Hi,<div><br></div><div>I think I will start with a more basic question.  I am new to modeller and bioinformatics in general. </div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif"><br></font></div><div>

<font class="Apple-style-span" face="arial, helvetica, sans-serif">If I have a target protein, i.e., 1<span class="Apple-style-span" style="font-family: arial, sans-serif; white-space: pre-wrap; ">ahoa<span></span><span> protein<span class="Apple-style-span" style="font-family: arial, helvetica, sans-serif; white-space: normal; "> I want to model, how can I prepare the input files (i.e. alignment and template files) for that protein??? any suggestions? tutorials or read about this?  the modeller tutorial assumes one knows how to prepare the files to be read by modeller, and I actually don&#39;t know that part.  Any advise would be strongly appreciated.</span></span></span></font></div>

<div><font class="Apple-style-span" face="Times" size="2"><span class="Apple-style-span" style="font-size: 10px;"><br></span></font></div><div><font class="Apple-style-span" face="Times" size="2"><span class="Apple-style-span" style="font-size: 10px;"><br>

</span></font><div class="gmail_quote">On Fri, Apr 2, 2010 at 12:33 PM, 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>
</font></blockquote></div><br><br clear="all"><br>-- <br>Daniel F.<br><br>Department of Statistics, Harvard University<br>1 Oxford Street, Cambridge, MA 02138<br>
</div>