Hi: My target protein is a member of GPCR.I used multiple template to build the model, there was no overlap among the templates. The final model was not reasonable. The C-tail and N-tail were away from transmember region, simultaneity,located flank of transmember region.I want to know, was there any restraints on 'MODELLER'? the following is alignment: >P1;proteinA structureX:proteinA aaaaaaaaaaaaaaaaaaaaaaaaaaaa----------------------------------* >P1;proteinB structureX:proteinB ----------------------------bbbbbbbbbbbbbbbbbbbbbbbbb---------* >P1;proteinC structureX:proteinC -----------------------------------------------------ccccccccc* >P1;model sequence:model aaaaaaaaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbbbbbbbbbbcccccccccc* The following was my script: from modeller import * from modeller.automodel import * env = environ() a = automodel(env, alnfile='model_mult.ali', knowns=('proteinA','proteinB', 'proteinC' ), sequence='model') a.starting_model = 1 a.ending_model = 1 a.make() was I missing something important? Or, did it in a wrong way? looking for your reply! thanks!