Dear Ben,
Thanks Ben,
That's exactly what I needed to know!
Daron
On May 31, 2013, at 3:35 AM, Modeller Caretaker modeller-care@salilab.org wrote:
> 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 > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage