<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Shya,<div>I'm sorry it is not very clear! The .ali file looks like this:</div><div><br></div><div>You can use an alignment file that sculptor can recognize. This file
looks like this (there must be exactly the same number of characters for
the target
and the template sequences (including dashes for gaps):
<pre style="face=courier">> title text for sequence of target to follow
VDFNGYWKMLSNENFEEYLRALDVNVALRKIANLLKPDKEIVQDGDHMIIRTLSTFRNYIMDFQVGKEFEEDLTGIDD
> title text for sequence of template (supplied PDB) to follow
-AFSGTWQVYAQENYEEFLRAISLPEEVIKLAKDVKPVTEIQQNGSDFTITSKTPGKTVTNSFTIGKEAEIT--TMDG
</pre><div>You can create this with any alignment program, or by using a web server such as <a href="http://toolkit.tuebingen.mpg.de/hhpred">http://toolkit.tuebingen.mpg.de/hhpred</a> and this will generate alignments. </div></div><div><br></div><div>Let me know if that isn't what you need to know!</div><div><br></div><div>All the best,</div><div>Tom T</div><div><br></div><div><br></div><div><div><div>On Dec 6, 2011, at 2:36 PM, Shya Biswas wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi all,<br>I was wondering how to generate .ali file that I need to run rosetta MR. I have most of the files for the run except this one. the documentation did not help a lot.<br>thanks,<br>Shya<br>
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<div style="font-size: 12px; "><div><div><div><div><br>Thomas C. Terwilliger<br>Mail Stop M888<br>Los Alamos National Laboratory<br>Los Alamos, NM 87545<br><br>Tel: 505-667-0072 email: <a href="mailto:terwilliger@LANL.gov">terwilliger@LANL.gov</a><br>Fax: 505-665-3024 SOLVE web site: <a href="http://solve.lanl.gov">http://solve.lanl.gov</a><br>PHENIX web site: http:www.phenix-online.org<br>ISFI Integrated Center for Structure and Function Innovation web site: <a href="http://techcenter.mbi.ucla.edu">http://techcenter.mbi.ucla.edu</a><br>TB Structural Genomics Consortium web site: <a href="http://www.doe-mbi.ucla.edu/TB">http://www.doe-mbi.ucla.edu/TB</a></div><div>CBSS Center for Bio-Security Science web site: <a href="http://www.lanl.gov/cbss">http://www.lanl.gov/cbss</a><br><br></div></div></div></div><br></div><br class="Apple-interchange-newline">
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