Did you try to build a model of your second protein (with say Phyre 
<a href="http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index">http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index</a>  )? <div>Then try to manually place a section of that model into your density? </div><div>

Or Molecular replacement with said model?<div><br></div><div>Kelly Daughtry<br clear="all">*******************************************************<br>Kelly Daughtry, Ph.D.<br>Post-Doctoral Fellow, Raetz Lab<br>Biochemistry Department<br>

Duke University<br>Alex H. Sands, Jr. Building<br>303 Research Drive<br>RM 250<br>Durham, NC 27710<br>P: 919-684-5178<br>*******************************************************<br>
<br><br><div class="gmail_quote">On Thu, Feb 9, 2012 at 2:15 AM, intekhab alam <span dir="ltr">&lt;<a href="mailto:faisaldbg@gmail.com">faisaldbg@gmail.com</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">

<div>Hi all</div>
<div>I have a 3A dataset for a protein-protein complex. I have successfully build the first protein and refined it to R/Rfree 24/28. I can see some density for my second protein but the density is a bit noisy. I have attached the coot image of the density.  I want to model the aminoacid having sequence as given </div>



<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span lang="EN-US">peptide:</span></p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><font color="#ff6666"><span lang="EN-US">MGKKGKNKKG</span><span lang="EN-US">R</span><span lang="EN-US">G</span><span lang="EN-US">R</span><span lang="EN-US">PGVF</span><span lang="EN-US">R</span><span lang="EN-US">T</span><span lang="EN-US">R</span><span lang="EN-US">G</span><span lang="EN-US">LTDEEYDEFKK</span><span lang="EN-US">RR</span><span lang="EN-US">ES</span><span lang="EN-US">R</span><span lang="EN-US">GGKYSIDDYLAD</span><span lang="EN-US">R</span><span lang="EN-US">E</span><span lang="EN-US">R</span><span lang="EN-US">EEELLE</span><span lang="EN-US">R</span><span lang="EN-US">DEEEAIFGDGFGLE</span></font></p>



<div><br clear="all">1.Based on map features which segemnt should i start with.</div>
<div>2. Is there anyway that i can  build the best fit segment of my second protein. <br></div>
<div>I tried autobuild but it failed to build any peptide for my second protein.</div>
<div> </div>
<div>Your help is highly appreciated.</div>
<div> </div>
<div>regards</div><span class="HOEnZb"><font color="#888888">
<div> </div>
<div>-- </div>
<div><br>INTEKHAB ALAM<br>LABORATORY OF STRUCTURAL BIOINFORMATICS<br>KOREA UNIVERSITY, SEOUL<br></div>
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<br></blockquote></div><br></div></div>