-------- Original Message --------
Subject: five ss bridges
Date: Thu, 02 Aug 2007 10:58:11 -0400
From: Dany Naranjo Feliciano <>
To:
-----Original Message-----
From: "Dany Naranjo Feliciano" <>
To:
Date: Thu, 02 Aug 2007 10:30:42 -0400
Subject: five ss bridges
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
Dany Naranjo Feliciano
Lic. Bioquímica
Grupo Biología Molecular
Centro Nacional de Sanidad Agropecuaria (CENSA)
Apartado 10. San José de las Lajas.
La Habana. CP 32700. Cuba
Teléfono 53-47-863014 ext 28
"Participe en Universidad 2008 del 11 al 15 de febrero del 2008.
Palacio de Convenciones. La Habana. Cuba.
http: //www.universidad2008.cu".
Ben Webb, Modeller Caretaker
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