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Re: [modeller_usage] Force B-hairpin loop when modelling

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
--
             http://www.salilab.org/modeller/
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