On 10/25/12 6:33 AM, Rienk Doetjes wrote: > I am working with a structure that, according to all available > information I have, contains a beta hairpin loop. Whenever I use > modeller to produce a homology model, this beta-hairpin will not be > formed. Is there a way I can force modeller to actually generate this > feature I want? Forcing the standard secondary structure does not seem > to work.

Modeller's secondary structure restraints are not particularly strong, and encourage beta strands, not hairpins. You might try finding a short template fragment that contains a suitable hairpin and aligning it with your model sequence in that region.

Ben Webb, Modeller Caretaker