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.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:
>P1:x
....
XXXX
/
XXXX
?
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
a.make()
Thank you very much
Christopher
