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