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.align2d()

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:

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

a.make()