Hi all

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 as multiple templates to reconstruct the original structure of the protein. First, I aligned the three parts as the following way:

N-terminus> aaaaaaaaa-------------------------------------* transmembrane> ----------------bbbbbbbbbbbbb---------------* C-terminus> --------------------------------------ccccccccc* original> aaaaaaaaabbbbbbbbbbbbbccccccccc*

then I used the following script to generate the original structure of my protein:

from modeller import * from modeller.automodel import *

env = environ() a = automodel(env, alnfile='bhro_mult.ali', knowns=('bhro_n','bhro_tm','bhro_c'), sequence='bhro') a.starting_model = 1 a.ending_model =1 a.make()

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. I was missing something important? Or, did it in a wrong way? I am new to modeller, any suggestions are appreciated!

Thanks in advance

yours Xin Liu