[modeller_usage] five ss bridges

["Dany Naranjo Feliciano" <>]

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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