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Wed Dec 2 17:41:11 PST 2020


ing to work backward toward the N-terminus.

If I am reading the phenix.autobuild documention correctly, it sounds like =
there are two modes:

(i)                 Standard mode - rebuild the whole protein from scratch,=
 which does give the possibility of adding my N-terminal residues.  However=
, I don=92t want my nearly complete existing model to be rebuilt, I just wa=
nt AutoBuild to try to add the missing N-terminal sequence to the existing =
model.

(ii)              Rebuild-in-place, which rebuilds the current model but do=
esn=92t add or subtract any atoms.  So that sounds like it=92s not what I=
=92m looking for because it won=92t add the N-terminal sequence AND it rebu=
ilds the existing model, which I want to keep exactly as is.

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 cu=
rrently existing residue in the input model exactly as they are?

Happy to hear any advice you can give.

Thanks,
Matthew

---
Matthew J. Whitley, Ph.D.
Research Instructor
Department of Pharmacology & Chemical Biology
University of Pittsburgh School of Medicine



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<p class=3D"MsoNormal"><span class=3D"DefaultFontHxMailStyle">Hello all,<o:=
p></o:p></span></p>
<p class=3D"MsoNormal"><span class=3D"DefaultFontHxMailStyle"><o:p>&nbsp;</=
o:p></span></p>
<p class=3D"MsoNormal"><span class=3D"DefaultFontHxMailStyle">I have a very=
 large protein with 16 copies in the asymmetric unit (nearly 15,000 total r=
esidues).&nbsp; Upon initial model building, ~30 residues at the N-terminus=
 of each identical chain were not built.&nbsp;
 After building the reliable parts of the model and filling in other gaps a=
nd then refining that partial (but nearly complete) model, the N-terminal d=
ensity has now improved to the degree that I can manually build a number of=
 the missing residues in Coot.&nbsp;
 However, that means manually building the same series of residues over and=
 over for each of the 16 identical chains.&nbsp; Is there a way to get Auto=
Build to add these N-terminal residues for me to spare me the tedium of rep=
etitive manual building?<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span class=3D"DefaultFontHxMailStyle"><o:p>&nbsp;</=
o:p></span></p>
<p class=3D"MsoNormal"><span class=3D"DefaultFontHxMailStyle">What I=92ve g=
leaned from the documentation so far:<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span class=3D"DefaultFontHxMailStyle"><o:p>&nbsp;</=
o:p></span></p>
<p class=3D"MsoNormal"><span class=3D"DefaultFontHxMailStyle">From the phen=
ix.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 m=
issing region.&nbsp; That=92s not the case
 for me because I=92m trying to work backward toward the N-terminus.<o:p></=
o:p></span></p>
<p class=3D"MsoNormal"><span class=3D"DefaultFontHxMailStyle"><o:p>&nbsp;</=
o:p></span></p>
<p class=3D"MsoNormal"><span class=3D"DefaultFontHxMailStyle">If I am readi=
ng the phenix.autobuild documention correctly, it sounds like there are two=
 modes:<o:p></o:p></span></p>
<p class=3D"MsoListParagraph" style=3D"margin-left:39.0pt;text-indent:-.5in=
;mso-list:l0 level1 lfo1">
<![if !supportLists]><span class=3D"DefaultFontHxMailStyle"><span style=3D"=
mso-list:Ignore">(i)<span style=3D"font:7.0pt &quot;Times New Roman&quot;">=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;
</span></span></span><![endif]><span class=3D"DefaultFontHxMailStyle">Stand=
ard mode - rebuild the whole protein from scratch, which does give the poss=
ibility of adding my N-terminal residues.&nbsp; However, I don=92t 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.<o:p></o:p></span></p>
<p class=3D"MsoListParagraph" style=3D"margin-left:39.0pt;text-indent:-.5in=
;mso-list:l0 level1 lfo1">
<![if !supportLists]><span class=3D"DefaultFontHxMailStyle"><span style=3D"=
mso-list:Ignore">(ii)<span style=3D"font:7.0pt &quot;Times New Roman&quot;"=
>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;
</span></span></span><![endif]><span class=3D"DefaultFontHxMailStyle">Rebui=
ld-in-place, which rebuilds the current model but doesn=92t add or subtract=
 any atoms.&nbsp; So that sounds like it=92s not what I=92m looking for bec=
ause it won=92t add the N-terminal sequence AND
 it rebuilds the existing model, which I want to keep exactly as is.<o:p></=
o:p></span></p>
<p class=3D"MsoNormal"><span class=3D"DefaultFontHxMailStyle"><o:p>&nbsp;</=
o:p></span></p>
<p class=3D"MsoNormal"><span class=3D"DefaultFontHxMailStyle">Is there some=
 series of options in AutoBuild that will allow me to just add missing resi=
dues (provided in the sequence file) but keep all the other currently exist=
ing residue in the input model exactly
 as they are?<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span class=3D"DefaultFontHxMailStyle"><o:p>&nbsp;</=
o:p></span></p>
<p class=3D"MsoNormal"><span class=3D"DefaultFontHxMailStyle">Happy to hear=
 any advice you can give.<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span class=3D"DefaultFontHxMailStyle"><o:p>&nbsp;</=
o:p></span></p>
<p class=3D"MsoNormal"><span class=3D"DefaultFontHxMailStyle">Thanks,<o:p><=
/o:p></span></p>
<p class=3D"MsoNormal"><span class=3D"DefaultFontHxMailStyle">Matthew<o:p><=
/o:p></span></p>
<p class=3D"MsoNormal"><o:p>&nbsp;</o:p></p>
<p class=3D"MsoNormal"><span style=3D"font-size:12.0pt">---<o:p></o:p></spa=
n></p>
<p class=3D"MsoNormal"><b><span style=3D"font-size:12.0pt">Matthew J. Whitl=
ey, Ph.D.<o:p></o:p></span></b></p>
<p class=3D"MsoNormal"><span style=3D"font-size:12.0pt">Research Instructor=
<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:12.0pt">Department of Pharm=
acology &amp; Chemical Biology<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:12.0pt">University of Pitts=
burgh School of Medicine<o:p></o:p></span></p>
<p class=3D"MsoNormal"><o:p>&nbsp;</o:p></p>
<p class=3D"MsoNormal"><span class=3D"DefaultFontHxMailStyle"><o:p>&nbsp;</=
o:p></span></p>
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