[modeller_usage] Problem when reconstruct the protein with know structure!

["liu xin" <>]

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

(sorry, last letter I submited a wrong alignment,the following is I used)

>P1;N-terminus

structureX:N-terminus
aaaaaaaaaa------------------------------*

>P1;tm-region

structureX:tm-region

----------bbbbbbbbbbbbbbbbbbbb----------*

>P1;C-terminus
structureX:C-terminus
------------------------------cccccccccc*

>P1;original

sequence:original
aaaaaaaaaabbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb*
 

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