<div dir="auto">Dear Matthew,<div dir="auto"><br></div><div dir="auto">You say you have 16 identical chains?</div><div dir="auto">Is the electron density also identical between them?</div><div dir="auto">How close are the NCS related copies?</div><div dir="auto"><br></div><div dir="auto">I would choose to use Coots built-in NCS tools to copy the model from one chain to the others. Takes a few seconds tops, and then normal refinement should take care of the rest.</div><div dir="auto"><br></div><div dir="auto">See e.g. here</div><div dir="auto"><a href="https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Applying-NCS-Edits">https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Applying-NCS-Edits</a></div><div dir="auto"><br></div><div dir="auto"><br></div><div dir="auto"><br></div><div dir="auto"><br></div><div dir="auto">Unless of course all these N-terminal residues are rather different, then it's a different story, but not quite sure about it from your description.</div><div dir="auto"><br></div><div dir="auto">Hope this helps</div><div dir="auto"><br></div><div dir="auto">Folmer</div><div dir="auto"><br></div><div dir="auto"><br></div><div dir="auto"><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">tir. 17. aug. 2021 08.16 skrev Whitley, Matthew J <<a href="mailto:mjw100@pitt.edu">mjw100@pitt.edu</a>>:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal"><span class="m_-821382505231193416DefaultFontHxMailStyle">Hello all,<u></u><u></u></span></p>
<p class="MsoNormal"><span class="m_-821382505231193416DefaultFontHxMailStyle"><u></u> <u></u></span></p>
<p class="MsoNormal"><span class="m_-821382505231193416DefaultFontHxMailStyle">I have a very large protein with 16 copies in the asymmetric unit (nearly 15,000 total residues). Upon initial model building, ~30 residues at the N-terminus of each identical chain were not built.
After building the reliable parts of the model and filling in other gaps and then refining that partial (but nearly complete) model, the N-terminal density has now improved to the degree that I can manually build a number of the missing residues in Coot.
However, that means manually building the same series of residues over and over for each of the 16 identical chains. Is there a way to get AutoBuild to add these N-terminal residues for me to spare me the tedium of repetitive manual building?<u></u><u></u></span></p>
<p class="MsoNormal"><span class="m_-821382505231193416DefaultFontHxMailStyle"><u></u> <u></u></span></p>
<p class="MsoNormal"><span class="m_-821382505231193416DefaultFontHxMailStyle">What I’ve gleaned from the documentation so far:<u></u><u></u></span></p>
<p class="MsoNormal"><span class="m_-821382505231193416DefaultFontHxMailStyle"><u></u> <u></u></span></p>
<p class="MsoNormal"><span class="m_-821382505231193416DefaultFontHxMailStyle">From the phenix.fit_loops documentation, it seems like that tool only works for filling in chain breaks, i.e. there is already modeled protein at each end of the missing region. That’s not the case
for me because I’m trying to work backward toward the N-terminus.<u></u><u></u></span></p>
<p class="MsoNormal"><span class="m_-821382505231193416DefaultFontHxMailStyle"><u></u> <u></u></span></p>
<p class="MsoNormal"><span class="m_-821382505231193416DefaultFontHxMailStyle">If I am reading the phenix.autobuild documention correctly, it sounds like there are two modes:<u></u><u></u></span></p>
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<u></u><span class="m_-821382505231193416DefaultFontHxMailStyle"><span>(i)<span style="font:7.0pt "Times New Roman"">
</span></span></span><u></u><span class="m_-821382505231193416DefaultFontHxMailStyle">Standard mode - rebuild the whole protein from scratch, which does give the possibility of adding my N-terminal residues. However, I don’t want my nearly complete existing model to be rebuilt,
I just want AutoBuild to try to add the missing N-terminal sequence to the existing model.<u></u><u></u></span></p>
<p class="m_-821382505231193416MsoListParagraph" style="margin-left:39.0pt">
<u></u><span class="m_-821382505231193416DefaultFontHxMailStyle"><span>(ii)<span style="font:7.0pt "Times New Roman"">
</span></span></span><u></u><span class="m_-821382505231193416DefaultFontHxMailStyle">Rebuild-in-place, which rebuilds the current model but doesn’t add or subtract any atoms. So that sounds like it’s not what I’m looking for because it won’t add the N-terminal sequence AND
it rebuilds the existing model, which I want to keep exactly as is.<u></u><u></u></span></p>
<p class="MsoNormal"><span class="m_-821382505231193416DefaultFontHxMailStyle"><u></u> <u></u></span></p>
<p class="MsoNormal"><span class="m_-821382505231193416DefaultFontHxMailStyle">Is there some series of options in AutoBuild that will allow me to just add missing residues (provided in the sequence file) but keep all the other currently existing residue in the input model exactly
as they are?<u></u><u></u></span></p>
<p class="MsoNormal"><span class="m_-821382505231193416DefaultFontHxMailStyle"><u></u> <u></u></span></p>
<p class="MsoNormal"><span class="m_-821382505231193416DefaultFontHxMailStyle">Happy to hear any advice you can give.<u></u><u></u></span></p>
<p class="MsoNormal"><span class="m_-821382505231193416DefaultFontHxMailStyle"><u></u> <u></u></span></p>
<p class="MsoNormal"><span class="m_-821382505231193416DefaultFontHxMailStyle">Thanks,<u></u><u></u></span></p>
<p class="MsoNormal"><span class="m_-821382505231193416DefaultFontHxMailStyle">Matthew<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span style="font-size:12.0pt">---<u></u><u></u></span></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt">Matthew J. Whitley, Ph.D.<u></u><u></u></span></b></p>
<p class="MsoNormal"><span style="font-size:12.0pt">Research Instructor<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">Department of Pharmacology & Chemical Biology<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">University of Pittsburgh School of Medicine<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span class="m_-821382505231193416DefaultFontHxMailStyle"><u></u> <u></u></span></p>
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