Dear Modellers,

first of all I'd like to thank you for helping with my last question.

Now I have another question. I have to build a model by homology modelling for a protein(only sequence available) which builds a homodimer. The template-structure is a homodimer as well. I used the following script to align the sequence and the structure.

from modeller import *

env = environ()
aln = alignment(env)
mdl = model(env, file='y', model_segment=('FIRST:A','LAST:B'))
aln.append_model(mdl, align_codes='y', atom_files='y.pdb')
aln.append(file='x.ali', align_codes='x')
aln.write(file='xy.ali', alignment_format='PIR')
aln.write(file='xy.pap', alignment_format='PAP')

In the resulting alignment there is a separation ("/") between the two chains of the template sequence. But in the sequence of the target there isn't a separation of course. Do i have to put a separation in the sequence of the target in the alignment file or in the input file for the alignment script? Or whats the best way to handle this problem ? If I put the separation in the resulting alignment the alignment of the chains wouldn't be good. Does the x.ali file of my target have to look like this: 



Is it sufficient to use the following script afterwards to build the model out of the alignment ?

from modeller import *
from modeller.automodel import *

env = environ()
a = automodel(env, alnfile='xy.ali',
              knowns='y', sequence='x',
              assess_methods=(assess.DOPE, assess.GA341))
a.starting_model = 1
a.ending_model = 5

Thank you very much