Subject: [modeller_usage] Problem in running Modeller 8v2
From: Nagesh Chakka <>
Date: Mon, 27 Mar 2006 14:29:08 +1000
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