Hi All, I have just installed Modeller version 8v2 and tried to run the following script.
# Homology modelling by the allhmodel 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 = '/home/nagesh/modelling/structure'
a = allhmodel(env, alnfile = 'inputAlignment_files/xenDpl.pir', # alignment filename knowns = '1I17', # codes of the templates sequence = 'xenopusDoppel') # 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
Running the script is giving the following message.
[nagesh@vogon ~/modelling]$ mod8v2 model_dpl_latest.top Traceback (most recent call last): File "<string>", line 1, in ? File "/usr/lib/modeller8v2/modlib/modeller/runtop.py", line 79, in run self.runlines(self.lines) File "/usr/lib/modeller8v2/modlib/modeller/runtop.py", line 129, in runlines self.set_top_vars(vars) File "/usr/lib/modeller8v2/modlib/modeller/runtop.py", line 256, in set_top_vars raise IndexError, "Variable name not recognized: %s" % varname.upper () IndexError: Variable name not recognized: MODELLER.AUTOMODEL
What can be the probable reason for this problem. Thank you in advance. Nagesh