Hi,
I´m trying to model 5 SS bridges.
When I try to tell modeller 9v1 to do that,I receive the following error:
Could not find platform independent libraries <prefix>
Could not find platform dependent libraries <exec_prefix>
Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
'import site' failed; use -v for traceback
File "test_ssmodel_fasciola.py", line 9
def special_patches(self, aln):
^
IndentationError: expected an indented block
 
What might be wrong?
The script,
#Homology modelling by the automodel class
from modeller import * # Load standar Modeller classes
from modeller.automodel import * # Load the automodel class
#Redefine the special_patches routine to include the additional disulfides
#(this routine)
class mymodel(automodel):
def special_patches(self, aln):
# A disulfide between residues 10-51,44-47,43-110,80-114,88-100:
self.patch(residue_type='DISU', residues=(self.residues['10'],
self.residues['51']))
self.patch(residue_type='DISU', residues=(self.residues['44'],
self.residues['47']))
self.patch(residue_type='DISU', residues=(self.residues['43'],
self.residues['110']))
self.patch(residue_type='DISU', residues=(self.residues['80'],
self.residues['114']))
self.patch(residue_type='DISU', residues=(self.residues['88'],
self.residues['100']))
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 = './'
a = mymodel(env,
alnfile = 'test_fasciola.ali', # alignment filename
knowns = '1gmy_A.pdb', # codes of the templates
sequence = 'Q8I7B2_sequence') # 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

 





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