Hi<br><br>I&#39;m following the modeller tutorial to make a search for templates  but  with no success. May be  I&#39;m doing something wrong. Below I detail what I did:<br><br>1) download the  supplemental  files:<br><br>
<ul><li>All PDB sequences:<br>
<a href="http://www.salilab.org/modeller/downloads/pdball.pir.gz">pdball.pir.gz</a>
</li><li>Clustered at 95% identity:<br>
<a href="http://www.salilab.org/modeller/downloads/pdb_95.cod.gz">pdb_95.cod.gz</a> (PDB codes of cluster representatives)<br>
<a href="http://www.salilab.org/modeller/downloads/pdb_95.grp.gz">pdb_95.grp.gz</a> (PDB codes in each cluster)<br>
<a href="http://www.salilab.org/modeller/downloads/pdb_95.pir.gz">pdb_95.pir.gz</a> (sequences of cluster representatives)
</li></ul>

2) I unpack them into the directory where Modeller should find them: /usr/lib/modeller9v7/modlib. In this point, I have a doubt: in the tutorial said that I should replace the files: CHAINS_3.* with the downloaded before. But I did not find them, at least in that directory. Anyway I renamed the files accordingly the tutorial as: <br>
<br>pdball.pir to CHAINS_all.seq<br>pdb_95.cod to CHAINS_3.0_40_xn.cod<br><br>With these modifications I run seqsearch.top and apparently it worked, but after many (3-4) hours I stopped it. it never writes any line in the log file.<br>
<br>seqsearch.top file used as input.<br>SET SEARCH_RANDOMIZATIONS = 100<br>SET FILE = &#39;TvLDH.ali&#39;<br>READ_SEQUENCE_DB<br>SEQUENCE_SEARCH ALIGN_CODES = &#39;TvLDH&#39;, DATA_FILE  = ON<br><br>Any help will be appreciated.<br>
<br>Sergio<br><br><br clear="all"><br>-- <br>Dr. Sergio Garay<br>Facultad de Bioquimica y Cs. Biológicas<br>Universidad Nacional del Litoral<br>Santa Fe - Argentina<br>C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA<br>Argentina<br>
Ph. +54 (342) 4575-213<br>Fax. +54 (342) 4575-221 <br>