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)