Hello Steve,<br><br>A reply from a newbie as well :)<br><br>If I understood your question correctly you have more or less this situation:<br><br><font style="font-family: courier new,monospace;" size="1">TEMPLATE  AAAAAAAAAA----------AAAAAAAAA<br>

SEQUENCE  AAAAAAAAAABBBBBBBBBBAAAAAAAAA<br></font><br>If you use the FASTA sequence of your template with its own structure, it will build a complete structure with those sections modelled as loops. You just need to provide MODELLER with the template structure, it&#39;s sequence (with gaps in the missing regions), and the sequence of the full thing.<br>

<br>Best Regards,<br><br clear="all">João [ .. ] Rodrigues<br><br>(Blog)   <a href="http://doeidoei.wordpress.com">http://doeidoei.wordpress.com</a><br>(MSN)   <a href="mailto:always_asleep_@hotmail.com">always_asleep_@hotmail.com</a><br>

(Skype) rodrigues.jglm<br>