Hi Parantu,

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 shah@embl-heidelberg.de Subject: [modeller_usage] Newbie question : restraining secondary structure To: modeller_usage@salilab.org Message-ID: Pine.LNX.4.44.0507171409470.861-100000@jack.EMBL-Heidelberg.DE 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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