Re: [modeller_usage] Loop modeling

On 01/27/2011 06:22 AM, bharat lal wrote: > I have modelled a protein using secondary structure restrained script... > The model seems to be perfectly fine .. but one portion of the model is > converted into a helix which has to be a loop according to the template > .. how can I force that region to be a loop ???

You can't *force* it, but if you unalign the target and template in this region, loop/coil is the most likely secondary structure you'll end up with. See http://salilab.org/archives/modeller_usage/2009/msg00170.html

Ben Webb, Modeller Caretaker