap="">_______________________________________________
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</pre>
</blockquote>
<pre class="moz-signature" cols="72">--
Marta Pérez Illana, Ph. D. student
Dept. of Macromolecular Structures Lab 15
Centro Nacional de Biotecnología (CNB-CSIC)
Darwin, 3
28049-Madrid (SPAIN)
Email: <a class="moz-txt-link-abbreviated" href="mailto:marta.perez@cnb.csic.es">marta.perez@cnb.csic.es</a>
Phone: (0034) 91 585 4508
<a class="moz-txt-link-freetext" href="http://wwwuser.cnb.csic.es/~sanmartinlab">http://wwwuser.cnb.csic.es/~sanmartinlab</a></pre>
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