liu xin wrote: > I divided the protein with know structure (bovine rhodopsin receptor) > into three part: N-terminus region, transmembrane region and C-terminus > region without change their initial coordinates, and I try to use the > three parts to reconstruct the original structure of the protein. ... > However, the generated model was different from the original one, > looking closely, I found the difference mainly occurred in the > N-terminus and C-terminus regions, their coordinates have changed > greatly when compared with the original structure.
Modeller will try to build models that resemble the template whenever it is aligned with your target sequence, but these restraints are on internal coordinates, not Cartesian coordinates, so there could well be rotation or translation of your three segments. In particular, by breaking the sequence into three, you have prevented Modeller from using the information present in your original structure about the distances between these three segments.
Ben Webb, Modeller Caretaker