I'm not an expert with modeller, but your problem, I guess, is a python
problem.
Python works with indented code, and, at the begining, it is lacking in
your script.
I hope it could be usefull,
Frederico G. C. Arnoldi
UNESP - Rio Claro - SP - Brazil.
Pay attetion on the "spaces" before the statements. Maybe the the
following script should work.
class mymodel(automodel):
def special_restraints(self, aln): ## an indentation
rsr = self.restraints ### another
rsr.make(aln, restraint_type='STRAND', residue_ids=('416', '418'))
env = environ() # create a new MODELLER environment to build this model
in
# directories for input atom files
env.io.atom_files_directory = './'
a = mymodel(env,
alnfile = 'ewq_msh23.ali', # alignment filename
knowns = '1EWQ', # codes of the templates
sequence = '1msh') # code of the target
a.starting_model= 1 # index of the first model
a.ending_model = 20 # index of the last model
# (determines how many models to
calculate)
a.make() # do the actual homology modelling
Message: 4
Date: Sun, 17 Jul 2005 14:20:39 +0200 (CEST)
From: Parantu Shah <>
Subject: [modeller_usage] Newbie question : restraining secondary
structure
To:
Message-ID:
<>
Content-Type: TEXT/PLAIN; charset=US-ASCII
Hi,
May be I am making a mistake in here but.
When I try to use the script in example 12 in the FAQ about
* Is it possible to restrain secondary structure in the target sequence?
modeller 8v1 gives following error message and quits
File "model-default.py", line 7
rsr = self.restraints:
^
IndentationError: expected an indented block
Any help is wellcome
best regards,
Parantu
----------------------------------------------------
* Here is the script file
from modeller.automodel import * # Load the automodel class
class mymodel(automodel):
def special_restraints(self, aln):
rsr = self.restraints
rsr.make(aln, restraint_type='STRAND', residue_ids=('416', '418'))
env = environ() # create a new MODELLER environment to build this model
in
# directories for input atom files
env.io.atom_files_directory = './'
a = mymodel(env,
alnfile = 'ewq_msh23.ali', # alignment filename
knowns = '1EWQ', # codes of the templates
sequence = '1msh') # code of the target
a.starting_model= 1 # index of the first model
a.ending_model = 20 # index of the last model
# (determines how many models to
calculate)
a.make() # do the actual homology modelling
-------------------------------------------------------------------------
Parantu Shah Ph: 0 6221 387 456 (0)
Graduate Student : 0 1797 731 953 (m)
Bork Group Fax: +49 6221 387 517
European Molecular Biology Laboratory
Heidelberg, Germany
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