Hi, I am new to modeller and I have trouble creating a homology model of a protein using model-addrsr. By predicting secondary structure, between residues "305-318" is alpha-helix. I modified the model-addrsr.py script as shown below and I got error messages. I would appreciate it if any one can give me any suggestion. Thanks.

from modeller import * from modeller.automodel import * # Load the automodel class

log.verbose() env = environ()

# directories for input atom files env.io.atom_files_directory = './:../atom_files'

class mymodel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms rsr.add(secondary_structure.alpha(self.residue_range('305:', '318:'))) a = mymodel(env, alnfile = 'seg.ali', # alignment filename knowns = '1u19A', # codes of the templates sequence = 'mrg1') # 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 homology modeling

The error: File "modelrsr.py", line 14 rsr.add(secondary_structure.alpha(self.residue_range('305:', '318:'))) ^ IndentationError: unindent does not match any outer indentation level

The .log file:

MODELLER 9v1, 2007/01/19, r4822

PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS

Copyright(c) 1989-2007 Andrej Sali All Rights Reserved

Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK

Kind, OS, HostName, Kernel, Processor: 4, Linux linux 2.6.11.4-21.7-default i686 Date and time of compilation : 2007/01/19 13:47:34 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2007/04/17 22:15:53