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Hi Kaushik,<br>
<br>
I think that's what Phenix Autobuild does: it ranks possible residue
fits into map-candidate by probability taking into account density
shapes, sequence and may be other factors. <br>
See around pages 62-64 here:<br>
<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/presentations/model_building_resolve_tt_2011-02-09.pdf">http://phenix-online.org/presentations/model_building_resolve_tt_2011-02-09.pdf</a><br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 2/10/16 22:14, Kaushik Hatti wrote:<br>
</div>
<blockquote
cite="mid:CAGMFGb=MuYKER+mSTT6gJjZRZaeRUC5s5GVMHqjyNM0CJPMCFQ@mail.gmail.com"
type="cite">
<div dir="ltr">Hello,
<div><br>
</div>
<div>In continuation to my earlier thread (subject:�sequence
independent model building possible?), I have built model into
density without knowledge of sequence for a data diffracted to
1.9A resolution.� Current R/Rfree is 15/19, phaser error=16.88
degrees with no Ramachandran outliers.</div>
<div><br>
</div>
<div>Is there a way we can differentiate between Glu/Gln,
Asp/Asn and sometimes Thr/Val directly from density?� I have
considered the local environment
(hydrophobic/hydrophilic/polarity pockets, possible hydrogen
bonds/other interactions, buried/exposed, etc...) in choosing
one over the other confusing pairs of amino acids.� However, I
am not absolutely certain in many places.</div>
<div><br>
</div>
<div>A BLAST of this sequence against all non-redundant protein
sequence database yield highest hit of 80% sequence identity.�
Hence, we are still not sure of sequence of the contaminant
protein which got crystallised and want to decipher sequence
directly from the structure.</div>
<div><br>
</div>
<div>Thanks for any pointers/suggestions,</div>
<div>Regards,</div>
<div>Kaushik</div>
<div><br>
</div>
<div>-- <br>
<div>
<div dir="ltr"><font color="#999999">Stupidity is everyone�s
birthright.� However, only the learned exercise it!<br>
--Kaushik (28Oct2014)</font></div>
</div>
</div>
</div>
<br>
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