Problem with evaluate_model.py - modeller_usage

26 Apr 2006


      Dear users,
I am trying to obtain the DOPE potential and the corresponding plot for my 
best model. I am using the evalute_model.py script from the web tutorial, 
but when I run it I get this error:
Traceback (most recent call last):
  File "evaluate_model.py", line 24, in ?
    normalize_profile=True, smoothing_window=15)
TypeError: assess_dope() got an unexpected keyword argument 'output'
Can somebody help me?.
Thanks a lot in advance.
I am using Modeller 8v0 and here is my scritp (my alignment file is called 
Ara.ali and the templates structures are located in ../templates/)
from modeller import *
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
env.libs.topology.read(file='$(LIB)/top_heav.lib') # read topology
env.libs.parameters.read(file='$(LIB)/par.lib') # read parameters
# directories for input atom files
env.io.atom_files_directory = '../templates/'
# read model file
mdl = model(env)
mdl.read(file='Ara.B99990012.pdb')
aln = alignment(env)
code = "Ara"
# generate topology
aln.append_model(mdl, atom_files='Ara.B99990012.pdb', align_codes=code)
aln.append_model(mdl, atom_files='Ara.B99990012.pdb', 
align_codes=code+'-ini')
mdl.generate_topology(aln, sequence=code+'-ini')
mdl.transfer_xyz(aln)
mdl.assess_dope(output='ENERGY_PROFILE NO_REPORT', file='Ara.profile',
                normalize_profile=True, smoothing_window=15)