Dear Modeller community,
I have a good structure template to model the missing segment of a protein chain; however, the portion I'm tyring to model should contain a sharp bend. I'm actually using one part of the template for one side of the chain and the other part of the template for the other side of the chain after the bend. When I align the template (wich overlaps with the structure containing the missing portion) the two template pieces look reasonable aside from missing the loop that constitues the bend. After running automodel the template structure is not even retained; instead, it just builds large loops in no particular orientation. Is it possible that the problem is that automodel's constraints make it unable to model the bend correctly? If so, would using the model() class without certain constraints allow me to model this bend?
Thanks in advance, Russell Green