Hi,<div><br></div><div>You should go through the tutorial ;-)<div><br></div><div>You&#39;ll need to perform a homology search using the PIR database which is prepared for you already -- see the Data sets section for pir_95.  You&#39;ll need to format your pdb into modeller&#39;s alignment format -- see the format section.</div>

<div><br></div><div>After this homology search, sift through the top hits and then build an alignment from those and your target.  You can align with however many templates you see fit.</div><div><br></div><div>Modeller has an automodel method which you can use that actually builds models between your template(s) and your target.</div>

<div><br></div><div>Checkout: <a href="http://salilab.org/modeller/tutorial/basic.html">http://salilab.org/modeller/tutorial/basic.html</a></div><div><br></div><div><br></div><div>Cheers,</div><div>Paul<br><div><br><div class="gmail_quote">

On Fri, Apr 2, 2010 at 9:33 AM, Daniel Fernandez <span dir="ltr">&lt;<a href="mailto:dfernan@gmail.com">dfernan@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;">

Hi,
<div><br></div><div>I am trying to use modeller to fill in missing side chain or backbone atoms in the <span style="font-family:arial, sans-serif;white-space:pre-wrap">1ahoa<span></span><span> protein.  Do you have any suggestion on how to do that using modeller, i.e., which one I should use as a template and as a target protein for that problem.  I am relatively new to the software and protein modelling literature.  Any help would be strongly appreciated.</span></span></div>



<div><font face="arial, sans-serif"><span style="white-space:pre-wrap"><br></span></font></div><div><font face="arial, sans-serif"><span style="white-space:pre-wrap">Best,</span></font></div>

<div><font face="arial, sans-serif"><span style="white-space:pre-wrap"><br></span></font></div><font color="#888888"><div><font face="arial, sans-serif"><span style="white-space:pre-wrap">Daniel</span></font></div>

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<br></blockquote></div><br><br clear="all"><br>-- <br>Paul Rigor <br>Pre-doctoral BIT Fellow and Graduate Student <br>Institute for Genomics and Bioinformatics <br>Donald Bren School of Information and Computer Sciences <br>

University of California, Irvine<br><a href="http://www.ics.uci.edu/~prigor">http://www.ics.uci.edu/~prigor</a><br>
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