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