[modeller_usage] using two templates in Modeller8v2

["Thomas K. Weldeghiorghis" <>]

Hi there,

I am new to modeller and I have trouble creating a homology model of a
protein using two templates.  I modified the model-default.py script as
shown below and I got error messages.  I would appreciate it if any one
can give me any suggestion.

Thanks.
Thomas


Here is model-default.py script I am using:
#####################################################################
# Homology modelling by the automodel class

from modeller.automodel import *    # Load the automodel class

log.verbose()    # request verbose output
env = environ()  # create a new MODELLER environment to build this model in

# directories for input atom files
env.io.atom_files_directory = './:../atom_files'

a = automodel(env,
              alnfile  = 'alignment1.ali',     # alignment filename
              knowns   = '2MDbis 1wu9',       # codes of the templates
              sequence = 'flq15691')           # code of the target
a.starting_model= 1                 # index of the first model
a.ending_model  = 1                 # index of the last model
                                    # (determines how many models to
calculate)
a.make()                            # do the actual homology modelling

#########################################################################

my alignment file looks:
###################################################################
>P1;2MDbis
structureX:2MDbis:1 : :148 : :Eb1:Homo sapience: 1.90: 0.19
.....
>P1;1wu9 structureX:1wu9:A    : :59  : :Eb1:Homo sapience: 1.90: 0.19
......
>P1;flq15691
sequence:flq15691:1: :286::q15691:Homo sapience: 2.00: -1.00
......
#####################################################################

I am getting the following error message
########################################################################
Traceback (most recent call last):
  File "model-default.py", line 18, in ?
    a.make()                            # do the actual homology modelling
  File
"/usr/local/programs/modeller-8v2/modlib/modeller/automodel/automodel.py",
line 100, in make
    self.homcsr(exit_stage)
  File
"/usr/local/programs/modeller-8v2/modlib/modeller/automodel/automodel.py",
line 318, in homcsr
    aln = self.read_alignment()
  File
"/usr/local/programs/modeller-8v2/modlib/modeller/automodel/automodel.py",
line 312, in read_alignment
    aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence])
  File "/usr/local/programs/modeller-8v2/modlib/modeller/alignment.py",
line 36, in append
    return self.__int_append('alignment.append', io, libs, vars)
  File "/usr/local/programs/modeller-8v2/modlib/modeller/alignment.py",
line 68, in __int_append
    libs=libs.modpt, **vars)
  File "/usr/local/programs/modeller-8v2/modlib/modeller/util/top.py",
line 33, in read_alignment
    return _modeller.read_alignment(aln, io, libs, *args)
_modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was not
found in the alignment file; ALIGN_CODES(       2) =  flq15691
###################################################################