<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 Marta, Rob,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>The underlying problem is that both Chimera and ChimeraX’s PDB code “preserves” sequence information simply by saving any SEQRES records that were present in the original input. mmCIF files do not have SEQRES records and therefore no such records make it into a PDB file saved from an mmCIF structure. Neither program looks at the structure per se to generate the SEQRES records.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>So what needs to happen is that instead of simply passing through pre-existing SEQRES records, the programs need to look at the structures being saved and construct corresponding SEQRES records. We have a ticket open for this in ChimeraX, and we will fix it. It <i class="">might</i> also be done in Chimera, but it’s less likely (depends on the difficulty).</div><div class=""><br class=""></div><div class="">--Eric</div><div class=""><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><div class=""><br class=""></div><div class=""><div><blockquote type="cite" class=""><div class="">On Mar 23, 2020, at 10:20 AM, Marta Perez Illana <<a href="mailto:marta.perez@cnb.csic.es" class="">marta.perez@cnb.csic.es</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" class="">
<div class=""><p class="">Hi Rob</p><p class="">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 class="">
</p><p class="">The only think I could do was use <b class="">chimerax, where the
unstrucutred sequence is kept after saving it as a mmCIF format</b>.</p>
<ul class="">
<li class=""> 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 class="">
</li>
<li class="">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 class="">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 class="">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 class="">If there is an alternative way I would also be more than
interested :) <br class="">
</p><p class="">Regards<br class="">
</p><p class="">Marta <br class="">
</p><p class=""><br class="">
</p>
<div class="moz-cite-prefix">On 23.03.20 15:02, Rob Blakemore wrote:<br class="">
</div>
<blockquote type="cite" cite="mid:CAACY4a5jWvjHVA=pU4v=f9RTCdUze0MZ3iVVnUU+mhTynuuUuw@mail.gmail.com" class="">
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<div dir="ltr" class="">
<div dir="ltr" class=""><br class="">
<div class="">Hi,</div>
<div class=""><br class="">
</div>
<div class="">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 class=""><br class="">
</div>
<div class="">
<div style="font-family: -webkit-standard;" class="">Details</div>
<div style="font-family: -webkit-standard;" class="">I'm
running Chimera 1.14 (build 42094) on MacOS Mojave
V10.14.6</div>
<div style="font-family: -webkit-standard;" class="">I'm
using 6VXX as the PDB file.</div>
</div>
<div class=""><br class="">
</div>
<div class="">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 class=""><br class="">
</div>
<div class="">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 class=""><br class="">
</div>
<div class="">Is there any way to preserve the unstructured residues
when saving these files? </div>
<div class=""><br class="">
</div>
<div class="">Thank you,</div>
<div class="">Rob Blakemore</div>
<div class=""><a href="mailto:robert.blakemore@tufts.edu" moz-do-not-send="true" class="">robert.blakemore@tufts.edu</a></div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
</div>
</div>
<br class="">
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</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>
</div>
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