On 05/30/2013 02:31 AM, Daron Standley wrote: > Although I'm not a very regular user of modeller, I believe it is well > known that long gaps, especially terminal gaps, look strange when > modeled using default options.
Sure. Typically, we just remove those regions and don't model them. Any modeling of these regions is just going to be fantasy anyway.
> "if distance of residue x from center is greater than some huge value > (2-3x the predicted Rg, based on sequence length), add a bias to the > potential for x toward the center of the protein"
The easiest way to do that would be to add an upper bound distance restraint between each C alpha and the center of gravity of the protein. An example is at http://salilab.org/modeller/9.11/manual/node105.html
Ben Webb, Modeller Caretaker