[modeller_usage] how to treat an unaligned 46-amino acid long insertion

[Thomas Evangelidis <tevang3 AT gmail.com>]

Dear modellers,

what's the best way to refine the structure of a 46 amino acid long insertion which is not aligned with any of the templates? As far as I know loop refinement can be applied to shorter parts of the protein. As a matter of fact I've already tested the slow mode but this part still looks disordered. I have also performed a PSI-BLAST search but haven't found any pdb structure which matches this part of my target sequence.

thanks in advance.
Tom