<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div dir="ltr">Hi Marta,</div><div dir="ltr"><br></div><div dir="ltr"> Thanks for the explanation of why you use split. Suppose Model Panel showed each chain, and you deleted all the unwanted chains. Would that work as well as split?</div><div dir="ltr"><br></div><div dir="ltr"> Definitely split should preserve the sequence information for missing structure, so we appreciate you bringing that to our attention.</div><div dir="ltr"><br></div><div dir="ltr"> Tom</div><div dir="ltr"><br><blockquote type="cite">On Mar 6, 2020, at 3:04 AM, Marta Perez Illana <marta.perez@cnb.csic.es> wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<p>Thanks a lot for the ideas and opening the topic, that was
absolutely great and appreciated. I just wanted to make sure that
I was not messing around myself with the splitting+sequence thing.
<br>
</p>
<p>Ideally I wouldn't use the split as you both suggested...
However, I frequently use the match maker with several homology
proteins coming from big viruses with lots of proteins... and
having less proteins in the session really helps me not to get
confused and focus and switching on and of every protein at each
time... So I am afraid that I really adore the split command.<br>
</p>
<p>Having the full sequence on the other side helps me out to
compare the homology proteins and see which areas are traced in
one protein but not in the other (or parts of the protein that are
subjected to protease fragmentation and not visualized in the
structure) , as well as to get full alignments based on
structure...</p>
<p>I am really grateful for all the help and sorry for being a bit
picky on the split+sequence...<br>
</p>
<p>Marta<br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 05.03.20 20:56, Tom Goddard wrote:<br>
</div>
<blockquote type="cite" cite="mid:A7D970B9-2EE5-4144-B7AC-4636ABA461E9@sonic.net">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
Hi Marta,
<div class=""><br class="">
</div>
<div class=""> The sequence for the missing structure should be
preserved by the split command but it currently is not being
preserved. We have opened a request for that</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/2913" class="" moz-do-not-send="true">https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/2913</a></div>
<div class=""><br class="">
</div>
<div class="">I agree with Elaine, that you should rarely need to
use the split command.</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Mar 2, 2020, at 9:15 AM, Marta Perez Illana
wrote:</div>
<br class="Apple-interchange-newline">
<div class=""><span style="caret-color: rgb(0, 0, 0);
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!important;" class="">Hi Elaine</span><br style="caret-color: rgb(0, 0, 0); font-family:
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<br style="caret-color: rgb(0, 0, 0); font-family:
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0px; text-transform: none; white-space: normal;
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<span style="caret-color: rgb(0, 0, 0); font-family:
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font-variant-caps: normal; font-weight: normal;
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0px; text-transform: none; white-space: normal;
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text-decoration: none; float: none; display: inline
!important;" class="">Thanks a lot for the quick reply!
I though that maybe there was a way to keep that info
of the non-traced amino acids after doing splitting.</span><br style="caret-color: rgb(0, 0, 0); font-family:
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<br style="caret-color: rgb(0, 0, 0); font-family:
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<span style="caret-color: rgb(0, 0, 0); font-family:
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!important;" class="">I use split because we work with
huge molecules, and therefore is really convenient for
focusing on a particular chain. And as well for fitting
as you mention... I will try the alternatives you
proposed! now knowing that making/saving new models
implies for sure kind of "loosing that info"...</span><br style="caret-color: rgb(0, 0, 0); font-family:
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<br style="caret-color: rgb(0, 0, 0); font-family:
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<span style="caret-color: rgb(0, 0, 0); font-family:
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!important;" class="">Regards</span><br style="caret-color: rgb(0, 0, 0); font-family:
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<br style="caret-color: rgb(0, 0, 0); font-family:
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<span style="caret-color: rgb(0, 0, 0); font-family:
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!important;" class="">Marta</span><br style="caret-color: rgb(0, 0, 0); font-family:
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<br style="caret-color: rgb(0, 0, 0); font-family:
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<br style="caret-color: rgb(0, 0, 0); font-family:
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0px; text-transform: none; white-space: normal;
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text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
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0px; text-transform: none; white-space: normal;
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!important;" class="">On 02/03/2020 18:05, Elaine Meng
wrote:</span><br style="caret-color: rgb(0, 0, 0);
font-family: Helvetica; font-size: 12px; font-style:
normal; font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start; text-indent:
0px; text-transform: none; white-space: normal;
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text-decoration: none;" class="">
<blockquote type="cite" style="font-family: Helvetica;
font-size: 12px; font-style: normal; font-variant-caps:
normal; font-weight: normal; letter-spacing: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;" class="">Hi Marta,<br class="">
When you open a structure from PDB or mmCIF format,
there is a special part of the file that gives the full
sequence of the structure used in the experiment, even
if parts of that structure are not visible in the
density (and therefore do not have atomic coordinates).
This is part of the model information.<br class="">
<br class="">
However, “split” makes new models, and it currently
loses various kinds of information. I believe this is
the case in both Chimera and ChimeraX. After splitting,
it must only look at the coordinates to get the
sequence.<br class="">
<br class="">
My personal opinion is to avoid using “split” unless it
is really necessary.<br class="">
<br class="">
In Chimera it sometimes helped with molecular surface
calculation, but in ChimeraX there is less reason to do
it. You can specify chains individually without
splitting. The main reason one might split is for
separately fitting the chains. However, if having the
full sequence is important, you can instead open
multiple copies of the original model and just delete
the parts of each that you don’t need.<br class="">
<br class="">
I hope this helps,<br class="">
Elaine<br class="">
-----<br class="">
Elaine C. Meng, Ph.D.<br class="">
UCSF Chimera(X) team<br class="">
Department of Pharmaceutical Chemistry<br class="">
University of California, San Francisco<br class="">
<br class="">
<blockquote type="cite" class="">On Mar 2, 2020, at 8:30
AM, Marta Perez Illana wrote:<br class="">
<br class="">
Hi all<br class="">
When I open a cif in chimerax and press the sequence
button the window shows up and there is everything
within the molecule, including the non-traced amino
acids (missing in the structure).<br class="">
<br class="">
Whereas if I do split the molecule to have just one
chain, then the sequence view only shows traced amino
acids, but not the non-traced ones anymore... Any
ideas on this please?<br class="">
<br class="">
P.D. With cif files this was a bit confusing in
regular chimera for me as well, since when saving the
cif it was kind of converted and I guess some info
regarding this non-traced aminoacids was missed...<br class="">
<br class="">
Thank you!!!<br class="">
Marta<br class="">
</blockquote>
</blockquote>
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<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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